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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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  • Subversion terminology. Difference between projects, modules and root directories

    - by aioobe
    I'm setting up a repository for me and some colleagues. I have a subversion repository at hand, and all required rights. The usual directory-skeleton has been set up for me (branches, tags and trunk). Now I'm about to create a directory for me and my colleagues to put our files in. I'm quite sure the right place to put it is in trunk. Now here and there in tutorials, I see terms like "modules" and "projects" such as in Checking Out a Project - svn checkout svn checkout http://host_name/svn_dir/repository_name/project/trunk proj Is proj in the above line some glorified directory in trunk? Should I do something else than a checkout on trunk, mkdir and then commit when creating a directory for me and my colleagues? Whats the difference between a project, a directory in trunk and a module?

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  • Can you define <=> in Ruby and then have ==, >, <, >=, and <= defined automatically?

    - by jeremy Ruten
    Here's part of my Note class: class Note attr_accessor :semitones, :letter, :accidental def initialize(semitones, letter, accidental = :n) @semitones, @letter, @accidental = semitones, letter, accidental end def <=>(other) @semitones <=> other.semitones end def ==(other) @semitones == other.semitones end def >(other) @semitones > other.semitones end def <(other) @semitones < other.semitones end end It seems to me like there should be a module that I could include that could give me my equality and comparison operators based on my <=> method. Is there one? I'm guessing a lot of people run into this kind of problem. How do you usually solve it? (How do you make it DRY?)

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  • How can I hide the taxonomy field for authenticated users but show it for other users in Drupal 6?

    - by Jaymie
    I have a Drupal (v6.17) Content Type which includes a Taxonomy field. I want to hide this from ordinary Authenticated Users, but want it available to my Site Contributor role users, so they can review and then assign tags to user-created nodes. I've tried overriding the Node Add/Edit form in Panels 3 by creating a panel variant especially for Authenticated Users, which would exclude the Taxonomy field. However, the Taxonomy field is bundled in with the "General Form" controls - without showing this, I don't get the Title and Body fields. Is there a way I can either include the Title and Body fields without Taxonomy, OR hide just the Taxonomy field when the authenticated user role creates a node. I realise there's a CCK field which might be able to help me out here, but how do I tie that to the Taxonomy module? Any help gratefully received.

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  • rake task can't access rails.cache

    - by mark
    Hi I want to call a rake task from a cron job that stores remote weather data in the rails cache. However, I must be doing something pretty wrong here because I cannot find any solution through countless fruitless searches. Say I define and call this task namespace :weather do desc "Store weather from remote source to cache" task :cache do Rails.cache.write('weather_data', Date.today) end end I get the error Anonymous modules have no name to be referenced by Which leads me to believe the rails cache isn't available. Outputting Rails.class from the rake file gives me Module but Rails.cache.class again returns the above error. Do I need to include something here? Am I just hopeless at internet? :) Thanks in advance.

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  • Error Messaged and Error Code design

    - by Ved
    We are designing set of web services which will return XML string in response. These are RESTFul services so I will have to send exception inside element. I am planing to design set of Error code which can help me determine where level occured just by looking at the code. For Example 1000 - Application Level 2000 - DB level 3000 - Network level so if I have error message then I can know right away that this was an application level error and it came from 1st business module. I am not very experience in this so I would love to here your thoughts and criticism. Thanks

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  • Generating/managing config files for hosted application

    - by mfinni
    I asked a question about config management, and haven't seen a reply. It's possible my question was too vague, so let's get down to brass tacks. Here's the process we follow when onboarding a new customer instance into our hosted application : how would you manage this? I'm leaning towards a Perl script to populate templates to generate shell scripts, config files, XML config files, etc. Looking briefly at CFengine and Chef, it seems like they're not going to reduce the amount of work, because I'd still have to manually specify all of the changes/edits within the tool. Doesn't seem to be much of a gain over touching the config files directly. We add a stanza to the main config file for the core (3rd-party) application. This stanza has values that defines the instance (customer) name the TCP listener port for this instance (not one currently used) the DB2 database name (serial numeric identifier, already exists, they get prestaged for us by the DBAs) three sub-config files, by name - they need to be created from 3 templates and be named after the instance The sub-config files define: The filepath for the DB2 volumes The filepath for the storage of objects The filepath for just one of the DB2 volumes (yes, redundant to the first item. We run some application commands, start the instance We do some LDAP thingies (make an OU for the instance, etc.) We add a stanza to the config file for our security listener that acts as a passthrough to LDAP instance name LDAP OU TCP port for instance DB2 database name We restart the security listener (off-hours), change the main config file from item 1, stop and restart the instance. It is now authenticating via LDAP. We add the stop and start commands for this instance to the HA failover scripts. We import an XML config file into the instance that defines things for the actual application for the customer - user names, groups, permissions, and business rules. The XML is supplied by the implementation team. Now, we configure the dataloading application We add a stanza to the existing top-level config file that points to a new customer-level config file. The new customer-level config file includes: the instance (customer) name the DB2 database name arbitrary number of sub-config files, by name Each of the sub-config files defines: filepaths to the directories for ingestion, feedback, backup, and failure those filepaths have a common path to a customer-specific folder, and then one folder for each sub-config file Each of those filepaths needs to be created We need to add this customer instance to our monitoring scripts that confirm the proper processes are running and can be logged into. Of course, those monitoring config files include the instance name, the TCP port, the DB2 database name, etc. There's also a reporting application that needs to be configured for the new instance. You get the idea. There's also XML that is loaded into WAS by the middleware team. We give them the values for them to plug into the XML - they could very easily hand us the template and we could give them back completed XML.

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  • Code completion in NetBeans' python plugin does not work properly

    - by T.K.
    I am asking on StackOverflow because surely I am doing something completely silly and I hope S.O. might provide me with a quick answer. I've installed the latest stable Python-plugin for NetBeans. It works great, and I tested code completion with various packages such as sys, os and so on. It works beautifully. However, it does not seem to pick up the code completion for the code in my own project. I created a package called mypackage (it has _init_.py as well), and in it I have a module called mymodule.py. Inside mymodule I've put a class called MyClass, complete with doc-strings and all. Please refer to this screenshot to describe what happens in code-completion: As you see, it's suggesting irrelevant things, as opposed to just MyClass. (Note that if I execute mymodule.MyClass() it works 100%, it's just that I would really like code completion on my own code) Hope I'm just doing something silly here... Any ideas?

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  • Rules Engine vs Expert System

    - by User1
    What is the difference between a rules engine and an expert system? Example1: Let's say that I have a program that determines the expiration date of a new driver's license. It takes inputs like visa expiration date, passport number, birthday, etc. It determines the expiration date of the driver's license from this input. It can even give an error if the input did not have enough valid identifications to allow a new driver's license. Example2: Let's say I am making an online version of the game Monopoly. I want the ability to change the rules of the game (say $400 for passing go or no one can buy properties until they land on the same property twice, etc). I have a module in the code to handle these rules. Are these both rules engines or are they expert systems? They both seem so similar. Is it just a synonym?

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  • Error running celeryd

    - by Eric Palakovich Carr
    I'm posting this question (and answer) so if anybody else has this problem in the future, you'll be able to google it. If you are trying to run celeryd in Django like so: python manage.py celeryd You can receive the following error immediately after it has started: celery@eric-desktop-dev has started. Traceback (most recent call last): File "manage.py", line 11, in <module> execute_manager(settings) <... snip ...> File "/usr/local/lib/python2.6/dist-packages/amqplib-0.6.1-py2.6.egg/amqplib/client_0_8/connection.py", line 134, in __init__ self._x_start_ok(d, login_method, login_response, locale) File "/usr/local/lib/python2.6/dist-packages/amqplib-0.6.1-py2.6.egg/amqplib/client_0_8/connection.py", line 704, in _x_start_ok args.write_longstr(response) File "/usr/local/lib/python2.6/dist-packages/amqplib-0.6.1-py2.6.egg/amqplib/client_0_8/serialization.py", line 352, in write_longstr self.write_long(len(s)) TypeError: object of type 'NoneType' has no len() A rather cryptic error message, with no real clue as to where to go to fix the problem. See below for the answer so you don't waste a bunch of time on this error like I did today :)

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  • accessing OCaml records

    - by hyperboreean
    How can I use some OCaml record that I've defined in some other file? Say for example that I have the file a.ml in which I define the r record: type r = { i: int; j: int; }; and a file b.ml in which I want to use the r record. Something like this: let s = {i = 12; j = 15;} clearly doesn't work - I know it has something to do with accessing the module in which the record is defined, but I've yet to get the syntax right.

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  • Serving files over HTTPS dynamically based on request.ssl? with Attachment_fu

    - by Marston A.
    I see there is a :user_ssl option in attachment_fu which checks the amazon_s3.yml file in order to serve files via https:// In the s3_backend.rb you have this method: def self.protocol @protocol ||= s3_config[:use_ssl] ? 'https://' : 'http://' end But this then makes it serve ALL s3 attachments with SSL. I'd like to make it dynamic depending if the current request was made with https:// i.e: if request.ssl? @protocol = "https://" else @protocol = "http://" end How can I make it work in this way? I've tried modifying the method and then get the NameError: undefined local variable or method `request' for Technoweenie::AttachmentFu::Backends::S3Backend:Module error

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  • Convert wife/husband/partner to a programmer.

    - by Stefan
    originally posted by Stefan: How many of you have had the thought of educate your partner and invite him/her to the beautiful world of programming? I once started to give my wife lessons twice a week, It was a competition between me and another programmer, we thought it would be nice to have our wives understand why we work as programmers and also have it as a hobby sitting all night long. Maybe we could get our wives to feel the power too? After a couple of months my wife didn't like the idea any more, it was too hard to understand she thought, same for my friends wife. So now we are thinking of some project that would be too fun for our wives to turn down just to get the spirit up again. It would be nice to hand over a project to my wife, "Can you debug this for me, please? There are some strange error on module xxx." :) Maybe I'm crazy, what do you think?

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  • Shutting Down SSH Tunnel in Paramiko Programatically

    - by PlaidFan
    We are attempting to use the paramiko module for creating SSH tunnels on demand to arbitrary servers for purposes of querying remote databases. We attempted to use the forward.py demo that ships with paramiko but the big limitation is there does not seem to be an easy way to close an SSH tunnel and the SSH connection once the socket server is started up. The limitation we have is that we cannot activate this from a shell and then kill the shell manually to stop the listner. We need to open the SSH connection, tunnel, perform some actions through the tunnel, close the tunnel, and close the SSH connection within python. I've seen references to a server.shutdown() method but it isn't clear how to implement it correctly. Any help would be greatly appreciated...

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  • How to find out who's causing an access violation error?

    - by Fernando
    I'm getting reports that my app is causing a GPF on some Vista machines. The error message is something like this: access violation at 0x75784062 ( tried to write to 0x00000006) In order to fix this, I first need to know exactly who is causing this GPF: my main exe, some third party component, one of my own activex components, a dll, etc... How can I find this out? What tools can pinpoint the exact module that caused this mess? Any help would be greatly appreciated. PS My app is coded in VB6 and my activex controls are written in Delphi 2007.

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  • Get python tarfile to skip files without read permission

    - by chris
    I'm trying to write a function that backs up a directory with files of different permission to an archive on Windows XP. I'm using the tarfile module to tar the directory. Currently as soon as the program encounters a file that does not have read permissions, it stops giving the error: IOError: [Errno 13] Permission denied: 'path to file'. I would like it to instead just skip over the files it cannot read rather than end the tar operation. This is the code I am using now: def compressTar(): """Build and gzip the tar archive.""" folder = 'C:\\Documents and Settings' tar = tarfile.open ("C:\\WINDOWS\\Program\\archive.tar.gz", "w:gz") try: print "Attempting to build a backup archive" tar.add(folder) except: print "Permission denied attempting to create a backup archive" print "Building a limited archive conatining files with read permissions." for root, dirs, files in os.walk(folder): for f in files: tar.add(os.path.join(root, f)) for d in dirs: tar.add(os.path.join(root, d))

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  • Add image gallery to node in Drupal

    - by vian
    I'm using Image module for Drupal 6 and the submodule of Image Gallery. Image gallery is identified by taxonomy term of certain vocabulary. What I need is to attach Image Gallery View supplied with Image Gallery to certain node. I am now trying to use Views Attach to do this. But how can I pass an argument of taxonomy term for gallery to the view? Also I added the taxonomy term for gallery to be defined for both images and my node type. Is it ok?

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  • C# getting version of unmanaged dll

    - by Richard
    I'm calling an unmanaged dll from my managed c# code and wanted to check I'm calling the right version. The code I'm trying to load the assembly (to then get the resource file and then get the version) is: cur_version = Assembly.LoadFile("X:\Workspace\yreceipts_pos\yRprintProcessor\Debug\yRprintProcessor.dll"); It's failing because of this error: The module was expected to contain an assembly manifest. (Exception from HRESULT: 0x80131018) Does anyone know how to get around this or have a better way to check the version of an unmanaged dll from managed c# code? Thanks in advance, Richard

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  • include_once fails!

    - by user220201
    Hi, I am new to php. I thought I knew enough but apparently do not. I am trying to use the OAuth.php from code.google.com. So I include OAuth.php in my code. Here is my php file - index.php <?php print 'Hello1'; include 'test.php'; print 'Hello2'; include 'OAuth.php'; print 'Hello3'; ?> Here test.php, OAuth.php and index.php are all in the same directory. Amazingly enough, I see Hello1 and Hello2 but not Hello3. What am I missing. Its driving me crazy. Any help is greatly greatly appreciated. I am using php5 with apache 2.2 and also have the oauth.so module installed and loaded from php.net. SV

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  • What's the .proto equivalent of List<T> in protobuf-net?

    - by Marc Bollinger
    To keep some consistency, we use code generation for a lot of our object models, and one of the offshoots of that has been generating the .proto files for ProtocolBuffers via a separate generation module. At this point though, I'm stumped at how to implement the generation for when it happens upon a List<T> object. It looks like this is possible via contracts: [ProtoMember(1)] public List<SomeType> MyList {get; set;} but outside of that, I'm not sure how or if it's possible to do this only from creating the .proto file/using the VS custom tool. Any thoughts?

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  • jQuery Toggle Cookie Support

    - by hell0w0rld
    I'm trying to implement the jQuery Cookie plugin into my slide toggle script, but so far haven't been successful. Here's my code (without any cookie implementation): jQuery: $(document).ready(function() { $('a.toggle').click(function() { var id = $(this).attr('name'); $('#module' + id).slideToggle('fast'); $('a.toggle[name='+id+']').toggle(); return false; }); }); HTML: <a class="toggle" name="1" href="#">- Hide</a> <a class="toggle hidden" name="1" href="#">+ Show</a> <div id="module1"><p>Hello World</p></div> Anyone know if it's easy enough to implement the jQuery Cookie plugin into my existing code so it remembers the open/closed state? Thank you.

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  • Spring 3 - Custom Security

    - by Eqbal
    I am in the process of converting a legacy application from proprietary technology to a Spring based web app, leaving the backend system as is. The login service is provided by the backend system through a function call that takes in some parameter (username, password plus some others) and provides an output that includes the authroizations for the user and other properties like firstname, lastname etc. What do I need to do to weave this into Spring 3.0 security module. Looks like I need to provide a custom AuthenticationProvider implementation (is this where I call the backend function?). Do I also need a custom User and UserDetailsService implementation which needs loadUserByName(String userName)? Any pointers on good documentation for this? The reference that came with the download is okay, but doesn't help too much in terms of implementing custom security.

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  • evaluating buffer in emacs python-mode on remote host

    - by Adrian
    Hello, I'm using emacs23 with tramp to modify python scripts on a remote host. I found that when I start the python shell within emacs it starts up python on the remote host. My problem is that when I then try to call python-send-buffer via C-c C-c it comes up with the error Traceback (most recent call last): File "", line 1, in ? ImportError: No module named emacs Traceback (most recent call last): File "", line 1, in ? NameError: name 'emacs' is not defined Now, I must admit that I don't really know what's going on here. Is there a way for me to configure emacs so that I can evaluate the buffer on the remote host? Many thanks.

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  • Prime Number - Data while loading

    - by Emroot
    Hi, I was trying in Ruby on Rails how to find a prime number. Here is my code : helper : app/helpers/test_helper.rb module TestHelper def prime_number? number index = 2 tmp = 0 while index <= number if tmp < 1 if (number % index) == 0 tmp += 1 end else return false end index += 1 end return true end end and my view : app/views/test/index.html.erb <% (2..100).each do |i| -%> <% if prime_number? i %> <%= i %> <% end -%> <% end -%> So my question is : How can you load data while it's calculating ? I mean if I replace 100 by 100000 in my view, how can I see data on my view while my helper method is calculating ? Do I need to use ajax or rails provide a tool for that ? Thank you.

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  • C# Assembly Xna.Framework.dll does not load

    - by jbsnorro
    When trying to load Microsoft.Xna.Framework.dll from any project, it throws a FileNotFoundException. The specified module could not be found. (Exception from HRESULT: 0x8007007E), with no innerException. Even the simple code like the following throws that exception: static void Main(string[] args) { Assembly.LoadFile(@"C:\Microsoft.Xna.Framework.dll"); } I run XP x64, but I've set the platform in the configuration manager to x86, because I know it shouldn't(doesn't) work on x64 or Any CPU. I've manually added the dll file to GAC, but that didn't solve the problem. I have also tried the M$ Assembly Binding Log Viewer to see if those logs had any useful information, but they didn't. Everything, the loading etc, was a success according to them. Any suggestions? please?

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