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• File management

  - by user343934

  I am working on python and biopython right now. I have a file upload form and whatever file is uploaded suppose(abc.fasta) then i want to pass same name in execute (abc.fasta) function parameter and display function parameter (abc.aln). Right now i am changing file name manually, but i want to have it automatically. Workflow goes like this. ----If submit is not true then display only header and form part --- if submit is true then call execute() and get file name from form input --- Then display the save file result in the same page. File name is same as input. My raw code is here -- http://pastebin.com/FPUgZSSe Any suggestions, changes and algorithm is appreciated Thanks

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• Google App Engine Database Index

  - by fjsj

  I need to store a undirected graph in a Google App Engine database. For optimization purposes, I am thinking to use database indexes. Using Google App Engine, is there any way to define the columns of a database table to create its index? I will need some optimization, since my app uses this stored undirected graph on a content-based filtering for item recommendation. Also, the recommender algorithm updates the weights of some graph's edges. If it is not possible to use database indexes, please suggest another method to reduce query time for the graph table. I believe my algorithm does more data retrieval operations from graph table than write operations. PS: I am using Python.

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• is this a correct way to generate rsa keys?

  - by calccrypto

  is this code going to give me correct values for RSA keys (assuming that the other functions are correct)? im having trouble getting my program to decrypt properly, as in certain blocks are not decrypting properly this is in python: import random def keygen(bits): p = q = 3 while p == q: p = random.randint(2**(bits/2-2),2**(bits/2)) q = random.randint(2**(bits/2-2),2**(bits/2)) p += not(p&1) # changes the values from q += not(q&1) # even to odd while MillerRabin(p) == False: # checks for primality p -= 2 while MillerRabin(q) == False: q -= 2 n = p * q tot = (p-1) * (q-1) e = tot while gcd(tot,e) != 1: e = random.randint(3,tot-1) d = getd(tot,e) # gets the multiplicative inverse while d<0: # i can probably replace this with mod d = d + tot return e,d,n one set of keys generated: e = 3daf16a37799d3b2c951c9baab30ad2d d = 16873c0dd2825b2e8e6c2c68da3a5e25 n = dc2a732d64b83816a99448a2c2077ced

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• Is this __import__ functionality correct?

  - by Jason Baker

  I have a package named jiva_tasks, which I'm trying to import via celery (using the CELERY_IMPORTS attribute of celeryconfig. The import statement that celery is using is this: __import__(module, [], [], ['']) Oddly enough, when this syntax is used, the module gets imported twice, once as jiva_tasks and another time as jiva_tasks. (with a period at the end). Now, chances are good that celery should be passing in globals rather than an empty list, but this seems broken to me. It seems odd that even if given the wrong arguments, __import__ would import something that isn't a valid python module name. I know that the way to fix this is to pass in globals, but I want to understand why I'm getting this result. Is this a bug, or is there something I don't understand about how __import__ is working? Update: It also seems to be working fine if I use importlib.

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• How to return a value when destroying/cleaning-up an object instance

  - by Mridang Agarwalla

  When I initiate a class in Python, I give it some values. I then call method in the class which does something. Here's a snippet: class TestClass(): def __init__(self): self.counter = 0 def doSomething(self): self.counter = self.counter + 1 print 'Hiya' if __name__ == "__main__": obj = TestClass() obj.doSomething() obj.doSomething() obj.doSomething() print obj.counter As you can see, everytime I call the doSomething method, it prints some text and increments an internal variable i.e. counter. When I initiate the class, i set the counter variable to 0. When I destroy the object, I'd like to return the internal counter variable. What would be a good way of doing this? I wanted to know if there were other ways apart from doing stuff like: accessing the variable directly. Like obj.counter. creating a method like getCounter. Thanks.

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• Faster way to convert from 24 bit wav pcm format to float?

  - by LMO

  I need to read data in from a wav file in 24 bit pcm format, and convert to float. I'm using Python 2.7.2. The wave package reads the data in as a string, so what I've tried is: # read in entire wav file wdata = f.readframes(nFrames) # unpack into signed integers and convert to float data = array.array('f') for i in range(0,nFrames*3,3): data.append(float(struct.unpack('<i', '\x00'+ wdata[i:i+3])[0])) # normalize sample values data = data / 0x800000 This is quite a bit faster than my earlier approaches, but still quite slow. Can anyone suggest a more efficient method?

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• Django or Drupal, which one should I use that suits best my needs ?

  - by HJ-INCPP

  Hello, I want to learn and use Drupal or Django for the following: dynamic web sites, medium database, multi-level users, paypal integration, content managment, speed (developing), security I like MVC, ORM and object-oriented prg. Which is better to jump into ? Which one is more mature, powerful, understandable, object-oriented and easier to use by the time ? What about Python Spring ... Also, which of these 3 are better documented, are better for a cv and have more extensions? Known languages: php, java, mysql Thank you !

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• Need to get the uploaded file to my local PC

  - by Suhail

  Hi, I have created a test form which will ask users to enter a name and upload the image file: <html lang="en"> <head> <title>Testing image upload</title> </head> <body> <form action="/services/upload" method="POST" enctype="multipart/form-data"> File Description: <input name='fdesc' type='text'><br> File name: <input type="file" name="fname"><br> <div><input type="submit"></div> </form> </body> </html> i need to get the file uploaded by the user and store it on my local PC. can this be done in python ? please let me know.

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• How to detect identical part(s) inside string?

  - by Horace Ho

  I try to break down the http://stackoverflow.com/questions/2711961/decoding-algorithm-wanted question into smaller questions. This is Part I. Question: two strings: s1 and s2 part of s1 is identical to part of s2 space is separator how to extract the identical part(s)? example 1: s1 = "12 November 2010 - 1 visitor" s2 = "6 July 2010 - 100 visitors" the identical parts are "2010", "-", "1" and "visitor" example 2: s1 = "Welcome, John!" s2 = "Welcome, Peter!" the identical parts are "Welcome," and "!" Python and Ruby preferred. Thanks

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• Trying to figure out URL dispatcher for sluggale URLs like stackoverflow

  - by TylerW

  I'm using the Tornado framework (Python). I have the sluggable URLs working. But I have 3 different entries in the URL dispatcher. I was wondering if someone could help me transform it into one line. This is what I have: (r"/post/([0-9]+)/[a-zA-Z0-9\-]+", SpotHandler), (r"/post/([0-9]+)/", SpotHandler), (r"/post/([0-9]+)", SpotHandler), I want it so that the following URLs all go to the same place. http://domain.com/post/14 http://domain.com/post/14/ http://domain.com/post/14/any-text-it-doesnt-matter-what-it-is

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• Django 1.2 crash course needed

  - by delusionalweekendwarrior

  I know Python but I've never used Django. What do I need to know about Django 1.2 to port my typical PHP CRUD web application in one weekend? (Yes I've read Joel Spolsky's Netscape article :-)) I'm reading this tutorial right now and it's excellent. I'm already playing around with inspectdb to generate my models from the existing schema. I'm planning to use the following features of Django this weekend: Fragment caching Static asset versioning (for far future expires) Schema migrations (or whatever they're called in Django) Auto-admin (and customize it later) The test framework ...other stuff I probably don't know about yet I'm familiar with all these concepts in other languages/frameworks, except for the ORM which I've never used. I know SQL pretty well though. Any links, sage bits of advice, gotchas, stuff not mentioned in the (excellent) tutorial/docs, or stuff that is mentioned but warrants repeating == very welcome. Thanks!

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• libxml2 install error: command 'gcc' failed with exit status 1? What are the dependencies of libxml2

  - by SIA

  Hi everybody!! I am trying to install libxml2 on unbuntu 9.10 and getting errors: $ sudo python setup.py develop Its a very lengthy error message but the last error is Setup script exited with error: Command 'gcc' failed with exit status 1. Can anybody tell me why i am getting this error? What are the dependencies or libraries required to install this? scenario: I am trying to setup the reddit.com clone, and when i run develop command, its generating a huge error as stated above. Please help!! Thanks in advance And my many thanks to Stackoverflow team for having such a life saving site.

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• How do I redirect stdin/stdout when I have a sequence of commands in Bash?

  - by Tom

  I've currently got a Bash command being executed (via Python's subprocess::Popen) which is reading from stdin, doing something and outputing to stdout. Something along the lines of: pid = subprocess.Popen( ["-c", "cmd1 | cmd2"], stdin = subprocess.PIPE, stdout = subprocess.PIPE, shell =True ) output_data = pid.communicate( "input data\n" ) Now, what I want to do is to change that to execute another command in that same subshell that will alter the state before the next commands execute, so my shell command line will now (conceptually) be: cmd0; cmd1 | cmd2 Is there any way to have the input sent to cmd1 instead of cmd0 in this scenario? I'm assuming the output will include cmd0's output (which will be empty) followed by cmd2's output. cmd0 shouldn't actually read anything from stdin, does that make a difference in this situation? I know this is probably just a dumb way of doing this, I'm trying to patch in cmd0 without altering the other code too significantly. That said, I'm open to suggestions if there's a much cleaner way to approach this.

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• Web programming: Apache modules: mod_python vs mod_php

  - by Olivier Pons

  Hi! I've been using for more than 12 years PHP with Apache (a.k.a mod_php) for my web development work. I've recenlty discovered python and its real power (I still don't understand why this is not always the best product that becomes the most famous). I've just discovered mod_python for Apache. I've already googled but without success things like mod_python vs mod_php. I wanted to know the differences between the two mod_php and mod_python in terms of: speed productivity maintainance (I know `python is most productive and maintainable language in the world, but is it the same for Web programming with Apache) availability of features e.g, cookies and session handling, databases, protocols, etc.

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• Pass logger instance to class

  - by mridang

  Hi Guys, I'm using a open-source Python library in my project. This library logs a lot of information using the logging class. ...but I can't see the output or log it to file. I know that i would have to create a logger instance and add a file-handler or a console-handler to it but how can i pass this logger instance to the class? Here's the init snippet of the class that I'm going to be using. class Periscope: ''' Main Periscope class''' def __init__(self): self.config = ConfigParser.SafeConfigParser({"lang": "en"}) if is_local: self.config_file = os.path.join(bd.xdg_config_home, "periscope", "config") if not os.path.exists(self.config_file): folder = os.path.dirname(self.config_file) if not os.path.exists(folder): logging.info("Creating folder %s" %folder) os.mkdir(folder) logging.info("Creating config file") configfile = open(self.config_file, "w") self.config.write(configfile) configfile.close() else: #Load it self.config.read(self.config_file) self.pluginNames = self.listExistingPlugins() self._preferedLanguages = None Any help? Thanks guys.

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• What are some good ways to do intermachine locking?

  - by mike

  Our server cluster consists of 20 machines, each with 10 pids of 5 threads. We'd like some way to prevent any two threads, in any pid, on any machine, from modifying the same object at the same time. Our code's written in Python and runs on Linux, if that helps narrow things down. Also, it's a pretty rare case that two such threads want to do this, so we'd prefer something that optimizes the "only one thread needs this object" case to be really fast, even if it means that the "one thread has locked this object and another one needs it" case isn't great. What are some of the best practices?

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• Why are closures broken within exec?

  - by Devin Jeanpierre

  In Python 2.6, >>> exec "print (lambda: a)()" in dict(a=2), {} 2 >>> exec "print (lambda: a)()" in globals(), {'a': 2} Traceback (most recent call last): File "<stdin>", line 1, in <module> File "<string>", line 1, in <module> File "<string>", line 1, in <lambda> NameError: global name 'a' is not defined >>> exec "print (lambda: a).__closure__" in globals(), {'a': 2} None I expected it to print 2 twice, and then print a tuple with a single cell. It is the same situation in 3.1. What's going on?

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• Tag Suggestion system, approaches and ideas

  - by Galois

  Hi guys! -- I am working on a (auto) tag suggestion system (NOT tag autocomplete). Lets say I want to suggest tags for a given question like here on SO (although SO's tagging system is auto-complete). My main idea is to get the intersection between the tags_set and the given question.split()_set. (In python the set_intersection is efficient enough). Also, in order to make it a little bit more accurate I might use words-distance to count as 'the same' very close words i.e movie == movies. For now I am not thinking about using any Collaborative Filtering technique looking for the tags to similar questions and so on, because I believe since the question text is pretty short (comparing with a blog article or a paper) it is not worth the effort. So I was wondering if you have any other (more) efficient approaches to suggest. Any ideas, specially from people who they have done something like that before, are more than welcome.

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• KeyError this says that key(partner) is not in dict ?

  - by Ansh Jain

  I am trying to make an chat application using python and django. I almost complete it and its working fine for 8-10 minutes when two persons are chatting after that certain time it shows an error. here is the traceback : - Traceback (most recent call last): File "\Django_chat\django_chat\chat\views.py", line 55, in receive message = chatSession.getMessage(request.session['partner'],request.session['uid'],afterTime) File "C:\Python26\lib\site-packages\django\contrib\sessions\backends\base.py", line 47, in __getitem__ return self._session[key] KeyError: 'partner' here is the receive module :- def receive(request): message received by this user chatSession = chat() data = request.POST afterTime = data['lastMsgTime'] try: message = chatSession.getMessage(request.session['partner'],request.session['uid'],afterTime) except: #partnerId = virtual_users.objects.get(id=request.session['uid']).partner print('there is an error in receive request') traceback.print_exc(file=open("/myapp.log","a")) msg = serializers.serialize("json", message) return HttpResponse(msg) Please Help me :( thanks Ansh J

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• Change Gmail message routing on individual mailboxes

  - by citadelgrad

  We are using dual delivery for one of our Google Apps doamins and need to be able to disable mail delivery to the Gmail account. You can manually update the settings on a per user basis through the Admin interface by unchecking the box next to "Google Apps Email" in the Email routing section. From the Google Apps API documentation for the python library it does not appear that I programmatically disable the email routing for "Google Apps Email" on a per user basis. Does anyone know if it's possible? The only routing related method I can find is at the Domain level and not the user level. gdata.apps.adminsettings.service Thank you!

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• Importing Classes Within a Module

  - by CodeJoust

  Currently, I have a parser with multiple classes that work together. For Instance: TreeParser creates multiple Product and Reactant modules which in turn create multiple Element classes. The TreeParser is called by a render method within the same module, which is called from the importer. Currently, using the class name in the imported module file works only if the file calling the module contains from module_name import *, so the classes are imported into the main namespace. Finally, if the package has dependencies (such as re and another another module within the same folder), where is the best place to require those modules? Within the __init__.py file or within the module itself? I don't really want to add the module name in front of every call to the class, in case I do call import *, however, is it possible to use a variable name of the current module to call the class, or use a workaround in the __init__.py file? I'm probably used to the ruby require '' method instead of python's module system.

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• Unittest and mock

  - by user1410756

  I'm testing with unittest in python and it's ok. Now, I have introduced mock and I need to resolve a question. This is my code: from mock import Mock import unittest class Matematica(object): def __init__(self, op1, op2): self.op1 = op1 self.op2 = op2 def adder(self): return self.op1 + self.op2 def subs(self): return abs(self.op1 - self.op2) def molt(self): return self.op1 * self.op2 def divid(self): return self.op1 / self.op2 class TestMatematica(unittest.TestCase): """Test della classe Matematica""" def testing(self): """Somma""" mat = Matematica(10,20) self.assertEqual(mat.adder(),30) """Sottrazione""" self.assertEqual(mat.subs(),10) class test_mock(object): def __init__(self, matematica): self.matematica = matematica def execute(self): self.matematica.adder() self.matematica.adder() self.matematica.subs() if __name__ == "__main__": result = unittest.TextTestRunner(verbosity=2).run(TestMatematica('testing')) a = Matematica(10,20) b = test_mock(a) b.execute() mock_foo = Mock(b.execute)#return_value = 'rafa') mock_foo() print mock_foo.called print mock_foo.call_count print mock_foo.method_calls This code is functionally and result of print is: True, 1, [] . Now, I need to count how many times are called self.matematica.adder() and self.matematica.subs() . THANKS

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• Trying to catch integrity error with sqlaclhemey

  - by Lostsoul

  I'm having problems with trying to catch a error. I'm using pyramid/sqlalchemy and made a sign up form with email as the primary key. The problem is when a duplicate email is entered it raises a IntegrityError, so I'm trying to catch that error and provide a message but no matter what I do I can't catch it(the error keeps appearing). try: new_user = Users(email, firstname, lastname, password) DBSession.add(new_user) return HTTPFound(location = request.route_url('new')) except IntegrityError: message1 = "Yikes! Your email already exists in our system. Did you forget your password?" I get the same message when I tried except exc.SQLAlchemyError (although I want to catch specific errors and not a blanket catch all). Is there something wrong with my python syntax? or is there something I need to do special in sqlalchemy to catch it?

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• Best option for Google App Engine Datastore and external database?

  - by Alex

  I need to get an App Engine app talking to and sharing data with an external database, The best option i can come up with is outputting the external database data to an xml file and then processing this in my app engine app and storing it inside the datastore, although the data being shared is sensitive data such as login details so outputting this to an xml file is not exactly a great idea, is it possible for the app engine app to directly query the database? or is there a secure option for using xml files? oh and im using python/django and the external database will be hosted on another domain

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• Why is it that I cannot insert this into Django correctly?

  - by alex

  new_thing = MyTable(last_updated=datetime.datetime.now()) new_thing.save() >>>>select * from MyTable\G; last_updated: 2010-04-01 05:26:21 However, in my Python console...this is what it says... >>> print datetime.datetime.now() 2010-04-01 10:26:21.643041 So obviously it's off by 5 hours. By the way, the database uses "SYSTEM" as its time, so they should match perfectly. mysql> SELECT current_time; +--------------+ | current_time | +--------------+ | 10:30:16 | +--------------+ >>> print datetime.datetime.now() 2010-04-01 10:30:17.793040

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