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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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  • How to access non-first matches with xpath in Selenium RC ?

    - by Gj
    I have 20 labels in my page: In [85]: sel.get_xpath_count("//label") Out[85]: u'20' And I can get the first one be default: In [86]: sel.get_text("xpath=//label") Out[86]: u'First label:' But, unlike the xpath docs I've found, I'm getting an error trying to subscript the xpath to get to the second label's text: In [87]: sel.get_text("xpath=//label[2]") ERROR: An unexpected error occurred while tokenizing input The following traceback may be corrupted or invalid The error message is: ('EOF in multi-line statement', (216, 0)) ERROR: An unexpected error occurred while tokenizing input The following traceback may be corrupted or invalid The error message is: ('EOF in multi-line statement', (1186, 0)) --------------------------------------------------------------------------- Exception Traceback (most recent call last) /Users/me/<ipython console> in <module>() /Users/me/selenium.pyc in get_text(self, locator) 1187 'locator' is an element locator 1188 """ -> 1189 return self.get_string("getText", [locator,]) 1190 1191 /Users/me/selenium.pyc in get_string(self, verb, args) 217 218 def get_string(self, verb, args): --> 219 result = self.do_command(verb, args) 220 return result[3:] 221 /Users/me/selenium.pyc in do_command(self, verb, args) 213 #print "Selenium Result: " + repr(data) + "\n\n" 214 if (not data.startswith('OK')): --> 215 raise Exception, data 216 return data 217 Exception: ERROR: Element xpath=//label[2] not found What gives?

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  • Django: Save data from form in DB

    - by Anry
    I have a model: class Cost(models.Model): project = models.ForeignKey(Project) cost = models.FloatField() date = models.DateField() For the model I created a class form: class CostForm(ModelForm): class Meta: model = Cost fields = ['date', 'cost'] view.py: def cost(request, offset): if request.method == 'POST': #HOW save data in DB? return HttpResponseRedirect('/') else: form = CostForm() In the template file determined: <form action="/cost/{{ project }}/" method="post" accept-charset="utf-8"> <label for="date">Date:</label><input type="text" name="date" value={{ current_date }} id="date" /> <label for="cost">Cost:</label><input type="text" name="cost" value="0" id="cost" /> <p><input type="submit" value="Add"></p> </form> How save data from form in DB? P.S. offset = project name Model: class Project(models.Model): title = models.CharField(max_length=150) url = models.URLField() manager = models.ForeignKey(User) timestamp = models.DateTimeField() I tried to write: def cost(request, offset): if request.method == 'POST': form = CostForm(request.POST) if form.is_valid(): instance = form.save(commit=False) instance.project = Project.objects.filter(title=offset) instance.date = request.date instance.cost = request.cost instance.save() return HttpResponseRedirect('/') else: form = CostForm() But it does not work :(

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  • Debugging IDAPython Scripts outside of IDAPro

    - by YaronK
    I'm kinda new to scripting for IDA - nevertheless, I've written a complex script I need to debug, as it is not working properly. It is composed of a few different files containing a few different classes. Writing line-by-line in the commandline is not effective for obvious reasons. Running a whole script from the File doesn't allow debugging. Is there a way of using the idc, idautils, idaapi not from within IDA? I've written the script on PyDev for Eclipse, I'm hoping for a way to run the scripts from within it. A similar question is, can the api classes I have mentioned work on idb files without IDA having them loaded? Thanks.

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  • Terminate subprocess in Windows, access denied

    - by Jesse Aldridge
    - import time import subprocess from os.path import expanduser chrome_path = expanduser('~\Local Settings\Application Data\Google\Chrome\Application\chrome.exe') proc = subprocess.Popen(chrome_path) time.sleep(4) proc.terminate() Output: WindowsError: [Error 5] Access is denied How can I kill the Chrome process?

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  • app-engine-patch and "object_detail" view didn't work

    - by Hugh
    Hi(Sorry for my ugly english) When I calling the flowing: http://192.168.62.90:8000/blog/entry/?agphdXR1bW4xOTEychALEgpibG9nX2VudHJ5GCYM will use this: urlpatterns = patterns('', (r'^media/(?P<path>.*)$', 'django.views.static.serve', {'document_root': settings.MEDIA_ROOT, 'show_indexes': True}), (r'^$', list_detail.object_list, entry_info), (r'^entry/(?P<object_id>.*)$', list_detail.object_detail, {'queryset': Entry.all(), 'template_name': 'sample_test_page.html'}), ) and the error is: Generic view must be called with either an object_id or a slug/slug_field. I want to know why this didn't work for me.

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  • How to update the filename of a Django's FileField instance ?

    - by pierre-guillaume-degans
    Hello, Here a simple django model: class SomeModel(models.Model): title = models.CharField(max_length=100) video = models.FileField(upload_to='video') I would like to save any instance so that the video's file name would be a valid file name of the title. For example, in the admin interface, I load a new instance with title "Lorem ipsum" and a video called "video.avi". The copy of the file on the server should be "Lorem Ipsum.avi" (or "Lorem_Ipsum.avi"). Thank you :)

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  • Whats wrong with this task queue setup?

    - by Peter Farmer
    I've setup this task queue implementation on a site I host for a customer, it has a cron job which runs each morning at 2am "/admin/tasks/queue", this queues up emails to be sent out, "/admin/tasks/email", and uses cursors so as to do the queuing in small chunks. For some reason last night /admin/tasks/queue kept getting run by this code and so sent out my whole quota of emails :/. Have I done something wrong with this code? class QueueUpEmail(webapp.RequestHandler): def post(self): subscribers = Subscriber.all() subscribers.filter("verified =", True) last_cursor = memcache.get('daily_email_cursor') if last_cursor: subscribers.with_cursor(last_cursor) subs = subscribers.fetch(10) logging.debug("POST - subs count = %i" % len(subs)) if len(subs) < 10: logging.debug("POST - Less than 10 subscribers in subs") # Subscribers left is less than 10, don't reschedule the task for sub in subs: task = taskqueue.Task(url='/admin/tasks/email', params={'email': sub.emailaddress, 'day': sub.day_no}) task.add("email") memcache.delete('daily_email_cursor') else: logging.debug("POST - Greater than 10 subscibers left in subs - reschedule") # Subscribers is 10 or greater, reschedule for sub in subs: task = taskqueue.Task(url='/admin/tasks/email', params={'email': sub.emailaddress, 'day': sub.day_no}) task.add("email") cursor = subscribers.cursor() memcache.set('daily_email_cursor', cursor) task = taskqueue.Task(url="/admin/tasks/queue", params={}) task.add("queueup")

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  • Bypass django form validation on new form instance

    - by Thomas Schultz
    Hello! I have a situation where we are trying to autofill some form data on the second page of a signup and I was wondering if there's a way to bypass the entire form validation when we pass in only a couple of fields? so we have something like form = NewForm(request.POST) Where request.POST only contains some of the fields in NewForm(). So the page loads and there is feedback about how some fields are not filled in yet. This all happens from the GET request of the second page. Is there a way to do something like... form = NewForm(request.POST, validate=False)

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  • Catch PyGTK TreeView reorder

    - by mkotechno
    I have a simple gtk.TreeView with a gtk.ListStore model and set_reorderable(True), I want to catch the signal/event emited when the user reorder through drag&drop the list, but the documentation does not help much: "The application can listen to these changes by connecting to the model's signals" So I tried to connect the model (ListStore) signals... but surprise! ListStore has no signals, so you are dispatched to TreeModel signals, then I tried to connect with the TreeModel "rows-reordered" signal with no lucky. How should I catch the list reorder performed by the user?

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  • how to count all distinct records in many-to-many relations in django ORM?

    - by marduk-pl
    hi, i have two models: class Project(models.Model): categories = models.ManyToManyField(Category) class Category(models.Model): name = models.CharField() now, i make some queryset: query = Project.objects.filter(id__in=[1,2,3,4]) and i like to get list of all distinct categories in this queryset with count of projects with refering to these categories - exactly i would like to get that results: category1 - 10 projects category2 - 5 projects that is opposite to this query: query2 = query.annotate(Count('categories')) what return me: project1 - 2categories project2 - 7categories how can i make it in django ORM?

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  • Sort by an object's type

    - by Richard Levasseur
    Hi all, I have code that statically registers (type, handler_function) pairs at module load time, resulting in a dict like this: HANDLERS = { str: HandleStr, int: HandleInt, ParentClass: HandleCustomParent, ChildClass: HandleCustomChild } def HandleObject(obj): for data_type in sorted(HANDLERS.keys(), ???): if isinstance(obj, data_type): HANDLERS[data_type](obj) Where ChildClass inherits from ParentClass. The problem is that, since its a dict, the order isn't defined - but how do I introspect type objects to figure out a sort key? The resulting order should be child classes follow by super classes (most specific types first). E.g. str comes before basestring, and ChildClass comes before ParentClass. If types are unrelated, it doesn't matter where they go relative to each other.

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  • Scraping a page from a secure URL which is possibly using a session ID

    - by VN44CA
    How to scrape a page like this. https://www.procom.ca/JobList.aspx?keywords=&Cities=&reference=&JobType=0 It is secure, and requires a referrer? I can't get anything using wget or httplib2. If you go through this page, you get a list and it works on a browser but not the command line. https://www.procom.ca/jobsearch.aspx I am interested in command line fetching. thx

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  • A web framework where AJAX was not an after thought

    - by Pirate for Profit
    AJAX is a pain in the ass because it essentially means you'll have to write two sets of similarish code: one for browsers with JavaScript enabled and those without. Not only this, but you have to connect JavaScript events to hook into your models and display the results. And if all that weren't bad enough, you need to send an address change with the request, otherwise the user won't be able to "click back" correctly (if confused look at what happens to the address bar when you click links in GMail). We're searching for something that had the foresight and design goals with all these concerns in mind. Performance and security are also obvious major concerns. We love config-based systems as well, where you don't have to write a lot of code you just drop it into an easily read config format. It's like asking for the holy grail right?

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  • Can this code be further optimized??

    - by kaki
    i understand that the code given below will not be compltely understood unless i explain my whole of previous and next lines of code. But this is part of the code which is causing so much of delay in my project and want to optimize this. i want to know which code part is faulty and how could this be replaced. i guess,few can say that use of this function is heavy compared and other ligher method are available to do this work please help, thanks in advance for i in range(len(lists)): save=database_index[lists[i]] #print save #if save[1]!='text0194'and save[1]!='text0526': using_data[save[0]]=save p=os.path.join("c:/begpython/wavnk/",str(str(str(save[1]).replace('phone','text'))+'.pm')) x1=open(p , 'r') x2=open(p ,'r') for i in range(6): x1.readline() x2.readline() gen = (float(line.partition(' ')[0]) for line in x1) r= min(enumerate(gen), key=lambda x: abs(x[1] - float(save[4]))) #print r[0] a1=linecache.getline(str(str(p).replace('.pm','.mcep')), (r[0]+1)) #print a1 p1=str(str(a1).rstrip('\n')).split(' ') #print p1 join_cost_index_end[save[0]]=p1 #print join_cost_index_end gen = (float(line.partition(' ')[0]) for line in x2) r= min(enumerate(gen), key=lambda x: abs(x[1] - float(save[3]))) #print r[0] a2=linecache.getline(str(str(p).replace('.pm','.mcep')), (r[0]+1)) #print a2 p2=str(str(a2).rstrip('\n')).split(' ') #print p2 join_cost_index_strt[save[0]]=p2 #print join_cost_index_strt j=j+1 #print j #print join_cost_index_end #print join_cost_index_strt enter code here here my database_index has about 2,50,000 entries`

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  • Remove padding in wxPython's wxWizard

    - by mridang
    Hi Guys, I'm using wxPython to create a wizard using the wxWizard control. I'm trying to a draw a colored rectangle but when I run the app, there seems to be a about a 10px padding on each side of the rectangle. This goes for all other controls too. I have to offset them a bit so that they appear exactly where I want them to. Is there any way I could remove this padding? Here's the source of my base Wizard page. class SimplePage(wx.wizard.PyWizardPage): """ Simple wizard page with unlimited rows of text. """ def __init__(self, parent, title): wx.wizard.PyWizardPage.__init__(self, parent) self.next = self.prev = None #self.sizer = wx.BoxSizer(wx.VERTICAL) title = wx.StaticText(self, -1, title) title.SetFont(wx.Font(18, wx.SWISS, wx.NORMAL, wx.BOLD)) #self.sizer.AddWindow(title, 0, wx.ALIGN_LEFT|wx.ALL, padding) #self.sizer.AddWindow(wx.StaticLine(self, -1), 0, wx.EXPAND|wx.ALL, padding) # self.SetSizer(self.sizer) self.Bind(wx.EVT_PAINT, self.OnPaint) def OnPaint(self, evt): """set up the device context (DC) for painting""" self.dc = wx.PaintDC(self) self.dc.BeginDrawing() self.dc.SetPen(wx.Pen("grey",style=wx.TRANSPARENT)) self.dc.SetBrush(wx.Brush("grey", wx.SOLID)) # set x, y, w, h for rectangle self.dc.DrawRectangle(0,0,500, 500) self.dc.EndDrawing() del self.dc def SetNext(self, next): self.next = next def SetPrev(self, prev): self.prev = prev def GetNext(self): return self.next def GetPrev(self): return self.prev def Activated(self, evt): """ Executed when page is being activated. """ return def Blocked(self, evt): """ Executed when page is about to be switched. Switching can be blocked by returning True. """ return False def Cancel(self, evt): """ Executed when wizard is about to be canceled. Canceling can be blocked by returning False. """ return True Thanks guys.

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  • lxml unicode entity parse problems

    - by Jon Hadley
    I'm using lxml as follows to parse an exported XML file from another system: xmldoc = open(filename) etree.parse(xmldoc) But im getting: lxml.etree.XMLSyntaxError: Entity 'eacute' not defined, line 4495, column 46 Obviously it's having problems with unicode entity names - but how would i get round this? Via open() or parse()?

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  • creating message box as sheets for mac in PyQt

    - by user971306
    I used message box as seperate dialog instead of sheets for mac OS, now i m working on it to spawn a sheet as message box instead of seperate one. I have tried setting the message box as a modal one: (messagebox.setWindowModality(QtCore.Qt.WindoModal)) and setting message box, parent dialog window flags as sheet (parentDialog.setWindowFlags(QtCore.Qt.Sheet) messagebox.setWindowFlags(QtCore.Qt.Sheet)) But the above commands are not working to create a sheet instead of seperate dialog. Does anyone have an idea of how to solve?

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  • Scrapy Could not find spider Error

    - by Nacari
    I have been trying to get a simple spider to run with scrapy, but keep getting the error: Could not find spider for domain:stackexchange.com when I run the code with the expression scrapy-ctl.py crawl stackexchange.com. The spider is as follow: from scrapy.spider import BaseSpider from __future__ import absolute_import class StackExchangeSpider(BaseSpider): domain_name = "stackexchange.com" start_urls = [ "http://www.stackexchange.com/", ] def parse(self, response): filename = response.url.split("/")[-2] open(filename, 'wb').write(response.body) SPIDER = StackExchangeSpider()` Another person posted almost the exact same problem months ago but did not say how they fixed it, http://stackoverflow.com/questions/1806990/scrapy-spider-is-not-working I have been following the turtorial exactly at http://doc.scrapy.org/intro/tutorial.html, and cannot figure out why it is not working.

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  • wx paste image into panel

    - by Moayyad Yaghi
    hello i need to find a way to copy an image from a software .. ( microsoft paint for example ) and paste it into my own pain tool that i made using wxpython .. how do i read the image that has been loaded into memory ? so i can paste it hope idea is clear enough thanks in advance

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  • Django Testing: Faking User Creation

    - by Ygam
    I want to better write this test: def test_profile_created(self): self.client.post(reverse('registration_register'), data={ 'username':'ygam', 'email':'[email protected]', 'password1':'ygam', 'password2':'ygam' }) """ Test if a profile is created on save """ user = User.objects.get(username='ygam') self.assertTrue(UserProfile.objects.filter(user=user).exists()) and I just came upon this code on django-registration tests that does not actually "create" the user: def test_registration_signal(self): def receiver(sender, **kwargs): self.failUnless('user' in kwargs) self.assertEqual(kwargs['user'].username, 'bob') self.failUnless('request' in kwargs) self.failUnless(isinstance(kwargs['request'], WSGIRequest)) received_signals.append(kwargs.get('signal')) received_signals = [] signals.user_registered.connect(receiver, sender=self.backend.__class__) self.backend.register(_mock_request(), username='bob', email='[email protected]', password1='secret') self.assertEqual(len(received_signals), 1) self.assertEqual(received_signals, [signals.user_registered]) However he used a custom function for this "_mock_request": class _MockRequestClient(Client): def request(self, **request): environ = { 'HTTP_COOKIE': self.cookies, 'PATH_INFO': '/', 'QUERY_STRING': '', 'REMOTE_ADDR': '127.0.0.1', 'REQUEST_METHOD': 'GET', 'SCRIPT_NAME': '', 'SERVER_NAME': 'testserver', 'SERVER_PORT': '80', 'SERVER_PROTOCOL': 'HTTP/1.1', 'wsgi.version': (1,0), 'wsgi.url_scheme': 'http', 'wsgi.errors': self.errors, 'wsgi.multiprocess':True, 'wsgi.multithread': False, 'wsgi.run_once': False, 'wsgi.input': None, } environ.update(self.defaults) environ.update(request) request = WSGIRequest(environ) # We have to manually add a session since we'll be bypassing # the middleware chain. session_middleware = SessionMiddleware() session_middleware.process_request(request) return request def _mock_request(): return _MockRequestClient().request() However, it may be too long of a function for my needs. I want to be able to somehow "fake" the account creation. I have not much experience on mocks and stubs so any help would do. Thanks!

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