rem stringlengths 0 322k | add stringlengths 0 2.05M | context stringlengths 8 228k |
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gc.rect(int(self.x+border_width/2.0), int(self.y+border_width/2.0), int(self.width-2*border_width+1), int(self.height-2*border_width+1)) | gc.rect(self.x+border_width/2.0-0.5, self.y+border_width/2.0-0.5, self.width-border_width/2.0, self.height-border_width/2.0) | def _draw_inset_border(self, gc, view_bounds=None, mode="default"): """ Draws the border of a component. Unlike the default Enable border, this one is drawn on the inside of the plot instead of around it. """ if not self.border_visible: return border_width = self.border_width gc.save_state() gc.set_line_width(border_... |
width+2*padding, height+2*padding) | width+2*padding + border_width, height+2*padding + border_width) | def _draw_mainlayer(self, gc, view_bounds=None, mode="default"): text_color = self.text_color_ highlight_color = self.highlight_color_ highlight_bgcolor = self.highlight_bgcolor_ padding = self.cell_padding |
x,y = self._cached_cell_coords[i,j+1] + self._text_offset + padding | x,y = self._cached_cell_coords[i,j+1] + self._text_offset + \ padding + border_width/2.0 | def _draw_mainlayer(self, gc, view_bounds=None, mode="default"): text_color = self.text_color_ highlight_color = self.highlight_color_ highlight_bgcolor = self.highlight_bgcolor_ padding = self.cell_padding |
gc.move_to(x, self.y-self.cell_border_width/2.0) gc.line_to(x, self.y+self.height+self.cell_border_width/2.0) | gc.move_to(x, self.y) gc.line_to(x, self.y+self.height) | def _draw_grid_lines(self, gc): gc.set_stroke_color(self.cell_border_color_) gc.set_line_dash(self.cell_border_style_) gc.set_line_width(self.cell_border_width) |
gc.move_to(self.x-self.cell_border_width/2.0, y) gc.line_to(self.x+self.width+self.cell_border_width/2.0, y) | gc.move_to(self.x, y) gc.line_to(self.x+self.width, y) | def _draw_grid_lines(self, gc): gc.set_stroke_color(self.cell_border_color_) gc.set_line_dash(self.cell_border_style_) gc.set_line_width(self.cell_border_width) |
x_points = arange(numcols+1) * cell_width + self.x y_points = arange(numrows+1) * cell_height + self.y | x_points = arange(numcols+1) * cell_width + self.cell_border_width/2.0 + self.x y_points = arange(numrows+1) * cell_height + self.cell_border_width/2.0 + self.y | def _compute_positions(self): |
self.bounds = [ cols * (width + margin), rows * (height + margin)] | self.bounds = [ cols * (width + margin) + self.cell_border_width, rows * (height + margin) + self.cell_border_width ] | def _update_bounds(self): if self.string_array is not None and len(self.string_array.shape) == 2: rows, cols = self.string_array.shape margin = 2*self.cell_padding + self.cell_border_width width, height = self._get_actual_cell_size() self.bounds = [ cols * (width + margin),# - self.cell_border_width, rows * (height + m... |
if self.control == self.control.GetCapture(): self.control.SetFocus() | self.control.SetFocus() | def _set_focus ( self ): "Sets the keyboard focus to this window" if self.control == self.control.GetCapture(): self.control.SetFocus() return |
def __init__(self, *args, **kwds): super(SuperTuple, self).__init__(*args, **kwds) for i, attr in enumerate(self.__class__.__names__): | def __new__(cls, *args, **kwds): self = tuple.__new__(cls, *args, **kwds) for i, attr in enumerate(cls.__names__): | def __init__(self, *args, **kwds): super(SuperTuple, self).__init__(*args, **kwds) for i, attr in enumerate(self.__class__.__names__): setattr(self, attr, self[i]) |
file_inspector = Instance(FileInspector, args=()) | filename = Str() line = Int(1) code = Str() | def getstats(cls, obj=None): self = cls(obj) return pstats.Stats(self) |
tui.Item('main_results', show_label=False), | tui.UItem('main_results'), | def getstats(cls, obj=None): self = cls(obj) return pstats.Stats(self) |
tui.Item('callee_results', show_label=False), | tui.UItem('callee_results'), | def getstats(cls, obj=None): self = cls(obj) return pstats.Stats(self) |
tui.Item('caller_results', show_label=False), tui.Item('file_inspector', show_label=False), | tui.UItem('caller_results'), tui.UItem('filename', style='readonly'), tui.UItem('code', editor=tui.CodeEditor(line='line')), | def getstats(cls, obj=None): self = cls(obj) return pstats.Stats(self) |
self.file_inspector.file_name = filename self.file_inspector.line = line else: self.file_inspector.file_name = '' self.file_inspector.line = 0 self.file_inspector.text = '' | with open(filename, 'ru') as f: code = f.read() self.code = code self.filename = filename self.line = line else: self.trait_set( code = '', filename = '', line = 1, ) | def update_sub_results(self, new): if new is None: return self.caller_results.total_time = new.cum_time self.caller_results.records = new.callers self.callee_results._resort() self.caller_results.selected_record = self.caller_results.activated_record = None |
""" Returns the width and height of the rendered text | """ Returns the bounding rect of the rendered text | def get_text_extent(self, text): """ Returns the width and height of the rendered text """ fm = self.gc.fontMetrics() rect = fm.boundingRect(text) return rect.width(), rect.height() |
return rect.width(), rect.height() | return rect.left(), -fm.descent(), rect.right(), fm.height() | def get_text_extent(self, text): """ Returns the width and height of the rendered text """ fm = self.gc.fontMetrics() rect = fm.boundingRect(text) return rect.width(), rect.height() |
fm = self.gc.fontMetrics() rect = fm.boundingRect(text) return rect.width(), rect.height(), -fm.descent(), fm.leading() | x1, y1, x2, y2 = self.get_text_extent(text) return x2, y2, y1, x1 | def get_full_text_extent(self, text): """ Returns the width, height, descent and leading of the rendered text. """ fm = self.gc.fontMetrics() rect = fm.boundingRect(text) return rect.width(), rect.height(), -fm.descent(), fm.leading() |
""" PDF currently ignores the alpha value | """ | def set_fill_color(self,color): """ PDF currently ignores the alpha value """ r,g,b = color[:3] try: a = color[3] except IndexError: a = 1.0 self.gc.setFillColorRGB(r, g, b) |
self.gc.setFillColorRGB(r, g, b) | self.gc.setFillColorRGB(r, g, b, a) | def set_fill_color(self,color): """ PDF currently ignores the alpha value """ r,g,b = color[:3] try: a = color[3] except IndexError: a = 1.0 self.gc.setFillColorRGB(r, g, b) |
""" PDF currently ignores the alpha value | """ | def set_stroke_color(self,color): """ PDF currently ignores the alpha value """ r,g,b = color[:3] try: a = color[3] except IndexError: a = 1.0 self.gc.setStrokeColorRGB(r, g, b) |
self.gc.setStrokeColorRGB(r, g, b) | self.gc.setStrokeColorRGB(r, g, b, a) | def set_stroke_color(self,color): """ PDF currently ignores the alpha value """ r,g,b = color[:3] try: a = color[3] except IndexError: a = 1.0 self.gc.setStrokeColorRGB(r, g, b) |
msg = "set_alpha not implemented on PDF yet." raise NotImplementedError, msg | self.gc.setFillAlpha(alpha) self.gc.setStrokeAlpha(alpha) super(GraphicsContext, self).set_alpha(alpha) | def set_alpha(self, alpha): """ """ msg = "set_alpha not implemented on PDF yet." raise NotImplementedError, msg |
import Image as PilImage | from reportlab.lib.utils import ImageReader from PIL import Image as PilImage | def draw_image(self, img, rect=None): """ draw_image(img_gc, rect=(x,y,w,h)) Draws another gc into this one. If 'rect' is not provided, then the image gc is drawn into this one, rooted at (0,0) and at full pixel size. If 'rect' is provided, then the image is resized into the (w,h) given and drawn into this GC at poi... |
pil_img = PilImage.new(format, (converted_img.width(), converted_img.height())) | pil_img = PilImage.fromstring(format, (converted_img.width(), converted_img.height()), converted_img.bmp_array.tostring()) | def draw_image(self, img, rect=None): """ draw_image(img_gc, rect=(x,y,w,h)) Draws another gc into this one. If 'rect' is not provided, then the image gc is drawn into this one, rooted at (0,0) and at full pixel size. If 'rect' is provided, then the image is resized into the (w,h) given and drawn into this GC at poi... |
self.gc.drawImage(pil_img, rect[0], rect[1], rect[2], rect[3]) | self.gc.drawImage(ImageReader(pil_img), rect[0], rect[1], rect[2], rect[3]) | def draw_image(self, img, rect=None): """ draw_image(img_gc, rect=(x,y,w,h)) Draws another gc into this one. If 'rect' is not provided, then the image gc is drawn into this one, rooted at (0,0) and at full pixel size. If 'rect' is provided, then the image is resized into the (w,h) given and drawn into this GC at poi... |
print "boo" | def save_state(self): """ Save the current graphic's context state. This should always be paired with a restore_state """ self.gc.CGContextSaveGState() print "boo" | |
portal_url = getattr(site, "portal_url", None) | portal_url = getattr(site, "portal_url", None) request = getattr(site, "REQUEST", None) | def __init__(self, context, expose_schema=True): """ @param expose_schema: Map AT schema accessors directly to template variables for engines which cannot traverse Zope content (Cheetah). """ security=getSecurityManager() #portal_state = getMultiAdapter((context, context.REQUEST), name=u'plone_portal_state') try: p... |
"request" : context.REQUEST, | "request" : request, | def __init__(self, context, expose_schema=True): """ @param expose_schema: Map AT schema accessors directly to template variables for engines which cannot traverse Zope content (Cheetah). """ security=getSecurityManager() #portal_state = getMultiAdapter((context, context.REQUEST), name=u'plone_portal_state') try: p... |
DeckPercentageTrump({"test": ">=", "value": 33.33, "ratio": 0.8}), | DeckPercentageTrump({"test": ">=", "value": 100/3, "ratio": 0.8}), | def __init__(self): self.objects = [ DeckPercentageTrump({"test": ">=", "value": 33.33, "ratio": 0.8}), # le test ne fonctionne pas comme souhaiter |
m = MP3(self.media) m.add_tags() m.tags['TIT2'] = id3.TIT2(encoding=2, text=u'text') m.save() | self.mp3.add_tags() self.mp3.tags['TIT2'] = id3.TIT2(encoding=2, text=u'text') self.mp3.save() | def write_tags(self): """Write all ID3v2.4 tags by mapping dub2id3_dict dictionnary with the respect of mutagen classes and methods""" |
self.metadata = self.get_file_metadata() | try: self.metadata = self.get_file_metadata() except: self.metadata = {'title': '', 'artist': '', 'album': '', 'date': '', 'comment': '', 'genre': '', 'copyright': '', } | def __init__(self, media): self.media = media self.item_id = '' self.source = self.media self.options = {} self.bitrate_default = '192' self.cache_dir = os.sep + 'tmp' self.keys2id3 = {'title': 'TIT2', 'artist': 'TPE1', 'album': 'TALB', 'date': 'TDRC', 'comment': 'COMM', 'genre': 'TCON', 'copyright': 'TCOP', } self.mp3... |
try: self.metadata = self.get_file_metadata() except: self.metadata = {'title': '', 'artist': '', 'album': '', 'date': '', 'comment': '', 'genre': '', 'copyright': '', } | self.metadata = self.get_file_metadata() | def __init__(self, media): self.media = media self.item_id = '' self.source = self.media self.options = {} self.bitrate_default = '192' self.cache_dir = os.sep + 'tmp' self.keys2id3 = {'title': 'TIT2', 'artist': 'TPE1', 'album': 'TALB', 'date': 'TDRC', 'comment': 'COMM', 'genre': 'TCON', 'copyright': 'TCOP', } self.mp3... |
self.mp3.close() | def get_file_metadata(self): metadata = {} for key in self.keys2id3.keys(): try: metadata[key] = self.mp3[key][0] except: metadata[key] = '' self.mp3.close() return metadata | |
self.osc_controller.add_method('/relay', 'i', self.relay_callback) | self.osc_controller.add_method('/media/relay', 'i', self.relay_callback) | def __init__(self, station, q, logger, m3u): Thread.__init__(self) self.station = station self.q = q self.logger = logger self.channel = shout.Shout() self.id = 999999 self.counter = 0 self.command = 'cat ' self.delay = 0 |
if not os.path.exists()self.record_dir): | if not os.path.exists(self.record_dir): | def __init__(self, station, q, logger, m3u): Thread.__init__(self) self.station = station self.q = q self.logger = logger self.channel = shout.Shout() self.id = 999999 self.counter = 0 self.command = 'cat ' self.delay = 0 |
self.record_callback('/write', [1]) | self.record_callback('/record', [1]) | def __init__(self, station, q, logger, m3u): Thread.__init__(self) self.station = station self.q = q self.logger = logger self.channel = shout.Shout() self.id = 999999 self.counter = 0 self.command = 'cat ' self.delay = 0 |
message = 'New track ! %s %s on | message = ' | def get_next_media(self): # Init playlist if self.lp != 0: old_playlist = self.playlist new_playlist = self.get_playlist() lp_new = len(new_playlist) |
self.tinyurl = tinyurl.create_one(self.channel.url + '/m3u/' + self.m3u.split(os.sep)[-1]) | def __init__(self, station, q, logger, m3u): Thread.__init__(self) self.station = station self.q = q self.logger = logger self.channel = shout.Shout() self.id = 999999 self.counter = 0 self.command = 'cat ' self.delay = 0 | |
def __init__(self, username, password): | def __init__(self, access_token_key, access_token_secret): | def __init__(self, username, password): import twitter self.username = username self.password = password self.api = twitter.Api(username=self.username, password=self.password) |
self.username = username self.password = password self.api = twitter.Api(username=self.username, password=self.password) | self.username = TWITTER_CONSUMER_KEY self.password = TWITTER_CONSUMER_SECRET self.access_token_key = access_token_key self.access_token_secret = access_token_secret self.api = twitter.Api(username=self.username, password=self.password, access_token_key=self.access_token_key, access_token_secret=self.access_token_secret... | def __init__(self, username, password): import twitter self.username = username self.password = password self.api = twitter.Api(username=self.username, password=self.password) |
message = 'New track ! %s | artist_names = artist.split(' ') artist_tags = ' message = 'New track ! %s %s on | def get_next_media(self): # Init playlist if self.lp != 0: old_playlist = self.playlist new_playlist = self.get_playlist() lp_new = len(new_playlist) |
def update_twitter(self): artist_names = self.artist.split(' ') artist_tags = ' message = '♫ %s %s on | def update_twitter(self, message=None): if not message: artist_names = self.artist.split(' ') artist_tags = ' message = '♫ %s %s on | def update_twitter(self): artist_names = self.artist.split(' ') artist_tags = ' #'.join(list(set(artist_names)-set(['&', '-']))) message = '♫ %s %s on #%s #%s' % (self.prefix, self.song, self.short_name, artist_tags) tags = '#' + ' #'.join(self.twitter_tags) message = message + ' ' + tags message = message[:113] + ' ' ... |
artist_names = self.artist.split(' ') artist_tags = ' message = '♫ %s %s on tags = ' message = message + ' ' + tags message = message[:107] + ' M3U : ' + self.m3u_tinyurl self.update_twitter(message) self.channel.set_metadata({'song': self.song, 'charset': 'utf8',}) | self.update_twitter_current() self.channel.set_metadata({'song': self.song, 'charset': 'utf8',}) | def run(self): while self.run_mode: self.q.get(1) self.next_media = 0 self.media = self.get_next_media() self.counter += 1 |
self.channel.close() self.channel.open() | try: self.channel.open() except: self.logger.write_error('Station ' + self.short_name + ' : could connect to the server ') continue | def run(self): while True: self.q.get(1) self.next_media = 0 self.media = self.get_next_media() self.counter += 1 |
media.metadata = {'artist': self.artist, 'title': self.title, 'album': self.short_name, 'genre': self.channel.genre} | media.metadata = {'artist': self.artist.encode('utf-8'), 'title': self.title.encode('utf-8'), 'album': self.short_name.encode('utf-8'), 'genre': self.channel.genre.encode('utf-8')} | def record_callback(self, path, value): value = value[0] if value == 1: self.rec_file = self.short_name + '-' + \ datetime.datetime.now().strftime("%x-%X").replace('/', '_') + '.' + self.channel.format self.recorder = Recorder(self.record_dir) self.recorder.open(self.rec_file) elif value == 0: self.recorder.close() if ... |
self.channel.set_metadata({'song': self.song, 'charset': 'utf8',}) | self.channel.set_metadata({'song': self.song, 'charset': 'utf-8',}) | def run(self): while self.run_mode: self.q.get(1) self.next_media = 0 self.media = self.get_next_media() self.counter += 1 if self.relay_mode: self.set_relay_mode() elif os.path.exists(self.media) and not os.sep+'.' in self.media: if self.lp == 0: self.logger.write_error('Station ' + self.short_name + ' has no media to... |
version='0.4.1', | version='0.5', | def _compile_po_files (self): data_files = [] |
condorSubmitFile.write('universe = ' + universe + '\n') condorSubmitFile.write('executable = ' + executable + '\n') condorSubmitFile.write('transfer_executable = ' + transfer_executable + '\n') | condorSubmitFile.write('universe = ' + universe + '\n' + 'executable = ' + executable + '\n' + 'transfer_executable = ' + transfer_executable + '\n' + 'when_to_transfer_output = ' + when_to_transfer_output + '\n' + 'Requirements = ' + requirements + '\n' + '+Owner = ' + owner + '\n' + 'log = ' + logfile + '\n' + 'outpu... | def run(config): os.environ['_CONDOR_SEC_DEFAULT_AUTHENTICATION_METHODS']='GSI' os.environ['X509_USER_PROXY']=config.proxyFile import glideKeeper import condorMonitor,condorManager gktid=glideKeeper.GlideKeeperThread(config.webURL,config.descriptFile,config.descriptSignature, config.runId, config.myClassadID, [(config.... |
condorSubmitFile.write('when_to_transfer_output = ' + when_to_transfer_output + '\n') condorSubmitFile.write('Requirements = ' + requirements + '\n') condorSubmitFile.write('+Owner = ' + owner + '\n') condorSubmitFile.write('log = ' + logfile + '\n') condorSubmitFile.write('output = ' + outputfile + '\n') condorSubmit... | def run(config): os.environ['_CONDOR_SEC_DEFAULT_AUTHENTICATION_METHODS']='GSI' os.environ['X509_USER_PROXY']=config.proxyFile import glideKeeper import condorMonitor,condorManager gktid=glideKeeper.GlideKeeperThread(config.webURL,config.descriptFile,config.descriptSignature, config.runId, config.myClassadID, [(config.... | |
summDir = workingDir + '/' + startTime + '/summaries/' os.makedirs(summDir) for l in range(0, runs, 1): for k in range(0, len(concurrencyLevel), 1): results=[] hours=[] minutes=[] seconds=[] jobStartInfo=[] jobExecuteInfo=[] jobFinishInfo=[] jobStatus=[] logFile = workingDir + '/' + startTime + '/con_' + concurrenc... | def run(config): os.environ['_CONDOR_SEC_DEFAULT_AUTHENTICATION_METHODS']='GSI' os.environ['X509_USER_PROXY']=config.proxyFile import glideKeeper import condorMonitor,condorManager gktid=glideKeeper.GlideKeeperThread(config.webURL,config.descriptFile,config.descriptSignature, config.runId, config.myClassadID, [(config.... | |
self.add_dir_obj(cWDictFile.symlinkSupport(web_stage_dir,'web',work_dir)) | self.add_dir_obj(cWDictFile.symlinkSupport(web_stage_dir,os.path.join(work_dir,'web'),"web")) | def __init__(self,work_dir, web_stage_dir=None): # if None, create a web subdir in the work_dir; someone else need to copy it to the place visible by web_url if web_stage_dir==None: web_stage_dir=os.path.join(work_dir,'web') cvWDictFile.frontendMainDicts.__init__(self,work_dir,web_stage_dir, workdir_name="web",simple_w... |
writeData = str(results[i][0]) + '\t' + str(results[i][1]) + '\t\t' + str(results[i][2]) + '\t\t' + results[i][3] + '\n' | writeData = str(results[i][0]) + '\t' + str(results[i][1]) + '\t' + str(results[i][2]) + '\t' + results[i][3] + '\n' | def run(config): os.environ['_CONDOR_SEC_DEFAULT_AUTHENTICATION_METHODS']='GSI' os.environ['X509_USER_PROXY']=config.proxyFile import glideKeeper import condorMonitor,condorManager gktid=glideKeeper.GlideKeeperThread(config.webURL,config.descriptFile,config.descriptSignature, config.runId, config.myClassadID, [(config.... |
times = "Concurrency Level = " + concurrencyLevel[k] + "\tExecute Time(Ave/Min/Max) = " + str(aveExeTime) + '/' + str(minExeTime) + '/' + str(maxExeTime) + "\tFinish Time(Ave/Min/Max) = " + str(aveFinTime) + "/" + str(minFinTime) + "/" + str(maxFinTime) + '\n' | times = "Concurrency_Level = " + concurrencyLevel[k] + "\t Execute_Time_(Ave/Min/Max) = " + str(aveExeTime) + '/' + str(minExeTime) + '/' + str(maxExeTime) + "\t Finish_Time_(Ave/Min/Max) = " + str(aveFinTime) + "/" + str(minFinTime) + "/" + str(maxFinTime) + '\n' | def run(config): os.environ['_CONDOR_SEC_DEFAULT_AUTHENTICATION_METHODS']='GSI' os.environ['X509_USER_PROXY']=config.proxyFile import glideKeeper import condorMonitor,condorManager gktid=glideKeeper.GlideKeeperThread(config.webURL,config.descriptFile,config.descriptSignature, config.runId, config.myClassadID, [(config.... |
FILE.write('executable=' + executable' '\n') | FILE.write('executable=' + executable + '\n') | def run(config): import glideKeeper gktid=glideKeeper.glideKeeperThread(config.webUrl,self.descriptName,config.descriptSignature, config.runId, config.gfactoryClassadID, [config.gfactoryNode],config.gFactoryConstraint, config.proxyFile) gktid.start() try: # most of the code goes here # first load the file, so we check... |
totalGlideins = int(int(concurrencyLevel[i]) + .1 * int(concurrencyLevel[i])) | requestedGlideins = int(concurrencyLevel[i]) totalGlideins = int(requestedGlideins + .1 * requestedGlideins)) | def run(config): import glideKeeper gktid=glideKeeper.glideKeeperThread(config.webUrl,self.descriptName,config.descriptSignature, config.runId, config.gfactoryClassadID, [config.gfactoryNode],config.gFactoryConstraint, config.proxyFile) gktid.start() try: # most of the code goes here # first load the file, so we check... |
filename = dir1 + 'submit' + '.condor' | filename = dir1 + 'submit.condor' | def run(config): import glideKeeper gktid=glideKeeper.glideKeeperThread(config.webUrl,self.descriptName,config.descriptSignature, config.runId, config.gfactoryClassadID, [config.gfactoryNode],config.gFactoryConstraint, config.proxyFile) gktid.start() try: # most of the code goes here # first load the file, so we check... |
if numberGlideins = totalGlideins: | if numberGlideins = requestedGlideins: | def run(config): import glideKeeper gktid=glideKeeper.glideKeeperThread(config.webUrl,self.descriptName,config.descriptSignature, config.runId, config.gfactoryClassadID, [config.gfactoryNode],config.gFactoryConstraint, config.proxyFile) gktid.start() try: # most of the code goes here # first load the file, so we check... |
final = [totalTime, concurrencyLevel[k]] | final = [totalTime, concurrencyLevel[i]] | def run(config): import glideKeeper gktid=glideKeeper.glideKeeperThread(config.webUrl,self.descriptName,config.descriptSignature, config.runId, config.gfactoryClassadID, [config.gfactoryNode],config.gFactoryConstraint, config.proxyFile) gktid.start() try: # most of the code goes here # first load the file, so we check... |
self.needed_glidein=needed_glideins | self.needed_glideins=needed_glideins | def request_glideins(self,needed_glideins): self.needed_glidein=needed_glideins |
factory_glidein_dict=glideinFrontendInterface.findGlideins(factory_pool_node,self.signature_type,self.factory_constraint,self.proxy_data!=None,get_only_matching=True) | factory_glidein_dict=glideinFrontendInterface.findGlideins(factory_pool_node,factory_identity,self.signature_type,self.factory_constraint,self.proxy_data!=None,get_only_matching=True) | def go_request_glideins(self): # query job collector pool_status=condorMonitor.CondorStatus() pool_status.load(None,[]) running_glideins=len(pool_status.fetchStored()) del pool_status self.running_glideins=running_glideins |
glidein_dict[(factory_pool_node,glidename)]=factory_glidein_dict[glidename] | glidein_el=factory_glidein_dict[glidename] if not glidein_el['attrs'].has_key('PubKeyType'): continue elif glidein_el['attrs']['PubKeyType']=='RSA': try: glidein_el['attrs']['PubKeyObj']=glideinFrontendInterface.pubCrypto.PubRSAKey(str(string.replace(glidein_el['attrs']['PubKeyValue'],'\\n','\n'))) glidein_dict[(fact... | def go_request_glideins(self): # query job collector pool_status=condorMonitor.CondorStatus() pool_status.load(None,[]) running_glideins=len(pool_status.fetchStored()) del pool_status self.running_glideins=running_glideins |
key_obj=key_builder.get_key_obj(self.classad_identity, | key_obj=key_builder.get_key_obj(self.classad_id, | def go_request_glideins(self): # query job collector pool_status=condorMonitor.CondorStatus() pool_status.load(None,[]) running_glideins=len(pool_status.fetchStored()) del pool_status self.running_glideins=running_glideins |
glideinkeeper_id,classad_id, | glidekeeper_id,classad_id, | def __init__(self, web_url,descript_fname,descript_signature, glideinkeeper_id,classad_id, factory_pools,factory_constraint, proxy_fname): threading.Thread.__init__(self) # consts self.signature_type = "sha1" self.max_request=100 |
gktid=glideKeeper.glideKeeperThread(config.webUrl,self.descriptName,config.descriptSignature, | gktid=glideKeeper.GlideKeeperThread(config.webUrl,self.descriptName,config.descriptSignature, | def run(config): import glideKeeper gktid=glideKeeper.glideKeeperThread(config.webUrl,self.descriptName,config.descriptSignature, config.runId, config.gfactoryClassadID, [config.gfactoryNode],config.gFactoryConstraint, config.proxyFile) gktid.start() try: # most of the code goes here # first load the file, so we check... |
gktid=glideKeeper.GlideKeeperThread(config.webUrl,self.descriptName,config.descriptSignature, | gktid=glideKeeper.GlideKeeperThread(config.webURL,self.descriptName,config.descriptSignature, | def run(config): import glideKeeper gktid=glideKeeper.GlideKeeperThread(config.webUrl,self.descriptName,config.descriptSignature, config.runId, config.gfactoryClassadID, [config.gfactoryNode],config.gFactoryConstraint, config.proxyFile) gktid.start() try: # most of the code goes here # first load the file, so we check... |
for k in range(0, len(concurrencyLevel), 1): requestedGlideins = int(concurrencyLevel[k]) totalGlideins = int(requestedGlideins + .1 * requestedGlideins) gktid.request_glideins(totalGlideins) | for l in range(0, runs, 1): main_log.write("Iteration %i\n"%l) for k in range(0, len(concurrencyLevel), 1): main_log.write("Concurrency %i\n"%int(concurrencyLevel[k])) requestedGlideins = int(concurrencyLevel[k]) totalGlideins = int(requestedGlideins + .1 * requestedGlideins) gktid.request_glideins(totalGlideins) ... | def run(config): os.environ['_CONDOR_SEC_DEFAULT_AUTHENTICATION_METHODS']='GSI' os.environ['X509_USER_PROXY']=config.proxyFile import glideKeeper gktid=glideKeeper.GlideKeeperThread(config.webURL,config.descriptFile,config.descriptSignature, config.runId, config.myClassadID, [(config.gfactoryNode,config.gfactoryClassad... |
workingDir = os.getcwd() loop = 0 dir1 = workingDir + '/test' + concurrencyLevel[k] + '/' os.makedirs(dir1) logfile = workingDir + '/test' + concurrencyLevel[k] + '.log' outputfile = 'test' + concurrencyLevel[k] + '.out' errorfile = 'test' + concurrencyLevel[k] + '.err' filename = 'submit.condor' condorSubmitFile = ope... | workingDir = os.getcwd() loop = 0 dir1 = workingDir + '/' + startTime + '/concurrency_' + concurrencyLevel[k] + '_run_' + str(l) + '/' os.makedirs(dir1) logfile = workingDir + '/' + startTime + '/con_' + concurrencyLevel[k] + '_run_' + str(l) + '.log' outputfile = 'concurrency_' + concurrencyLevel[k] + '.out' errorfile... | def run(config): os.environ['_CONDOR_SEC_DEFAULT_AUTHENTICATION_METHODS']='GSI' os.environ['X509_USER_PROXY']=config.proxyFile import glideKeeper gktid=glideKeeper.GlideKeeperThread(config.webURL,config.descriptFile,config.descriptSignature, config.runId, config.myClassadID, [(config.gfactoryNode,config.gfactoryClassad... |
self.gFactoryNode=val | self.gfactoryNode=val | def load_config(self): # first load file, so we check it is readable fd=open(self.config,'r') try: lines=fd.readlines() finally: fd.close() |
self.gFactoryConstraint=val | self.gfactoryConstraint=val | def load_config(self): # first load file, so we check it is readable fd=open(self.config,'r') try: lines=fd.readlines() finally: fd.close() |
[config.gfactoryNode],config.gFactoryConstraint, | [config.gfactoryNode],config.gfactoryConstraint, | def run(config): import glideKeeper gktid=glideKeeper.GlideKeeperThread(config.webURL,self.descriptName,config.descriptSignature, config.runId, config.gfactoryClassadID, [config.gfactoryNode],config.gFactoryConstraint, config.proxyFile) gktid.start() try: # most of the code goes here # first load the file, so we check... |
threading.Thread(self) | threading.Thread.__init__(self) | def __init__(self, web_url,descript_fname,descript_signature, glideinkeeper_id,classad_id, factory_pools,factory_constraint, proxy_fname): threading.Thread(self) # consts self.signature_type = "sha1" self.max_request=100 |
self.assertTrue(e.time > (datetime.datetime.now() + datetime.timedelta(minutes=10)).time(), "The time on the entry is not older than 10 minutes!") | timestamp = datetime.datetime.combine(e.date, e.time) self.assertTrue(timestamp < datetime.datetime.now() - datetime.timedelta(minutes=10), "The time on the entry is not older than 10 minutes!") | def testTimeOutOfRange(self): try: e = get_object_or_404(Entry, pk=1) self.assertTrue(e.time > (datetime.datetime.now() + datetime.timedelta(minutes=10)).time(), "The time on the entry is not older than 10 minutes!") except Http404, e: self.fail("Entry 1 doesn't exist.") res = self.client.get("/undo/1") self.assertEq... |
return HttpResponseRedirect(reverse("program_log.views.showdaily",)) | return HttpResponseRedirect(reverse("log-show-daily",)) | def addentry(request,slot): s = ProgramSlot.objects.get(pk=slot) if request.POST: n = request.POST['notes'] if n == 'Description': n = '' e = Entry.objects.create(slot=s,notes=n) return HttpResponseRedirect(reverse("program_log.views.showdaily",)) |
return (find_name_email_pairs(row) for row in soup.findAll('tr') if row['class'].startswith('blockTableInnerRow')) | return (find_name_email_pairs(row) for row in soup.findAll('tr')) | def safe_lookup(td): try: return td.a.string.strip().lower() except: return td.string.strip().title() |
prog.refresh_feed() | try: prog.refresh_feed() except: pass | def feed(request, program, feed): prog = get_object_or_404(ProgrammingFeed, pk=feed) prog.refresh_feed() ret = {"feed": prog, "program":program, "entries":prog.programmingaudio_set.all()} return render_to_response("programming/sciam.html", ret, context_instance=RequestContext(request)) |
slots = ProgramSlot.objects.filter(time__start__gte=now).select_related('program', 'time') | slots = ProgramSlot.objects.filter(active=True, time__start__gte=now).select_related('program', 'time') | def next_n_hours(n): now = datetime.now().time() now = time(now.hour) end_hour = now.hour + n end = now.replace(hour=end_hour%24) |
other = ProgramSlot.objects.filter(time__end__lte=end).order_by('time__start') | other = ProgramSlot.objects.filter(active=True, time__end__lte=end).order_by('time__start') | def next_n_hours(n): now = datetime.now().time() now = time(now.hour) end_hour = now.hour + n end = now.replace(hour=end_hour%24) |
def db_restart(): | def local_db_restart(): | def db_restart(): "Delete and rebuild database on the local" with settings(warn_only=True): local("rm kelpdb") local("python2.6 manage.py syncdb") local("python2.6 manage.py loaddata fixtures/*") |
local("python2.6 manage.py syncdb") local("python2.6 manage.py loaddata fixtures/*") | local("python2.6 manage.py syncdb --noinput") local("python2.6 manage.py loaddata fixtures/*") | def db_restart(): "Delete and rebuild database on the local" with settings(warn_only=True): local("rm kelpdb") local("python2.6 manage.py syncdb") local("python2.6 manage.py loaddata fixtures/*") |
sudo("su -c 'rm ../kelpdb' www-data") sudo("su -c './manage.py syncdb' www-data") sudo("su -c './manage.py loaddata fixtures/*' www-data)") | with settings(warn_only=True): sudo("su -c 'rm ../kelpdb' www-data") sudo("su -c 'python manage.py syncdb --noinput' www-data") sudo("su -c 'python manage.py loaddata fixtures/*' www-data)") | def restart_database(): "Delete and rebuild the database on the remote" with cd("/home/kelp/kelp"): sudo("su -c 'rm ../kelpdb' www-data") sudo("su -c './manage.py syncdb' www-data") sudo("su -c './manage.py loaddata fixtures/*' www-data)") |
if fs is None: fs = fs2.copy() else: if len(fs2) > 0 or overlap_mode == "intersection-strict": | if len(fs2) > 0 or overlap_mode == "intersection-strict": if fs is None: fs = fs2.copy() else: | def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet ): features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} for f in HTSeq.GFF_Reader( gff_filename ): if f.iv.chrom not in features.step_vectors.keys(): features.add_chrom( f.iv.chrom ) if f.type... |
if len( fs ) == 0: | if fs is None or len( fs ) == 0: | def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet ): features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} for f in HTSeq.GFF_Reader( gff_filename ): if f.iv.chrom not in features.step_vectors.keys(): features.add_chrom( f.iv.chrom ) if f.type... |
self.step_vectors[ chrom ][ strand ][ 0 : chrom_lengths[chrom] ] = set() | self.step_vectors[ chrom ][ "+" ][ : ] = set() self.step_vectors[ chrom ][ "-" ][ : ] = set() | def __init__( self, chrom_lengths, stranded=True ): GenomicArray.__init__( self, chrom_lengths, stranded, 'O' ) for chrom in self.step_vectors: if self.stranded: self.step_vectors[ chrom ][ strand ][ 0 : chrom_lengths[chrom] ] = set() else: self.step_vectors[ chrom ][ 0 : chrom_lengths[chrom] ] = set() |
self.step_vectors[ chrom ][ 0 : chrom_lengths[chrom] ] = set() | self.step_vectors[ chrom ][ : ] = set() | def __init__( self, chrom_lengths, stranded=True ): GenomicArray.__init__( self, chrom_lengths, stranded, 'O' ) for chrom in self.step_vectors: if self.stranded: self.step_vectors[ chrom ][ strand ][ 0 : chrom_lengths[chrom] ] = set() else: self.step_vectors[ chrom ][ 0 : chrom_lengths[chrom] ] = set() |
rr = r if not pe_mode else r[0] sys.stderr.write( ( "Warning: Skipping read '%s', because chromosome " + "'%s', to which it has been aligned, did not appear in the GFF file.\n" ) % ( rr.read.name, iv.chrom ) ) | if not pe_mode: rr = r else: rr = r[0] if r[0] is not None else r[1] if not quiet: sys.stderr.write( ( "Warning: Skipping read '%s', because chromosome " + "'%s', to which it has been aligned, did not appear in the GFF file.\n" ) % ( rr.read.name, iv.chrom ) ) | def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet ): features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} # Try to open samfile to fail early in case it is not there open( sam_filename ).close() for f in HTSeq.GFF_Reader( gff_filename ): if ... |
"Public License v3. Part of the 'HTSeq' framework." ) | "Public License v3. Part of the 'HTSeq' framework, version %s." % HTSeq.__version__ ) | def main(): optParser = optparse.OptionParser( usage = "%prog [options] sam_file gff_file", description= "This script takes an alignment file in SAM format and a " + "feature file in GFF format and calculates for each feature " + "the number of reads mapping to it. See " + "http://www-huber.embl.de/users/anders/HTSe... |
help = "suppress progress report" ) | help = "suppress progress report and warnings" ) | def main(): optParser = optparse.OptionParser( usage = "%prog [options] sam_file gff_file", description= "This script takes an alignment file in SAM format and a " + "feature file in GFF format and calculates for each feature " + "the number of reads mapping to it. See " + "http://www-huber.embl.de/users/anders/HTSe... |
except Exception: | except: | def main(): optParser = optparse.OptionParser( usage = "%prog [options] sam_file gff_file", description= "This script takes an alignment file in SAM format and a " + "feature file in GFF format and calculates for each feature " + "the number of reads mapping to it. See " + "http://www-huber.embl.de/users/anders/HTSe... |
except: sys.stderr.write( "Error occured when reading first line of sam file." ) raise try: | def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet, minaqual ): if quiet: warnings.filterwarnings( action="ignore", module="HTSeq" ) features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} # Try to open samfile to fail early in case it is not th... | |
try: | if not pe_mode: | def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet, minaqual ): if quiet: warnings.filterwarnings( action="ignore", module="HTSeq" ) features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} # Try to open samfile to fail early in case it is not th... |
except AttributeError: pass | else: sys.stderr.write( "Error occured in %s.\n" % read_seq_pe_file.get_line_number_string() ) | def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet, minaqual ): if quiet: warnings.filterwarnings( action="ignore", module="HTSeq" ) features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} # Try to open samfile to fail early in case it is not th... |
features.add_value( f.attr[ id_attribute ], f.iv ) | feature_id = f.attr[ id_attribute ] | def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet ): features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} for f in HTSeq.GFF_Reader( gff_filename ): if f.iv.chrom not in features.step_vectors.keys(): features.add_chrom( f.iv.chrom ) if f.type... |
count_reads_in_features( args[0], args[1], opts.stranded == "yes", opts.mode, opts.featuretype, opts.idattr, opts.quiet ) def my_showwarning( message, category, filename, lineno = None, line = None ): sys.stderr.write( "Warning: %s\n" % message ) if __name__ == "__main__": | def main(): optParser = optparse.OptionParser( usage = "%prog [options] sam_file gff_file", description= "This script takes an alignment file in SAM format and a " + "feature file in GFF format and calculates for each feature " + "the number of reads mapping to it. See " + "http://www-huber.embl.de/users/anders/HTSeq... | |
main() | count_reads_in_features( args[0], args[1], opts.stranded == "yes", opts.mode, opts.featuretype, opts.idattr, opts.quiet ) | def my_showwarning( message, category, filename, lineno = None, line = None ): sys.stderr.write( "Warning: %s\n" % message ) |
sys.stderr.write( ( "Warning: Skipping read '%s', aligned to %s, because " + "chromosome '%s' did not appear in the GFF file.\n" ) % ( r.read.name, r.iv, r.iv.chrom ) ) | rr = r if not pe_mode else r[0] sys.stderr.write( ( "Warning: Skipping read '%s', because chromosome " + "'%s', to which it has been aligned, did not appear in the GFF file.\n" ) % ( rr.read.name, iv.chrom ) ) | def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet ): features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} for f in HTSeq.GFF_Reader( gff_filename ): if f.iv.chrom not in features.step_vectors.keys(): features.add_chrom( f.iv.chrom ) if f.type... |
print "attr:", attrStr | def parse_GFF_attribute_string( attrStr, extra_return_first_value=False ): """Parses a GFF attribute string and returns it as a dictionary. If 'extra_return_first_value' is set, a pair is returned: the dictionary and the value of the first attribute. This might be useful if this is the ID. """ if attrStr.endswith( "\n... | |
print seqname, length | def get_sequence_lengths( self ): seqname = None seqlengths = {} for line in FileOrSequence.__iter__( self ): if line.startswith( ">" ): if seqname is not None: seqlengths[ seqname ] = length print seqname, length mo = _re_fasta_header_line.match( line ) seqname = mo.group(1) length = 0 else: assert seqname is not None... | |
pass else: algnt = SAM_Alignment( line ) yield algnt | continue algnt = SAM_Alignment( line ) yield algnt | def __iter__( self ): for line in FileOrSequence.__iter__( self ): if line.startswith( "@" ): # do something with the header line pass |
def __init__( self, dict chrom_lengths, bool stranded=True ): | def __init__( self, chrom_lengths, stranded=True ): | def __init__( self, dict chrom_lengths, bool stranded=True ): GenomicArray.__init__( self, chrom_lengths, stranded, 'O' ) for chrom in self.step_vectors: if self.stranded: self.step_vectors[ chrom ][ strand ][ 0 : self.chrom_lengths[chrom] ] = set() else: self.step_vectors[ chrom ][ 0 : self.chrom_lengths[chrom] ] = se... |
self.step_vectors[ chrom ][ strand ][ 0 : self.chrom_lengths[chrom] ] = set() | self.step_vectors[ chrom ][ strand ][ 0 : chrom_lengths[chrom] ] = set() | def __init__( self, dict chrom_lengths, bool stranded=True ): GenomicArray.__init__( self, chrom_lengths, stranded, 'O' ) for chrom in self.step_vectors: if self.stranded: self.step_vectors[ chrom ][ strand ][ 0 : self.chrom_lengths[chrom] ] = set() else: self.step_vectors[ chrom ][ 0 : self.chrom_lengths[chrom] ] = se... |
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