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  • Encrypt file using M2Crypto

    - by Bear
    It is known that I can read the whole file content in memory and encrypt it using the following code. contents = fin.read() cipher = M2Crypto.EVP.Cipher(alg="aes_128_cbc", key = aes_key, iv = aes_iv, op = 1) encryptedContents = cipher.update(contents) encryptedContents += cipher.final() But what if the file size is large, is there a way for me to pass the input stream to M2Crypto instead of reading the whole file first?

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  • Parse large XML file w/ script or use BioPython API ?

    - by jeremy04
    Hey guys this is my first question on here. I'm trying to make a local copy of the UniprotKB in SQL. The UniprotKB is 2.1GB, and it comes in XML and a special text format used by SwissProt Here are my options: 1) Use a SAX parser (XML) - I chose Ruby, and Nokogiri. I started writing the parser, but my initial reaction: how would I map the XML schema to the SAX parser? 2) BioPython - I already have BioSQL/Biopython installed, which literally created my SQL schema for me, and I was able to successfully insert one SwissProt/Uniprot txt file into the database. I'm running it right now (crosses fingers) on the entire 2.1gb. Here is the code I'm running: from Bio import SeqIO from BioSQL import BioSeqDatabase from Bio import SwissProt server = BioSeqDatabase.open_database(driver = "MySQLdb", user = "root", passwd = "", host="localhost", db = "bioseqdb") db = server["uniprot"] iterator = SeqIO.parse(open("/path/to/uniprot_sprot.dat", "r"), "swiss") db.load(iterator) server.commit() Edit: it's now crashing because the transactions are getting locked (since the tables are Innodb) Error Number: 1205 Lock wait timeout exceeded; try restarting transaction. I'm using MySQL version: 5.1.43 Should I switch my database to Postgrelsql ?

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  • Load image from string

    - by zaf
    Given a string containing jpeg image data, is it possible to load this directly in pygame? I've tried using StringIO but failed and I don't completely understand the 'file-like' object concept. Currently, as a workaround, I'm saving to disk and then loading an image the standard way: # imagestring contains a jpeg f=open('test.jpg','wb') f.write(imagestring) f.close() image=pygame.image.load('test.jpg') Any suggestions on improving this so that we avoid creating a temp file?

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  • Parse raw HTTP Headers

    - by Cev
    I have a string of raw HTTP and I would like to represent the fields in an object. Is there any way to parse the individual headers from an HTTP string? 'GET /search?sourceid=chrome&ie=UTF-8&q=ergterst HTTP/1.1\r\nHost: www.google.com\r\nConnection: keep-alive\r\nAccept: application/xml,application/xhtml+xml,text/html;q=0.9,text/plain;q=0.8,image/png,*/*;q=0.5\r\nUser-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_6; en-US) AppleWebKit/534.13 (KHTML, like Gecko) Chrome/9.0.597.45 Safari/534.13\r\nAccept-Encoding: gzip,deflate,sdch\r\nAvail-Dictionary: GeNLY2f-\r\nAccept-Language: en-US,en;q=0.8\r\n [...]'

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  • Elegant Disjunctive Normal Form in Django

    - by Mike
    Let's say I've defined this model: class Identifier(models.Model): user = models.ForeignKey(User) key = models.CharField(max_length=64) value = models.CharField(max_length=255) Each user will have multiple identifiers, each with a key and a value. I am 100% sure I want to keep the design like this, there are external reasons why I'm doing it that I won't go through here, so I'm not interested in changing this. I'd like to develop a function of this sort: def get_users_by_identifiers(**kwargs): # something goes here return users The function will return all users that have one of the key=value pairs specified in **kwargs. Here's an example usage: get_users_by_identifiers(a=1, b=2) This should return all users for whom a=1 or b=2. I've noticed that the way I've set this up, this amounts to a disjunctive normal form...the SQL query would be something like: SELECT DISTINCT(user_id) FROM app_identifier WHERE (key = "a" AND value = "1") OR (key = "b" AND value = "2") ... I feel like there's got to be some elegant way to take the **kwargs input and do a Django filter on it, in just 1-2 lines, to produce this result. I'm new to Django though, so I'm just not sure how to do it. Here's my function now, and I'm completely sure it's not the best way to do it :) def get_users_by_identifiers(**identifiers): users = [] for key, value in identifiers.items(): for identifier in Identifier.objects.filter(key=key, value=value): if not identifier.user in users: users.append(identifier.user) return users Any ideas? :) Thanks!

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  • How can this code be made more Pythonic?

    - by usethedeathstar
    This next part of code does exactly what I want it to do. dem_rows and dem_cols contain float values for a number of things i can identify in an image, but i need to get the nearest pixel for each of them, and than to make sure I only get the unique points, and no duplicates. The problem is that this code is ugly and as far as I get it, as unpythonic as it gets. If there would be a pure-numpy-solution (without for-loops) that would be even better. # next part is to make sure that we get the rounding done correctly, and than to get the integer part out of it # without the annoying floatingpoint-error, and without duplicates fielddic={} for i in range(len(dem_rows)): # here comes the ugly part: abusing the fact that i overwrite dictionary keys if I get duplicates fielddic[int(round(dem_rows[i]) + 0.1), int(round(dem_cols[i]) + 0.1)] = None # also very ugly: to make two arrays of integers out of the first and second part of the keys field_rows = numpy.zeros((len(fielddic.keys())), int) field_cols = numpy.zeros((len(fielddic.keys())), int) for i, (r, c) in enumerate(fielddic.keys()): field_rows[i] = r field_cols[i] = c

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  • Possible to change function name in definition?

    - by Bird Jaguar IV
    I tried several ways to change the function name in the definition, but they failed. >>> def f(): pass >>> f.__name__ 'f' >>> def f(): f.__name__ = 'new name' >>> f.__name__ 'f' >>> def f(): self.__name__ = 'new name' >>> f.__name__ 'f' But I can change the name attribute after defining it. >>> def f(): pass >>> f.__name__ = 'new name' >>> f.__name__ 'new name' Any way to change/set it in the definition (other than using a decorator)?

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  • Dynamically create class attributes

    - by ahojnnes
    Hi, I need to dynamically create class attributes from a DEFAULTS dictionary. defaults = { 'default_value1':True, 'default_value2':True, 'default_value3':True, } class Settings(object): default_value1 = some_complex_init_function(defaults[default_value1], ...) default_value2 = some_complex_init_function(defaults[default_value2], ...) default_value3 = some_complex_init_function(defaults[default_value3], ...) I could also achive this by having sth. like __init__ for class creation, in order to dynamically create these attributes from dictionary and save a lot of code and stupid work. How would you do this? Thank you very much in advance!

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  • how to create multiple selections in text edit box in qt4?

    - by Ronny
    Qt3.3 used to allow for multiple selections in the QTextEdit widget by calling the setSelection() function and specifying a different selection id (selNum) as the last argument in that function. In Qt4, to create a selection, I do it by creating a QTextCursor object and call the setPosition() or movePosition() methods. I have no problems being able to create a single selection of text. I am, however, unable to find a way to create multiple selections. The methods in Qt4 do not have an argument which allows you to set a selection id, nor can i find any other function in the QTextCursor or QTextEdit which looks like it might allow me to do so. Has this feature been completely removed from Qt4? or has is there a new and different way of doing it? Thanks. Ronny

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  • Django: Extending User Model - Inline User fields in UserProfile

    - by Jack Sparrow
    Is there a way to display User fields under a form that adds/edits a UserProfile model? I am extending default Django User model like this: class UserProfile(models.Model): user = models.OneToOneField(User, unique=True) about = models.TextField(blank=True) I know that it is possible to make a: class UserProfileInlineAdmin(admin.TabularInline): and then inline this in User ModelAdmin but I want to achieve the opposite effect, something like inverse inlining, displaying the fields of the model pointed by the OneToOne Relationship (User) in the page of the model defining the relationship (UserProfile). I don't care if it would be in the admin or in a custom view/template. I just need to know how to achieve this. I've been struggling with ModelForms and Formsets, I know the answer is somewhere there, but my little experience in Django doesn't allow me to come up with the solution yet. A little example would be really helpful!

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  • Numpy array, how to select indices satisfying multiple conditions?

    - by Bob
    Suppose I have a numpy array x = [5, 2, 3, 1, 4, 5], y = ['f', 'o', 'o', 'b', 'a', 'r']. I want to select the elements in y corresponding to elements in x that are greater than 1 and less than 5. I tried x = array([5, 2, 3, 1, 4, 5]) y = array(['f','o','o','b','a','r']) output = y[x > 1 & x < 5] # desired output is ['o','o','b','a'] but this doesn't work. How would I do this?

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  • more efficient way to pickle a string

    - by gatoatigrado
    The pickle module seems to use string escape characters when pickling; this becomes inefficient e.g. on numpy arrays. Consider the following z = numpy.zeros(1000, numpy.uint8) len(z.dumps()) len(cPickle.dumps(z.dumps())) The lengths are 1133 characters and 4249 characters respectively. z.dumps() reveals something like "\x00\x00" (actual zeros in string), but pickle seems to be using the string's repr() function, yielding "'\x00\x00'" (zeros being ascii zeros). i.e. ("0" in z.dumps() == False) and ("0" in cPickle.dumps(z.dumps()) == True)

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  • Django: What's the correct way to get the requesting IP address?

    - by swisstony
    I'm trying to develop an app using Django 1.1 on Webfaction. I'd like to get the IP address of the incoming request, but when I use request.META['REMOTE_ADDR'] it returns 127.0.0.1. There seems to be a number of different ways of getting the address, such as using HTTP_X_FORWARDED_FOR or plugging in some middleware called SetRemoteAddrFromForwardedFor. Just wondering what the best approach was?

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  • How to achieve interaction between GUI class with logic class

    - by volting
    Im new to GUI programming, and haven't done much OOP. Im working on a basic calculator app to help me learn GUI design and to brush up on OOP. I understand that anything GUI related should be kept seperate from the logic, but Im unsure how to implement interaction between logic an GUI classes when needed i.e. basically passing variables back and forth... Im using TKinter and when I pass a tkinter variable to my logic it only seems to hold the string PY_VAR0. def on_equal_btn_click(self): self.entryVariable.set(self.entryVariable.get() + "=") calculator = Calc(self.entryVariable) self.entryVariable.set(calculator.calculate()) Im sure that im probably doing something fundamentally wrong and probabaly really stupid, I spent a considerable amount of time experimenting (and searching for answers online) but Im getting no where. Any help would be appreciated. Thanks, V The Full Program (well just enough to show the structure..) import Tkinter class Gui(Tkinter.Tk): def __init__(self,parent): Tkinter.Tk.__init__(self,parent) self.parent = parent self.initialize() def initialize(self): self.grid() self.create_widgets() """ grid config """ #self.grid_columnconfigure(0,weight=1,pad=0) self.resizable(False, False) def create_widgets(self): """row 0 of grid""" """Create Text Entry Box""" self.entryVariable = Tkinter.StringVar() self.entry = Tkinter.Entry(self,width=30,textvariable=self.entryVariable) self.entry.grid(column=0,row=0, columnspan = 3 ) self.entry.bind("<Return>", self.on_press_enter) """create equal button""" equal_btn = Tkinter.Button(self,text="=",width=4,command=self.on_equal_btn_click) equal_btn.grid(column=3, row=0) """row 1 of grid""" """create number 1 button""" number1_btn = Tkinter.Button(self,text="1",width=8,command=self.on_number1_btn_click) number1_btn.grid(column=0, row=1) . . . def on_equal_btn_click(self): self.entryVariable.set(self.entryVariable.get() + "=") calculator = Calc(self.entryVariable) self.entryVariable.set(calculator.calculate()) class Calc(): def __init__(self, equation): self.equation = equation def calculate(self): #TODO: parse string and calculate... return self.equation if __name__ == "__main__": app = Gui(None) app.title('Calculator') app.mainloop()

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  • Divide numpy array

    - by BandGap
    Hi all I have some data represented in a 1300x1341 matrix. I would like to split this matrix in several pieces (e.g. 9) so that I can loop over and process them. The data needs to stay ordered in the sense that x[0,1] stays below (or above if you like) x[0,0] and besides x[1,1]. Just like if you had imaged the data, you could draw 2 vertical and 2 horizontal lines over the image to illustrate the 9 parts. If I use numpys reshape (eg. matrix.reshape(9,260,745) or any other combination of 9,260,745) it doesn't yield the required structure since the above mentioned ordering is lost... Did I misunderstand the reshape method or can it be done this way? What other pythonic/numpy way is there to do this?

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  • Selenium selected option in dropdown not displayed correctly

    - by luckyfool
    I have the following issue with Selenium Webdriver. There are two dropdown menus on a page i am testing "brand" and "items". The options of "items" depend on which brand you choose. I am trying to iterate through all possible choices and print brand-item pairs. I use two possible ways to pick an option from each dropdown menu Using Select(): def retryingSelectOption(name,n): result=False attempts=0 while attempts<5: try: element=Select(driver.find_element_by_name(name)) element.select_by_index(n) print element.all_selected_options[0].text result=True break except StaleElementReferenceException: pass attempts+=1 return result And using .click(): def retryingClickOption(name,n): result=False attempts=0 while attempts<5: try: driver.find_element_by_name(name).find_elements_by_tag_name("option")[n].click() result=True break except StaleElementReferenceException: pass attempts+=1 return result My problem is that at ,what seem to me as random moments (sometimes it works sometimes it does not), even though the above functions return True and printing out the selected option shows me the correct answer, the browser still displays the previous option. So basically Selenium tells me i have picked the right option but the browser displays the previous one.No idea what is wrong.

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  • Use Twisted's getPage as urlopen?

    - by RadiantHex
    Hi folks, I would like to use Twisted non-blocking getPage method within a webapp, but it feels quite complicated to use such function compared to urlopen. This is an example of what I'm trying to achive: def web_request(request): response = urllib.urlopen('http://www.example.org') return HttpResponse(len(response.read())) Is it so hard to have something similar with getPage?

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  • Modify passed, nested dict/list

    - by Gerenuk
    I was thinking of writing a function to normalize some data. A simple approach is def normalize(l, aggregate=sum, norm_by=operator.truediv): aggregated=aggregate(l) for i in range(len(l)): l[i]=norm_by(l[i], aggregated) l=[1,2,3,4] normalize(l) l -> [0.1, 0.2, 0.3, 0.4] However for nested lists and dicts where I want to normalize over an inner index this doesnt work. I mean I'd like to get l=[[1,100],[2,100],[3,100],[4,100]] normalize(l, ?? ) l -> [[0.1,100],[0.2,100],[0.3,100],[0.4,100]] Any ideas how I could implement such a normalize function? Maybe it would be crazy cool to write normalize(l[...][0]) Is it possible to make this work?? Or any other ideas? Also not only lists but also dict could be nested. Hmm... EDIT: I just found out that numpy offers such a syntax (for lists however). Anyone know how I would implement the ellipsis trick myself?

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  • What is the difference between type.__getattribute__ and object.__getattribute__?

    - by Neil G
    Given: In [37]: class A: ....: f = 1 ....: In [38]: class B(A): ....: pass ....: In [39]: getattr(B, 'f') Out[39]: 1 Okay, that either calls super or crawls the mro? In [40]: getattr(A, 'f') Out[40]: 1 This is expected. In [41]: object.__getattribute__(A, 'f') Out[41]: 1 In [42]: object.__getattribute__(B, 'f') --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-42-de76df798d1d> in <module>() ----> 1 object.__getattribute__(B, 'f') AttributeError: 'type' object has no attribute 'f' What is getattribute not doing that getattr does? In [43]: type.__getattribute__(B, 'f') Out[43]: 1 What?! type.__getattribute__ calls super but object's version doesn't? In [44]: type.__getattribute__(A, 'f') Out[44]: 1

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  • Serving large generated files using Google App Engine?

    - by John Carter
    Hiya, Presently I have a GAE app that does some offline processing (backs up a user's data), and generates a file that's somewhere in the neighbourhood of 10 - 100 MB. I'm not sure of the best way to serve this file to the user. The two options I'm considering are: Adding some code to the offline processing code that 'spoofs' it as a form upload to the blob store, and going thru the normal blobstore process to serve the file. Having the offline processing code store the file somewhere off of GAE, and serving it from there. Is there a much better approach I'm overlooking? I'm guessing this is functionality that isn't well suited to GAE. I had thought of storing in the datastore as db.Text or Dd.Blob but there I encounter the 1 MB limit. Any input would be appreciated,

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