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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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  • Pygame program that can get keyboard input with caps

    - by None
    I have a Pygame program that needs text input. The way it does this is to get keyboard input and when a key is pressed it renders that key so it is added to the screen. Essentially it acts like a text field. The problem is, when you hold shift it doesn't do anything. I relize this is because the program ignores shift input and instead writes the text if it's number is under 128. I have thought of setting a variable when shift is pressed then capitalizing if it was true, but string capitalization only woks on letters, not things like numbers or semicolons. Is there maybe a number I can add to the ascii number typed to modify it if shift is pressed, or something else?

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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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  • django sync db question

    - by Hulk
    In django models say this model exist in details/models.py class OccDetails(models.Model): title = models.CharField(max_length = 255) occ = models.ForeignKey(Occ) So when sync db is made the following fields get created and later to this of two more fields are added and sync db is made the new fields doesnt get created.How is this to be solved,Also what is auto_now=true in the below these are the new fields created_date = models.DateTimeField(auto_now_add=True) modified_date = models.DateTimeField(auto_now_add=True, auto_now=True)

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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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  • how to profile my code??

    - by kaki
    i want to how to profile my code... i have gone through the docs , but as there were no example codes given i could not get anything from it. i have a large code and it is taking so much time hence want to profile and increase its speed. i havent written my code in method , there are few in between but not completely. i dont have any main in my code..i want to know how to use profiling.. looking for some example or sample code of about how to profile.. i tried psyco i.e just addded two line at the top of my code import psyco psyco.full() is this write,it did not show any improvement. and other way of speeding up ,please suggest. thanks in advance..

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  • Tokenize a command string

    - by pocoa
    I have string like this: command "http://www.mysite.com" some_param="string param" some_param2=50 I want to tokenize this string into: command "http://www.mysite.com" some_param="string param" some_param2=50 I know it's possible to split with spaces but these parameters can also be seperated by commas, like: command "http://www.mysite.com", some_param="string param", some_param2=50 I tried to do it like this: \w+\=?\"?.+\"? but it didn't work.

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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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  • 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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  • Explicit disable MySQL query cache in some parts of program

    - by jack
    In a Django project, some cronjob programs are mainly used for administrative or analysis purposes, e.g. generating site usage stats, rotating user activities log, etc. We probably do not hope MySQL to cache queries in those programs to save memory usage and improve query cache efficiency. Is it possible to turn off MySQL query cache explicitly in those programs while keep it enabled for other parts including all views.py?

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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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  • Trying to set up nested while loops using a boolean switch

    - by thorn100
    First time posting. I'm trying to set up a while loop that will ask the user for the employee name, hours worked and hourly wage until the user enters 'DONE'. Eventually I'll modify the code to calculate the weekly pay and write it to a list, but one thing at a time. The problem is once the main while loop executes once, it just stops. Doesn't error out but just stops. I have to kill the program to get it to stop. I want it to ask the three questions again and again until the user is finished. Thoughts? Please note that this is just an exercise and not meant for any real world application. def getName(): """Asks for the employee's full name""" firstName=raw_input("\nWhat is your first name? ") lastName=raw_input("\nWhat is your last name? ") fullName=firstName.title() + " " + lastName.title() return fullName def getHours(): """Asks for the number of hours the employee worked""" hoursWorked=0 while int(hoursWorked)<1 or int(hoursWorked) > 60: hoursWorked=raw_input("\nHow many hours did the employee work: ") if int(hoursWorked)<1 or int(hoursWorked) > 60: print "Please enter an integer between 1 and 60." else: return hoursWorked def getWage(): """Asks for the employee's hourly wage""" wage=0 while float(wage)<6.00 or float(wage)>20.00: wage=raw_input("\nWhat is the employee's hourly wage: ") if float(wage)<6.00 or float(wage)>20.00: print ("Please enter an hourly wage between $6.00 and $20.00") else: return wage ##sentry variables employeeName="" employeeHours=0 employeeWage=0 booleanDone=False #Enter employee info print "Please enter payroll information for an employee or enter 'DONE' to quit." while booleanDone==False: while employeeName=="": employeeName=getName() if employeeName.lower()=="done": booleanDone=True break print "The employee's name is", employeeName while employeeHours==0: employeeHours=getHours() if employeeHours.lower()=="done": booleanDone=True break print employeeName, "worked", employeeHours, "this week." while employeeWage==0: employeeWage=getWage() if employeeWage.lower()=="done": booleanDone=True break print employeeName + "'s hourly wage is $" + employeeWage

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  • How do you efficiently bulk index lookups?

    - by Liron Shapira
    I have these entity kinds: Molecule Atom MoleculeAtom Given a list(molecule_ids) whose lengths is in the hundreds, I need to get a dict of the form {molecule_id: list(atom_ids)}. Likewise, given a list(atom_ids) whose length is in the hunreds, I need to get a dict of the form {atom_id: list(molecule_ids)}. Both of these bulk lookups need to happen really fast. Right now I'm doing something like: atom_ids_by_molecule_id = {} for molecule_id in molecule_ids: moleculeatoms = MoleculeAtom.all().filter('molecule =', db.Key.from_path('molecule', molecule_id)).fetch(1000) atom_ids_by_molecule_id[molecule_id] = [ MoleculeAtom.atom.get_value_for_datastore(ma).id() for ma in moleculeatoms ] Like I said, len(molecule_ids) is in the hundreds. I need to do this kind of bulk index lookup on almost every single request, and I need it to be FAST, and right now it's too slow. Ideas: Will using a Molecule.atoms ListProperty do what I need? Consider that I am storing additional data on the MoleculeAtom node, and remember it's equally important for me to do the lookup in the molecule-atom and atom-molecule directions. Caching? I tried memcaching lists of atom IDs keyed by molecule ID, but I have tons of atoms and molecules, and the cache can't fit it. How about denormalizing the data by creating a new entity kind whose key name is a molecule ID and whose value is a list of atom IDs? The idea is, calling db.get on 500 keys is probably faster than looping through 500 fetches with filters, right?

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  • How Can I Populate Default Form Data with a ManyToMany Field?

    - by b14ck
    Ok, I've been crawling google and Django documentation for over 2 hours now (as well as the IRC channel on freenode), and haven't been able to figure this one out. Basically, I have a model called Room, which is displayed below: class Room(models.Model): """ A `Partyline` room. Rooms on the `Partyline`s are like mini-chatrooms. Each room has a variable amount of `Caller`s, and usually a moderator of some sort. Each `Partyline` has many rooms, and it is common for `Caller`s to join multiple rooms over the duration of their call. """ LIVE = 0 PRIVATE = 1 ONE_ON_ONE = 2 UNCENSORED = 3 BULLETIN_BOARD = 4 CHILL = 5 PHONE_BOOTH = 6 TYPE_CHOICES = ( ('LR', 'Live Room'), ('PR', 'Private Room'), ('UR', 'Uncensored Room'), ) type = models.CharField('Room Type', max_length=2, choices=TYPE_CHOICES) number = models.IntegerField('Room Number') partyline = models.ForeignKey(Partyline) owner = models.ForeignKey(User, blank=True, null=True) bans = models.ManyToManyField(Caller, blank=True, null=True) def __unicode__(self): return "%s - %s %d" % (self.partyline.name, self.type, self.number) I've also got a forms.py which has the following ModelForm to represent my Room model: from django.forms import ModelForm from partyline_portal.rooms.models import Room class RoomForm(ModelForm): class Meta: model = Room I'm creating a view which allows administrators to edit a given Room object. Here's my view (so far): def edit_room(request, id=None): """ Edit various attributes of a specific `Room`. Room owners do not have access to this page. They cannot edit the attributes of the `Room`(s) that they control. """ room = get_object_or_404(Room, id=id) if not room.is_owner(request.user): return HttpResponseForbidden('Forbidden.') if is_user_type(request.user, ['admin']): form_type = RoomForm elif is_user_type(request.user, ['lm']): form_type = LineManagerEditRoomForm elif is_user_type(request.user, ['lo']): form_type = LineOwnerEditRoomForm if request.method == 'POST': form = form_type(request.POST, instance=room) if form.is_valid(): if 'owner' in form.cleaned_data: room.owner = form.cleaned_data['owner'] room.save() else: defaults = {'type': room.type, 'number': room.number, 'partyline': room.partyline.id} if room.owner: defaults['owner'] = room.owner.id if room.bans: defaults['bans'] = room.bans.all() ### this does not work properly! form = form_type(defaults, instance=room) variables = RequestContext(request, {'form': form, 'room': room}) return render_to_response('portal/rooms/edit.html', variables) Now, this view works fine when I view the page. It shows all of the form attributes, and all of the default values are filled in (when users do a GET)... EXCEPT for the default values for the ManyToMany field 'bans'. Basically, if an admins clicks on a Room object to edit, the page they go to will show all of the Rooms default values except for the 'bans'. No matter what I do, I can't find a way to get Django to display the currently 'banned users' for the Room object. Here is the line of code that needs to be changed (from the view): defaults = {'type': room.type, 'number': room.number, 'partyline': room.partyline.id} if room.owner: defaults['owner'] = room.owner.id if room.bans: defaults['bans'] = room.bans.all() ### this does not work properly! There must be some other syntax I have to use to specify the default value for the 'bans' field. I've really been pulling my hair out on this one, and would definitely appreciate some help. Thanks!

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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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  • Spaceship objects

    - by Jam
    I'm trying to make a program which creates a spaceship and I'm using the status() method to display the ship's name and fuel values. However, it doesn't seem to be working. I think I may have messed something up with the status() method. I'm also trying to make it so that I can change the fuel values, but I don't want to create a new method to do so. I think I've taken a horrible wrong turn somewhere in there. Help please! class Ship(object): def __init__(self, name="Enterprise", fuel=0): self.name=name self.fuel=fuel print "The spaceship", name, "has arrived!" def status(): print "Name: ", self.name print "Fuel level: ", self.fuel status=staticmethod(status) def main(): ship1=Ship(raw_input("What would you like to name this ship?")) fuel_level=raw_input("How much fuel does this ship have?") if fuel_level<0: self.fuel=0 else: self.fuel(fuel_level) ship2=Ship(raw_input("What would you like to name this ship?")) fuel_level2=raw_input("How much fuel does this ship have?") if fuel_level2<0: self.fuel=0 else: self.fuel(fuel_level2) ship3=Ship(raw_input("What would you like to name this ship?")) fuel_level3=raw_input("How much fuel does this ship have?") if fuel_level3<0: self.fuel=0 else: self.fuel(fuel_level3) Ship.status() main() raw_input("Press enter to exit.")

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  • Porting Django's templates engine to C

    - by sandra
    Hi folks, I recently wrote a simple and tiny embedded HTTP server for my C++ app (QT) and I played a little bit with Ry's http-parser and loved it. This guy is crazy. So I told to myself: "Hey! Why not port the django template engine to C?" That'd be awesome! I know, it won't be an easy task (not at all, I know) but I'd really love to implement this. So I came here for inspiration, ideas, opinions... I'd really love to have some pointers on the subject, ideas, what is already done, which major problems I'll encounter (and how to solve them) - How not to reinvent the wheel... anyway, you got the idea :) Thanks a million times! P.S. Simple code snippets, and links to tools and libs are very welcome! P.P.S. I'm already aware of grantlee, I took a look into its sources. Well... that's C++ and its specific to Qt.

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  • Parsing names with pyparsing

    - by johnthexiii
    I have a file of names and ages, john 25 bob 30 john bob 35 Here is what I have so far from pyparsing import * data = ''' john 25 bob 30 john bob 35 ''' name = Word(alphas + Optional(' ') + alphas) rowData = Group(name + Suppress(White(" ")) + Word(nums)) table = ZeroOrMore(rowData) print table.parseString(data) the output I am expecting is [['john', 25], ['bob', 30], ['john bob', 35]] Here is the stacktrace Traceback (most recent call last): File "C:\Users\mccauley\Desktop\client.py", line 11, in <module> eventType = Word(alphas + Optional(' ') + alphas) File "C:\Python27\lib\site-packages\pyparsing.py", line 1657, in __init__ self.name = _ustr(self) File "C:\Python27\lib\site-packages\pyparsing.py", line 122, in _ustr return str(obj) File "C:\Python27\lib\site-packages\pyparsing.py", line 1743, in __str__ self.strRepr = "W:(%s)" % charsAsStr(self.initCharsOrig) File "C:\Python27\lib\site-packages\pyparsing.py", line 1735, in charsAsStr if len(s)>4: TypeError: object of type 'And' has no len()

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  • sqlalchemy relation through another (declarative)

    - by clayg
    Is anyone familiar with ActiveRecord's "has_many :through" relations for models? I'm not really a Rails guy, but that's basically what I'm trying to do. As a contrived example consider Projects, Programmers, and Assignments: from sqlalchemy import create_engine from sqlalchemy.orm import sessionmaker from sqlalchemy import Column, ForeignKey from sqlalchemy.types import Integer, String, Text from sqlalchemy.orm import relation from sqlalchemy.ext.declarative import declarative_base Base = declarative_base() class Assignment(Base): __tablename__ = 'assignment' id = Column(Integer, primary_key=True) description = Column(Text) programmer_id = Column(Integer, ForeignKey('programmer.id')) project_id = Column(Integer, ForeignKey('project.id')) def __init__(self, description=description): self.description = description def __repr__(self): return '<Assignment("%s")>' % self.description class Programmer(Base): __tablename__ = 'programmer' id = Column(Integer, primary_key=True) name = Column(String(64)) assignments = relation("Assignment", backref='programmer') def __init__(self, name=name): self.name = name def __repr__(self): return '<Programmer("%s")>' % self.name class Project(Base): __tablename__ = 'project' id = Column(Integer, primary_key=True) name = Column(String(64)) description = Column(Text) assignments = relation("Assignment", backref='project') def __init__(self, name=name, description=description): self.name = name self.description = description def __repr__(self): return '<Project("%s", "%s...")>' % (self.name, self.description[:10]) engine = create_engine('sqlite://') Base.metadata.create_all(engine) Session = sessionmaker(bind=engine) session = Session() Projects have many Assignments. Programmers have many Assignments. (understatement?) But in my office at least, Programmers also have many Projects - I'd like this relationship to be inferred through the Assignments assigned to the Programmer. I'd like the Programmer model to have a attribute "projects" which will return a list of Projects associated to the Programmer through the Assignment model. me = session.query(Programmer).filter_by(name='clay').one() projects = session.query(Project).\ join(Project.assignments).\ join(Assignment.programmer).\ filter(Programmer.id==me.id).all() How can I describe this relationship clearly and simply using the sqlalchemy declarative syntax? Thanks!

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  • How to use thread in Django

    - by zomboid
    I want to check users' subscribed dates for certain period. And send mail to users whose subscription is finishing (ex. reminds two days). I think the best way is using thread and timer to check dates. But I have no idea how to call this function. I don't want to make a separate program or shell. I want to combine this procedure to my django code. I tried to call this function in my settings.py file. But it seems it is not a good idea. It calls the fucntion and creates thread everytime i imported settings.

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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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