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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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  • 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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  • Fabfiles With Command Line Arguments

    - by phasetwenty
    Is there a clean way to have your fabfile take command line arguments? I'm writing an installation script for a tool that I want to be able to specify an optional target directory via the command line. I wrote some code to test what would happen if I passed in some command line arguments: # fabfile.py import sys def install(): _get_options() def _get_options(): print repr(sys.argv[1:]) A couple of runs: $ fab install ['install'] Done. $ fab install --electric-boogaloo Usage: fab [options] <command>[:arg1,arg2=val2,host=foo,hosts='h1;h2',...] ... fab: error: no such option: --electric-boogaloo

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  • Django Forms Help needed

    - by user320993
    Hi All, Im new to django and trying to make a user registration form with few validations. Apart from this I also want a username suggestion code which will tell the user if the username he is trying to register is available or already in use. Then it should give few suggestions that might be available to choose from. Can anyone who might have worked on the same or somewhat same project help me with this. Thanks

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  • How can I set the line style of a specific cell in a QTableView?

    - by Bob Nelson
    I am working with a QT GUI. I am implementing a simple hex edit control using a QTableView. My initial idea is to use a table with seventeen columns. Each row of the table will have 16 hex bytes and then an ASCII representation of that data in the seventeenth column. Ideally, I would like to edit/set the style of the seventeenth column to have no lines on the top and bottom of each cell to give the text a free flowing appearance. What is the best way to approach this using the QTableView?

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  • Django - how to write users and profiles handling in best way?

    - by SpankMe
    Hey, I am writing simple site that requires users and profiles to be handled. The first initial thought is to use django's build in user handling, but then the user model is too narrow and does not contain fields that I need. The documentation mentions user profiles, but user profiles section has been removed from djangobook covering django 1.0 (ideally, the solution should work with django 1.2), and the Internet is full of different solutions, not making the choice easier (like user model inheritance, user profiles and django signals, and so on). I would like to know, how to write this in good, modern, fast and secure way. Should I try to extend django builtin user model, or maybe should I create my own user model wide enough to keep all the information I need? Below you may find some specifications and expectations from the working solution: users should be able to register and authenticate every user should have profile (or model with all required fields) users dont need django builtin admin panel, but they need to edit their profiles/models via simple web form Please, let me know how do you solve those issues in your applications, and what is the best current way to handle users with django. Any links to articles/blogs or code examples are highly appreciated!

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  • Real-time data on webpage with Django and jQuery

    - by Steven Hepting
    I would like a webpage that constantly updates a graph with new data as it arrives. Regularly, all the data you have is passed to a Django view at the beginning of the request. However, I need the page to be able to update itself with fresh information every few seconds to redraw the graph. Background The webpage will be similar to this http://www.panic.com/blog/2010/03/the-panic-status-board/. The data coming in will temperature values to be graphed measured by an Arduino and saved to the Django database (I've already done this part).

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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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  • TypeError: 'NoneType' object does not support item assignment

    - by R S John
    I am trying to do some mathematical calculation according to the values at particular index of a NumPy array with the following code X = np.arange(9).reshape(3,3) temp = X.copy().fill(5.446361E-01) ind = np.where(X < 4.0) temp[ind] = 0.5*X[ind]**2 - 1.0 ind = np.where(X >= 4.0 and X < 9.0) temp[ind] = (5.699327E-1*(X[ind]-1)**4)/(X[ind]**4) print temp But I am getting the following error Traceback (most recent call last): File "test.py", line 7, in <module> temp[ind] = 0.5*X[ind]**2 - 1.0 TypeError: 'NoneType' object does not support item assignment Would you please help me in solving this? Thanks

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  • Creating self-referential tables with polymorphism in SQLALchemy

    - by Jace
    I'm trying to create a db structure in which I have many types of content entities, of which one, a Comment, can be attached to any other. Consider the following: from datetime import datetime from sqlalchemy import create_engine from sqlalchemy import Column, ForeignKey from sqlalchemy import Unicode, Integer, DateTime from sqlalchemy.orm import relation, backref from sqlalchemy.ext.declarative import declarative_base Base = declarative_base() class Entity(Base): __tablename__ = 'entities' id = Column(Integer, primary_key=True) created_at = Column(DateTime, default=datetime.utcnow, nullable=False) edited_at = Column(DateTime, default=datetime.utcnow, onupdate=datetime.utcnow, nullable=False) type = Column(Unicode(20), nullable=False) __mapper_args__ = {'polymorphic_on': type} # <...insert some models based on Entity...> class Comment(Entity): __tablename__ = 'comments' __mapper_args__ = {'polymorphic_identity': u'comment'} id = Column(None, ForeignKey('entities.id'), primary_key=True) _idref = relation(Entity, foreign_keys=id, primaryjoin=id == Entity.id) attached_to_id = Column(Integer, ForeignKey('entities.id'), nullable=False) #attached_to = relation(Entity, remote_side=[Entity.id]) attached_to = relation(Entity, foreign_keys=attached_to_id, primaryjoin=attached_to_id == Entity.id, backref=backref('comments', cascade="all, delete-orphan")) text = Column(Unicode(255), nullable=False) engine = create_engine('sqlite://', echo=True) Base.metadata.bind = engine Base.metadata.create_all(engine) This seems about right, except SQLAlchemy doesn't like having two foreign keys pointing to the same parent. It says ArgumentError: Can't determine join between 'entities' and 'comments'; tables have more than one foreign key constraint relationship between them. Please specify the 'onclause' of this join explicitly. How do I specify onclause?

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  • Django: Admin with multiple sites & languages

    - by lazerscience
    Hi everybody! I'm supposed to build some Django apps, that allow you to administer multiple sites through one backend. The contrib.sites framework is quite perfect for my purposes. I can run multiple instances of manage.py with different settings for each site; but how should django's admin deal with different settings for different sites, eg. if they have different sets of languages, a different (default) language? So there are some problem s to face if you have to work on objects coming from different sites in one admin... I think settings.ADMIN_FOR is supposed to be quite helpful for cases like this, but theres hardly any documentation about it and I think it's not really used in the actual Django version (?). So any ideas/solutions are welcome and much appreciated! Thanks a lot...

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  • adding a header to pyqt list

    - by Moayyad Yaghi
    hello i want to add a headers and index to a list in pyqt , it's really not important what list of QT (qlistwidget , qlistview , qtablewidget, qtreeview) in short .. i want something like the spin box delegate example in the pyqt demo ... but instead of the index in the column headers i want a strings ... hope the idea is clear enough thanx in advance

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  • Can DBRefs contain additional fields?

    - by Soviut
    I've encountered several situations when using MongoDB that require the use of DBRefs. However, I'd also like to cache some fields from the referenced document in the DBRef itself. {$ref:'user', $id:'10285102912A', username:'Soviut'} For example, I may want to have the username available even though the user document is referenced. This would provide me all the benefits of a single document approach; Faster querying and eliminating the need to do manual dereferencing in my code. While at the same time allowing me to use references where they make sense. The idea being that when the referenced document is updated (a user changes their name, for example) my business layer can automatically update all the documents that reference it. Ultimately, I'm wondering if it's considered good form to store additional fields on my DBRefs? Will it break anything? Will I lose my data each time a reference is rewritten? Will drivers like pymongo support it?

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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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  • Can this be done with the ORM? - Django

    - by RadiantHex
    Hi folks, I have a few item listed in a database, ordered through Reddit's algorithm. This is it: def reddit_ranking(post): t = time.mktime(post.created_on.timetuple()) - 1134000000 x = post.score if x>0: y=1 elif x==0: y=-0 else: y=-1 if x<0: z=1 else: z=x return (log(z) + y * t/45000) I'm wondering if there is any clever way of using Django's ORM, in order to UPDATE the models in bulk. Without doing this: items = Item.objects.filter(created_on__gte=datetime.now()-timedelta(days=7)) for item in items: item.reddit_rank = reddit_rank(item) item.save() I know about the F() object, but I can't figure out if this function can be performed inside the ORM. Any ideas? Help would be very much appreciated!

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  • Regex for Matching First Alphanumeric Character skipping (The |An? )

    - by TheLizardKing
    I have a list of artists, albums and tracks that I want to sort using the first letter of their respective name. The issue arrives when I want to ignore "The ", "A ", "An " and other various non-alphanumeric characters (Talking to you "Weird Al" Yankovic and [dialog]). Django has a nice start '^(An?|The) +' but I want to ignore those and a few others of my choice. I am doing this in Django, using a MySQL db with utf8_bin collation.

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  • Multi-part template issue with Jinja2

    - by Alan Harris-Reid
    Hi, When creating templates I typically have 3 separate parts (header, body, footer) which I combine to pass a singe string to the web-server (CherryPy in this case). My first approach is as follows... from jinja2 import Environment, FileSystemLoader env = Environment(loader=FileSystemLoader('')) tmpl = env.get_template('Body.html') page_body = tmpl.render() tmpl = env.get_template('Header.html') page_header = tmpl.render() tmpl = env.get_template('Footer.html') page_footer = tmpl.render() page_code = page_header + page_body + page_footer but this contains repetitious code, so my next approach is... def render_template(html_file): from jinja2 import Environment, FileSystemLoader env = Environment(loader=FileSystemLoader('')) tmpl = env.get_template(html_file) return tmpl.render() page_header = render_template('Header.html') page_body = render_template('Body.html') page_footer = render_template('Footer.html) However, this means that each part is created in its own environment - can that be a problem? Are there any other downsides to this approach? I have chosen the 3-part approach over the child-template approach because I think it may be more flexible (and easier to follow), but I might be wrong. Anyone like to convince me that using header, body and footer blocks might be better? Any advice would be appreciated. Alan

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  • pylab.savefig() and pylab.show() image difference

    - by Jack1990
    I'm making an script to automatically create plots from .xvg files, but there's a problem when I'm trying to use pylab's savefig() method. Using pylab.show() and saving from there, everything's fine. Using pylab.show() Using pylab.savefig() def producePlot(timestep, energy_values,type_line = 'r', jump = 1,finish = 100): fc = sp.interp1d(timestep[::jump], energy_values[::jump],kind='cubic') xnew = numpy.linspace(0, finish, finish*2) pylab.plot(xnew, fc(xnew),type_line) pylab.xlabel('Time in ps ') pylab.ylabel('kJ/mol') pylab.xlim(xmin=0, xmax=finish) def produceSimplePlot(timestep, energy_values,type_line = 'r', jump = 1,finish = 100): pylab.plot(timestep, energy_values,type_line) pylab.xlabel('Time in ps ') pylab.ylabel('kJ/mol') pylab.xlim(xmin=0, xmax=finish) def linearRegression(timestep, energy_values, type_line = 'g'): #, jump = 1,finish = 100): from scipy import stats import numpy #print 'fuck' timestep = numpy.asarray(timestep) slope, intercept, r_value, p_value, std_err = stats.linregress(timestep,energy_values) line = slope*timestep+intercept pylab.plot(timestep, line, type_line) def plottingTime(Title,file_name, timestep, energy_values ,loc, jump , finish): pylab.title(Title) producePlot(timestep,energy_values, 'b',jump, finish) linearRegression(timestep,energy_values) import numpy Average = numpy.average(energy_values) #print Average pylab.legend(("Average = %.2f" %(Average),'Linear Reg'),loc) #pylab.show() pylab.savefig('%s.jpg' %file_name[:-4], bbox_inches= None, pad_inches=0) #if __name__ == '__main__': #plottingTime(Title,timestep1, energy_values, jump =10, finish = 4800) def specialCase(Title,file_name, timestep, energy_values,loc, jump, finish): #print 'Working here ...?' pylab.title(Title) producePlot(timestep,energy_values, 'b',jump, finish) import numpy from pylab import * Average = numpy.average(energy_values) #print Average pylab.legend(("Average = %.2g" %(Average), Title),loc) locs,labels = yticks() yticks(locs, map(lambda x: "%.3g" % x, locs)) #pylab.show() pylab.savefig('%s.jpg' %file_name[:-4] , bbox_inches= None, pad_inches=0) Thanks in advance, John

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