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  • Empty dict-like collection problem in SQLAlchemy

    - by maksymko
    I have a mapping in SQLAlchemy that looks like this: t_property_value = sa.Table('property_value', MetaData, autoload = True, autoload_with = engine) orm.mapper(PropertyValue, t_property_value) t_estate = sa.Table('estate', MetaData, autoload = True, autoload_with = engine) orm.mapper(Estate, t_estate, properties = dict( property_hash = orm.relation(PropertyValue, collection_class = column_mapped_collection(t_property_value.c.property_id)) )) Now, everything seems to be fine, when I load the Estate object and it has some relations to PropertyValue objects. However, when it does not, then property_hash attribute is None, instead of being something dict-like, so I can not add new relations like this: estate.property_hash[prop_id] = PropertyValue(...) because I get the "'NoneType' object does not support item assignment" error. So, is there any way to force SQLAlchemy to create proper empty collection?

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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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  • How do I make BeautifulSoup parse the contents of textarea tags as HTML?

    - by brofield
    Before 3.0.5, BeautifulSoup used to treat the contents of <textarea as HTML. It now treats it as text. The document I am parsing has HTML inside the textarea tags, and I am trying to process it. I've tried: for textarea in soup.findAll('textarea'): contents = BeautifulSoup.BeautifulSoup(textarea.contents) textarea.replaceWith(contents.html(text=True)) But I'm getting errors. I can't find this in the documentation, and the alternative parsers aren't helping. Anyone know how I can parse the textareas as HTML?

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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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  • Changing printer preferences in Windows programmatically

    - by Andrew Alexander
    I've written a script that installs several printers for a new user. I want to change the settings on some of these so that they can print on both sides of the page. I BELIEVE this involves modifying an attribute with printui, however it might need VB script or possibly another .NET language (I'd either use VB, C# or IronPython). I can add a comment to a given printer, but how do I select preferences and modify them? Pseudocode would look like this: printui.exe /n printername /??? [how to change quality desired] OR calls to the relevant Windows API.

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  • how to let the parser print help message rather than error and exit

    - by fluter
    Hi, I am using argparse to handle cmd args, I wanna if there is no args specified, then print the help message, but now the parse will output a error, and then exit. my code is: def main(): print "in abing/start/main" parser = argparse.ArgumentParser(prog="abing")#, usage="%(prog)s <command> [args] [--help]") parser.add_argument("-v", "--verbose", action="store_true", default=False, help="show verbose output") subparsers = parser.add_subparsers(title="commands") bkr_subparser = subparsers.add_parser("beaker", help="beaker inspection") bkr_subparser.set_defaults(command=beaker_command) bkr_subparser.add_argument("-m", "--max", action="store", default=3, type=int, help="max resubmit count") bkr_subparser.add_argument("-g", "--grain", action="store", default="J", choices=["J", "RS", "R", "T", "job", "recipeset", "recipe", "task"], type=str, help="resubmit selection granularity") bkr_subparser.add_argument("job_ids", nargs=1, action="store", help="list of job id to be monitored") et_subparser = subparsers.add_parser("errata", help="errata inspection") et_subparser.set_defaults(command=errata_command) et_subparser.add_argument("-w", "--workflows", action="store_true", help="generate workflows for the erratum") et_subparser.add_argument("-r", "--run", action="store_true", help="generate workflows, and run for the erratum") et_subparser.add_argument("-s", "--start-monitor", action="store_true", help="start monitor the errata system") et_subparser.add_argument("-d", "--daemon", action="store_true", help="run monitor into daemon mode") et_subparser.add_argument("erratum", action="store", nargs=1, metavar="ERRATUM", help="erratum id") if len(sys.argv) == 1: parser.print_help() return args = parser.parse_args() args.command(args) return how can I do that? thanks.

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  • Access to field in extended flatpage in django

    - by Stanislav Feldman
    How to access field in extended flatpage in django? I wrote this: class ExtendedFlatPage(FlatPage): teaser = CharField(max_length=150) class ExtendedFlatPageForm(FlatpageForm): teaser = CharField(max_length=150) class Meta: model = ExtendedFlatPage class ExtendedFlatPageAdmin(FlatPageAdmin): form = ExtendedFlatPageForm fieldsets = ( (None, {'fields': ('url', 'title', 'teaser', 'content', 'sites',)}), ) admin.site.unregister(FlatPage) admin.site.register(ExtendedFlatPage, ExtendedFlatPageAdmin) And creation in admin is ok. But then in flatpages/default.html I tried this: <html> <body> <h1>{{ flatpage.title }}</h1> <strong>{{ flatpage.teaser }}</strong> <p>{{ flatpage.content }}</p> </body> </html> And there was no flatpage.teaser! What is wrong?

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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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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