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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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  • 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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  • Non-global middleware in Django

    - by hekevintran
    In Django there is a settings file that defines the middleware to be run on each request. This middleware setting is global. Is there a way to specify a set of middleware on a per-view basis? I want to have specific urls use a set of middleware different from the global set.

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  • How to limit choice field options based on another choice field in django admin

    - by umnik700
    I have the following models: class Category(models.Model): name = models.CharField(max_length=40) class Item(models.Model): name = models.CharField(max_length=40) category = models.ForeignKey(Category) class Demo(models.Model): name = models.CharField(max_length=40) category = models.ForeignKey(Category) item = models.ForeignKey(Item) In the admin interface when creating a new Demo, after user picks category from the dropdown, I would like to limit the number of choices in the "items" drop-down. If user selects another category then the item choices should update accordingly. I would like to limit item choices right on the client, before it even hits the form validation on the server. This is for usability, because the list of items could be 1000+ being able to narrow it down by category would help to make it more manageable. Is there a "django-way" of doing it or is custom JavaScript the only option here?

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  • How to add packages into .exe file using py2exe?

    - by aF
    Hello, I have an app with two packages.. My setup.py is like this: sys.argv.append('py2exe') setup( options = {'py2exe': {'bundle_files': 1}}, windows = [{'script': "SoundLog.py"}], zipfile = None, ) After creating the .exe I have to put the packages in the same folder as the .exe file. How can I include them in the .exe? Thanks in advance!

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  • Django - The included urlconf doesn't have any patterns in it

    - by unsorted
    My website, which was working before, suddenly started breaking with the error "ImproperlyConfigured at / The included urlconf resume.urls doesn't have any patterns in it" The project base is called resume. In settings.py I have set ROOT_URLCONF = 'resume.urls' Here's my resume.urls, which sits in the project root directory. from django.conf.urls.defaults import * # Uncomment the next two lines to enable the admin: from django.contrib import admin admin.autodiscover() urlpatterns = patterns('', # Example: # (r'^resume/', include('resume.foo.urls')), # Uncomment the admin/doc line below and add 'django.contrib.admindocs' # to INSTALLED_APPS to enable admin documentation: (r'^admin/doc/', include('django.contrib.admindocs.urls')), # Uncomment the next line to enable the admin: (r'^admin/', include(admin.site.urls)), (r'^accounts/login/$', 'django.contrib.auth.views.login'), #(r'^employer/', include(students.urls)), (r'^ajax/', include('urls.ajax')), (r'^student/', include('students.urls')), (r'^club/(?P<object_id>\d+)/$', 'resume.students.views.club_detail'), (r'^company/(?P<object_id>\d+)/$', 'resume.students.views.company_detail'), (r'^program/(?P<object_id>\d+)/$', 'resume.students.views.program_detail'), (r'^course/(?P<object_id>\d+)/$', 'resume.students.views.course_detail'), (r'^career/(?P<object_id>\d+)/$', 'resume.students.views.career_detail'), (r'^site_media/(?P<path>.*)$', 'django.views.static.serve', {'document_root': 'C:/code/django/resume/media'}), ) I have a folder called urls and a file ajax.py inside. (I also created a blank init.py in the same folder so that urls would be recognized.) This is ajax.py. from django.conf.urls.defaults import * urlpatterns = patterns('', (r'^star/(?P<object_id>\d+)$', 'resume.students.ajax-calls.star'), ) Anyone know what's wrong? This is driving me crazy. Thanks,

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  • Enable PyGTK Eventbox motion-notify-event while is a Layout child

    - by mkotechno
    I noticed when a Eventbox is added into a Layout some events are missed, this does not happend for example adding it to a Fixed (very similar widget), I tried to restore the event mask in this way with no sucess: import pygtk import gtk def foo(widget, event): print event pygtk.require('2.0') window = gtk.Window(gtk.WINDOW_TOPLEVEL) window.connect('destroy', lambda x: gtk.main_quit()) eventbox = gtk.EventBox() eventbox.connect('button-press-event', foo) # works eventbox.connect('motion-notify-event', foo) # fail eventbox.set_events( gtk.gdk.BUTTON_MOTION_MASK| # restoring missed masks gtk.gdk.BUTTON1_MOTION_MASK| gtk.gdk.BUTTON2_MOTION_MASK| gtk.gdk.BUTTON3_MOTION_MASK) layout = gtk.Layout() image = gtk.image_new_from_file('/home/me/picture.jpg') layout.add(image) eventbox.add(layout) window.add(eventbox) window.show_all() gtk.main() How should I restore the missed event/mask?

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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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  • How to do call function after client finishes download from tornado web server?

    - by Shabbyrobe
    I would like to be able to run some cleanup functions if and only if the client successfully completes the download of a file I'm serving using Tornado. I installed the firefox throttle tool and had it slow the connection down to dialup speed and installed this handler to generate a bunch of rubbish random text: class CrapHandler(BaseHandler): def get(self, token): crap = ''.join(random.choice(string.ascii_uppercase + string.digits) for x in range(100000)) self.write(crap) print "done" I get the following output from tornado immediately after making the request: done I 100524 19:45:45 web:772] 200 GET /123 (192.168.45.108) 195.10ms The client then plods along downloading for about 20 seconds. I expected that it would print "done" after the client was done. Also, if I do the following I get pretty much the same result: class CrapHandler(BaseHandler): @tornado.web.asynchronous def get(self, token): crap = ''.join(random.choice(string.ascii_uppercase + string.digits) for x in range(100000)) self.write(crap) self.finish() print "done" Am I missing something fundamental here? Can tornado even support what I'm trying to do? If not, is there an alternative that does?

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  • App Engine HTTP 500s

    - by pocoa
    This request caused a new process to be started for your application, and thus caused your application code to be loaded for the first time. This request may thus take longer and use more CPU than a typical request for your application. I've handled all the situations, also DeadlineExceededError too. But sometimes I see these error messages in error logs. That request took about 10k ms, so it's not exceeded the limit too. But there is no other specific message about this error. All I know is that it returned HTTP 500. Is there anyone know the reason of these error messages? Thank you.

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  • Is there a simple way to make lists behave as files (with ftplib)

    - by Brent.Longborough
    I'd like to use ftplib to upload program-generated data as lists. The nearest method I can see for doing this is ftp.storlines, but this requires a file object with a readlines() method. Obviously I could create a file, but this seems like overkill as the data isn't persistent. Is there anything that could do this?: session = ftp.new(...) upload = convertListToFileObject(mylist) session.storlines("STOR SOMETHING",upload) session.quit

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  • inheritance from str or int

    - by wiso
    Why I have problem creating a class the inherite from str (or also int) class C(str): def __init__(self, a, b): str.__init__(self,a) self.b = b C("a", "B") TypeError: str() takes at most 1 argument (2 given) tha same appened if I try to use int instead of str, but it works with custom classes. I need to use __new__ instead of __init__? why?

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  • Django db encoding

    - by realshadow
    Hey, I have a little problem with encoding. The data in db is ok, when I select the data in php its ok. Problem comes when I get the data and try to print it in the template, I get - Å port instead of Šport, etc. Everything is set to utf-8 - in settings.py, meta tags in template, db table and I even have unicode method specified for the model, but nothing seems to work. I am getting pretty hopeless here... Here is some code: class Category_info(models.Model): objtree_label_id = models.AutoField(primary_key = True) node_id = models.IntegerField(unique = True) language_id = models.IntegerField() label = models.CharField(max_length = 255) type_id = models.IntegerField() class Meta: db_table = 'objtree_labels' def __unicode__(self): return self.label I have even tried with return u"%s" % self.label. Here is the view: def categories_list(request): categories_list = Category.objects.filter(parent_id = 1, status = 1) paginator = Paginator(categories_list, 10) try: page = int(request.GET.get('page', 1)) except ValueError: page = 1 try: categories = paginator.page(page) except (EmptyPage, InvalidPage): categories = paginator.page(paginator.num_pages) return render_to_response('categories_list.html', {'categories': categories}) Maybe I am just blind and/or stupid, but it just doesnt work. So any help is appreciated, thanks in advance. Regards

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  • gae error : Error: Server Error, how to debut it .

    - by zjm1126
    when i upload my project to google-app-engine , it show this : Error: Server Error The server encountered an error and could not complete your request. If the problem persists, please report your problem and mention this error message and the query that caused it. why ? how can i debug this error ? thanks

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  • Euclidian Distances between points

    - by R S
    I have an array of points in numpy: points = rand(dim, n_points) And I want to: Calculate all the l2 norm (euclidian distance) between a certain point and all other points Calculate all pairwise distances. and preferably all numpy and no for's.

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  • Selective emboldeing of text in a webpage

    - by Eknath Iyer
    while printing out utf-8 characters onto a webpage, if encapsulate them with they get emboldened, but anything else, the page turns blank. Why? def main(): print "Content-type: text/html\r\n\r\n"; print '<html>' print '<head>' print '<style type="text/css">' print '.highlight { background-color: yellow }' print '.color1 { color: green; }' print '.color2 { color: blue; }' print '.color3 { color: purple; }' print '.color4 { color: red; }' print '.color5 { color: teal; }' print '.color6 { color: yellow; }' print '.color7 { color: orange; }' print '.color8 { color: violet; }' print '</style></head>' print '<body>' form = cgi.FieldStorage() ch = form.getvalue('choice') if ch == 'English': in_sent = form.getvalue('f1') in_sent = in_sent.lower() cho=0 elif ch == 'Hindi': in_sent = trans_he(form.getvalue('transl1').decode("utf-8")).strip() cho=1 #cho = 0 for english #cho = 1 for hindi adict=[] print '<center><u> User Input Sentence ==> <b>', in_sent,'</b></u></center><br>' in_sent=in_sent.strip().split(' ') colordict={} counter=1 for word in in_sent: colordict[word]=counter counter = counter + 1 f = open('bidirectional.alignment.txt','rb').read() records=f.strip().split('\n\n\n') for record in records: el=[] el2 = [] #basic file processing is done here. record = record.strip().split('\n') source = record[cho] target = record[(cho+1)%2] source_sent = source.split(' # ')[1] target_sent = target.split(' # ')[1] source_words = source_sent.strip().split(' ') target_words = target_sent.strip().split(' ') trans_index = source.split(' # ')[2].strip().split(' ') for word in in_sent: if word in source_words: if int(trans_index[source_words.index(word)]) > 0: tword=target_words[(int(trans_index[source_words.index(word)])-1)] target_sent = target_sent.replace(tword+' ','<b>'+tword+' </b>') # When the <b> tag is used here(for the 'target_sent = ...' statement). it is fine. But when <b> is replaced by something like in the next line or even <i> or <u>, it doesn't show an output at all source_sent = source_sent.replace(word+' ','<span class="color1">'+word+' </span>') el2.append(source_sent) el2.append(target_sent) el.append(target_sent.count('<b>')) el.append(el2) if target_sent.count('<b>') > 0: adict.append(el) print '<table><tr><td><center><h1>SOURCE LANGUAGE</h1></center></td><td><center> <h1>TARGET LANGUAGE</h1></center></td></tr>' for entry in adict: print '<tr><td>',entry[1][0],'</td><td>',trans_eh(entry[1][1]).encode("utf-8"),'</td> </tr>' print '</table></body>' print '</html>' main()

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  • Can PyAMF support service deployment by way of the filesystem?

    - by Chris R
    I'm evaluating PyAMF to replace our current PHP (ugh) AMF services framework, and I'm unable to find the one crucial piece of information that would allow me to provide a compelling use case for changing over: Right now, new PHP AMF services are deployed simply by putting the .php files in the filesystem; the next time they're accessed, the new service is in play. Removal of a service is as simple as deleting the .php file that provided it, and updating it is correspondingly simple. I need that same ease-of-deployment from PyAMF. If we have to rewrite our installers to deploy these services, it'll be a nonstarter. So, what I need to know is, can PyAMF support new service discovery by way of the filesystem, can it support service upgrading and removal by way of same, and if so, what is the best way to set it up to do this? I'm open to any of the various server options; I can easily have cherrypy, django, whatever installed and running on its own, and even -- with a bit more sturm nd drang -- have mod_python or mod_wsgi made available.

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