prompt large_stringlengths 72 9.34k | completion large_stringlengths 0 7.61k |
|---|---|
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | y_val = 0
x_val += 1 |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | plt.savefig(filename) |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | plt.show() |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | shape = type_format[values[stitcher.TYPE_ATTR]] |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | color = 'b'
alpha = 0.2 |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | color = 'r' |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | color = 'y' |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | dotted_line.append((src, trg)) |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | normal_line.append((src, trg)) |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | plt.savefig(filename) |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | plt.show() |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | for nghb in graph.neighbors(item):
if nghb in tmp.nodes():
x_val = pos[nghb][0]
y_val = pos[nghb][1]
if (x_val, y_val) in list(cache.values()):
x_val = pos[nghb][0] + random.randint(10, SPACE)
... |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | x_val = pos[nghb][0]
y_val = pos[nghb][1]
if (x_val, y_val) in list(cache.values()):
x_val = pos[nghb][0] + random.randint(10, SPACE)
y_val = pos[nghb][0] + random.randint(10, SPACE)
cache[ite... |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | x_val = pos[nghb][0] + random.randint(10, SPACE)
y_val = pos[nghb][0] + random.randint(10, SPACE) |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | axes.plot([cache[src][0], cache[trg][0]],
[cache[src][1], cache[trg][1]],
[SPACE, SPACE], color='blue') |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | n_cols += 1 |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | show |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | _plot_subplot |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | show_3d |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | _plot_3d_subplot |
<|file_name|>vis.py<|end_file_name|><｜fim▁begin｜>
"""
Visualize possible stitches with the outcome of the validator.
"""
import math
import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import stitcher
SPACE = 25
TYPE_FORMAT = {'a': '^', 'b':... | _get_size |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | completed.add(f.split('.')[0]) |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | logger = logging.getLogger(logger_name or filename)
fmt = '[%(asctime)s] %(levelname)s %(message)s'
datefmt = "%Y-%m-%d %H:%M:%S"
formatter = logging.Formatter(fmt=fmt, datefmt=datefmt)
handler = logging.handlers.RotatingFileHandler(filename, maxBytes=1024 * 1024 * 1024, backupCount=10)
handler.... |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | def __init__(self, sbid, url):
self.sbid = sbid
self.url = url |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | self.sbid = sbid
self.url = url |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | """Download the PDF or search for the webpage for any PDF link
Args:
url, assuming the input url is valid
"""
def _urlfetch(url, sbid, filename=None, retry=10):
"""
A wrapper for either urlopen or urlretrieve. It depends on the whether
there is a filename as input
... |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | """
A wrapper for either urlopen or urlretrieve. It depends on the whether
there is a filename as input
"""
if filename and os.path.exists(filename):
log.warn("%s\tDUPLICATED\t%s" % (sbid, url))
return None
sleep_time = random.random() + 0.5
... |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | """
Returns:
[{'ScienceBaseID': a1b2c3d4, 'webLinks__uri': 'http://balabala'}, {}]
"""
l = []
with open(csv_filepath, 'r') as f:
reader = csv.DictReader(f, delimiter=',', quotechar='"')
for row in reader:
if 'Action' in row and row['Action'].lower() == 'ignore for... |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | """
Return downloaded tasks
"""
completed = set()
for f in os.listdir(output_folder):
filepath = os.path.join(output_folder, f)
with open(filepath, 'r') as ff:
head_line = ff.readline()
#if os.stat(filepath).st_size > MINIMUM_PDF_SIZE:
if head_line.startsw... |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | """main function
"""
global TASKS
TASKS = get_tasks(csv_filepath)
excluded = set()
if exclude_downloaded:
excluded = get_completed_tasks(output_folder)
for i in range(128):
t = threading.Thread(target=crawler, args=(output_folder, excluded))
t.start()
main_thre... |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | """
Thread working function
"""
finished = 0
print "thread %i has started, exclude %i items" %\
(threading.current_thread().ident, len(excluded))
global TASKS
while True:
task = None
try:
task = TASKS.pop()
except IndexError:
print "th... |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | print crawl(argv[1], '/scratch/pdfs') |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | log.warn("%s\tDUPLICATED\t%s" % (sbid, url))
return None |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | result = urllib.urlretrieve(url, filename)
log.info("%s\tOK\t%s" % (sbid, url)) |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | result = urllib2.urlopen(url).read() |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | sleep_time = random.randint(0, 2 ** i - 1) |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | pdf_name = url.split('/')[-1].split('.')[0]
_urlfetch(url, sbid, os.path.join(output_folder, "%s.%s.pdf" % (sbid, pdf_name))) |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | page = _urlfetch(url, sbid)
soup = bs4.BeautifulSoup(page)
anchors = soup.findAll('a', attrs={'href': re.compile(".pdf$", re.I)})
if not anchors:
log.warn("%s\tNO_PDF_DETECTED\t%s" % (sbid, url))
return None
for a in anchors:
href = a['href']
... |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | log.warn("%s\tNO_PDF_DETECTED\t%s" % (sbid, url))
return None |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | continue |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | l.append(row) |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | completed.add(f.split('.')[0]) |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | os.remove(filepath)
print 'deleted: ', filepath, head_line |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | excluded = get_completed_tasks(output_folder) |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | continue |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | break |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | continue |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | print "%i has finished %i" % (threading.current_thread().ident, finished) |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | import sys
main(sys.argv) |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | create_logger |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | __init__ |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | retrieve |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | _urlfetch |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | get_tasks |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | get_completed_tasks |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | crawl |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | crawler |
<|file_name|>crawler.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
crawler.py
~~~~~~~~~~~~~~
A brief description goes here.
"""
import csv
import urllib2
import urllib
import re
import os
import urlparse
import threading
import logging
import logging.handlers
import time
imp... | main |
<|file_name|>epitopefinder_plotdistributioncomparison.py<|end_file_name|><｜fim▁begin｜>#!python
"""Script for plotting distributions of epitopes per site for two sets of sites.
Uses matplotlib. Designed to analyze output of epitopefinder_getepitopes.py.
Written by Jesse Bloom."""
import os
import sys
import random
... | if 'ymax' in d:
ymax = epitopefinder.io.ParseFloatValue(d, 'ymax') |
<|file_name|>epitopefinder_plotdistributioncomparison.py<|end_file_name|><｜fim▁begin｜>#!python
"""Script for plotting distributions of epitopes per site for two sets of sites.
Uses matplotlib. Designed to analyze output of epitopefinder_getepitopes.py.
Written by Jesse Bloom."""
import os
import sys
import random
... | """Main body of script."""
random.seed(1) # seed random number generator in case P values are being computed
if not epitopefinder.plot.PylabAvailable():
raise ImportError("Cannot import matplotlib / pylab, which are required by this script.")
# output is written to out, currently set to standard... |
<|file_name|>epitopefinder_plotdistributioncomparison.py<|end_file_name|><｜fim▁begin｜>#!python
"""Script for plotting distributions of epitopes per site for two sets of sites.
Uses matplotlib. Designed to analyze output of epitopefinder_getepitopes.py.
Written by Jesse Bloom."""
import os
import sys
import random
... | raise ImportError("Cannot import matplotlib / pylab, which are required by this script.") |
<|file_name|>epitopefinder_plotdistributioncomparison.py<|end_file_name|><｜fim▁begin｜>#!python
"""Script for plotting distributions of epitopes per site for two sets of sites.
Uses matplotlib. Designed to analyze output of epitopefinder_getepitopes.py.
Written by Jesse Bloom."""
import os
import sys
import random
... | raise IOError("Script must be called with exactly one argument specifying the input file") |
<|file_name|>epitopefinder_plotdistributioncomparison.py<|end_file_name|><｜fim▁begin｜>#!python
"""Script for plotting distributions of epitopes per site for two sets of sites.
Uses matplotlib. Designed to analyze output of epitopefinder_getepitopes.py.
Written by Jesse Bloom."""
import os
import sys
import random
... | raise IOError("Failed to find infile %s" % infilename) |
<|file_name|>epitopefinder_plotdistributioncomparison.py<|end_file_name|><｜fim▁begin｜>#!python
"""Script for plotting distributions of epitopes per site for two sets of sites.
Uses matplotlib. Designed to analyze output of epitopefinder_getepitopes.py.
Written by Jesse Bloom."""
import os
import sys
import random
... | raise ValueError("%s specifies more than one file" % xf) |
<|file_name|>epitopefinder_plotdistributioncomparison.py<|end_file_name|><｜fim▁begin｜>#!python
"""Script for plotting distributions of epitopes per site for two sets of sites.
Uses matplotlib. Designed to analyze output of epitopefinder_getepitopes.py.
Written by Jesse Bloom."""
import os
import sys
import random
... | (site, n) = line.split(',')
(site, n) = (int(site), int(n))
xlist.append(n) |
<|file_name|>epitopefinder_plotdistributioncomparison.py<|end_file_name|><｜fim▁begin｜>#!python
"""Script for plotting distributions of epitopes per site for two sets of sites.
Uses matplotlib. Designed to analyze output of epitopefinder_getepitopes.py.
Written by Jesse Bloom."""
import os
import sys
import random
... | raise ValueError("%s failed to specify information for any sites" % xf) |
<|file_name|>epitopefinder_plotdistributioncomparison.py<|end_file_name|><｜fim▁begin｜>#!python
"""Script for plotting distributions of epitopes per site for two sets of sites.
Uses matplotlib. Designed to analyze output of epitopefinder_getepitopes.py.
Written by Jesse Bloom."""
import os
import sys
import random
... | title = None |
<|file_name|>epitopefinder_plotdistributioncomparison.py<|end_file_name|><｜fim▁begin｜>#!python
"""Script for plotting distributions of epitopes per site for two sets of sites.
Uses matplotlib. Designed to analyze output of epitopefinder_getepitopes.py.
Written by Jesse Bloom."""
import os
import sys
import random
... | pvalue = None
pvaluewithreplacement = None |
<|file_name|>epitopefinder_plotdistributioncomparison.py<|end_file_name|><｜fim▁begin｜>#!python
"""Script for plotting distributions of epitopes per site for two sets of sites.
Uses matplotlib. Designed to analyze output of epitopefinder_getepitopes.py.
Written by Jesse Bloom."""
import os
import sys
import random
... | pvalue = int(pvalue)
pvaluewithreplacement = epitopefinder.io.ParseBoolValue(d, 'pvaluewithreplacement')
if pvalue < 1:
raise ValueError("pvalue must be >= 1")
if len(epitopesbysite2_list) >= len(epitopesbysite1_list):
raise ValueError("You cannot use pvalue since... |
<|file_name|>epitopefinder_plotdistributioncomparison.py<|end_file_name|><｜fim▁begin｜>#!python
"""Script for plotting distributions of epitopes per site for two sets of sites.
Uses matplotlib. Designed to analyze output of epitopefinder_getepitopes.py.
Written by Jesse Bloom."""
import os
import sys
import random
... | raise ValueError("pvalue must be >= 1") |
<|file_name|>epitopefinder_plotdistributioncomparison.py<|end_file_name|><｜fim▁begin｜>#!python
"""Script for plotting distributions of epitopes per site for two sets of sites.
Uses matplotlib. Designed to analyze output of epitopefinder_getepitopes.py.
Written by Jesse Bloom."""
import os
import sys
import random
... | raise ValueError("You cannot use pvalue since epitopesbysite2_list is not a subset of epitopesbysite1_list -- it does not contain fewer sites with specified epitope counts.") |
<|file_name|>epitopefinder_plotdistributioncomparison.py<|end_file_name|><｜fim▁begin｜>#!python
"""Script for plotting distributions of epitopes per site for two sets of sites.
Uses matplotlib. Designed to analyze output of epitopefinder_getepitopes.py.
Written by Jesse Bloom."""
import os
import sys
import random
... | ymax = epitopefinder.io.ParseFloatValue(d, 'ymax') |
<|file_name|>epitopefinder_plotdistributioncomparison.py<|end_file_name|><｜fim▁begin｜>#!python
"""Script for plotting distributions of epitopes per site for two sets of sites.
Uses matplotlib. Designed to analyze output of epitopefinder_getepitopes.py.
Written by Jesse Bloom."""
import os
import sys
import random
... | main() # run the script |
<|file_name|>epitopefinder_plotdistributioncomparison.py<|end_file_name|><｜fim▁begin｜>#!python
"""Script for plotting distributions of epitopes per site for two sets of sites.
Uses matplotlib. Designed to analyze output of epitopefinder_getepitopes.py.
Written by Jesse Bloom."""
import os
import sys
import random
... | main |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | """
Operator which generates noise timestreams.
This passes through each observation and every process generates data
for its assigned samples. The dictionary for each observation should
include a unique 'ID' used in the random number generation. The
observation dictionary can optionally incl... |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | super().__init__()
self._out = out
self._oversample = 2
self._realization = realization
self._component = component
self._noisekey = noise
self._rate = rate
self._altfft = altFFT |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | """
Generate noise timestreams.
This iterates over all observations and detectors and generates
the noise timestreams based on the noise object for the current
observation.
Args:
data (toast.Data): The distributed data.
Raises:
KeyError:... |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | """
Simulate one chunk of noise for all detectors.
Args:
tod (toast.tod.TOD): TOD object for the observation.
nse (toast.tod.Noise): Noise object for the observation.
curchunk (int): The local index of the chunk to simulate.
chunk_first (int): Fir... |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | obsindx = obs['id'] |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | print("Warning: observation ID is not set, using zero!") |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | telescope = obs['telescope_id'] |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | global_offset = obs['global_offset'] |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | nse = obs[self._noisekey] |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | raise KeyError('Observation does not contain noise under '
'"{}"'.format(self._noisekey)) |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | raise RuntimeError('noise simulation for uniform distributed '
'samples not implemented') |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | times = tod.local_times() |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | times = None |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | rate = 1 / np.median(np.diff(
times[local_offset : local_offset+chunk_samp])) |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | rate = self._rate |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | continue |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | continue |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | ref = tod.cache.reference(cachename) |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | ref = tod.cache.create(cachename, np.float64,
(tod.local_samples[1], )) |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | __init__ |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | exec |
<|file_name|>sim_det_noise.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2015-2018 by the parties listed in the AUTHORS file.
# All rights reserved. Use of this source code is governed by
# a BSD-style license that can be found in the LICENSE file.
"""
sim_det_noise.py implements the noise simulation operator, OpSi... | simulate_chunk |
<|file_name|>__init__.py<|end_file_name|><｜fim▁begin｜>"""
This package supplies tools for working with automated services
connected to a server. It was written with IRC in mind, so it's not
very generic, in that it pretty much assumes a single client connected
to a central server, and it's not easy for a client to add ... | "connection",
"irc2num" |
<|file_name|>unassignedbugs.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python2
import urllib2
import urllib
from BeautifulSoup import BeautifulSoup
import smtplib
import ConfigParser
# Retreive user information
config = ConfigParser.ConfigParser()
config.read('config.cfg')
user = config.get('data','user')
passwor... | |
<|file_name|>unassignedbugs.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python2
import urllib2
import urllib
from BeautifulSoup import BeautifulSoup
import smtplib
import ConfigParser
# Retreive user information
config = ConfigParser.ConfigParser()
config.read('config.cfg')
user = config.get('data','user')
passwor... | print url
# open bugtracker / parse
page = urllib2.urlopen(url)
soup = BeautifulSoup(page)
data = soup.findAll('td',{'class':'task_id'})
msg = ""
pages = False
# Is there another page with unassigned bugs
if soup.findAll('a',{'id': 'next' }) == []:
page = False
else:
... |
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