import logging
import time
import uuid
import numpy as np
import tweepy
from past import autotranslate
autotranslate(['logging_twitter.handler'])
from logging_twitter.handler import TwitterHandler
class TwitterHelper:
def __init__(self,
consumer_key,
consumer_secret,
access_key,
access_secret,
debug=False):
self.consumer_key = consumer_key
self.consumer_secret = consumer_secret
self.access_key = access_key
self.access_secret = access_secret
self.debug = debug
if not self.debug:
auth = tweepy.OAuthHandler(self.consumer_key, self.consumer_secret)
auth.set_access_token(self.access_key, self.access_secret)
self.tweet_api = tweepy.API(auth)
def active_twitter_logger_for(self, logger_name, target_twitter_user):
_logger = logging.getLogger("salad")
_logger.addHandler(logging.StreamHandler())
_logger.setLevel(logging.INFO)
__TMPDIR_LOCK = threading.Lock()
if six.PY3:
if onWindows():
# create '/tmp' folder if not present
# required by autotranslate module
# TODO: remove when https://github.com/PythonCharmers/python-future/issues/295
# is fixed
if not os.path.exists("/tmp"):
with __TMPDIR_LOCK:
try:
os.makedirs("/tmp")
except OSError as exception:
_logger.error(
u"Cannot create '\\tmp' folder in root needed for"
"'cwltool' Python 3 installation.")
exit(1)
with __TMPDIR_LOCK:
from past import autotranslate # type: ignore
from past.translation import remove_hooks # type: ignore
autotranslate(['avro', 'avro.schema'])
import avro
import avro.schema # pylint: disable=no-name-in-module,import-error
remove_hooks()
# sentiment.py
#
# Copyright 2014 Ben Klein <*****@*****.**>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
# MA 02110-1301, USA.
#
#
# This file is to let python3 run these old python2 sentiment analyses
#
#Because this file should appear to hold the functions itself.
#Runs on an older version of python...
from past import autotranslate
autotranslate('sentiment_analysis')
from sentiment_analysis import *
from basic_sentiment_analysis import *
import os
import socket
import threading
import time
import sys
from future import standard_library
from future.utils import PY3
with standard_library.hooks():
import http.server
import socketserver
import pytest
import tornado.testing
from past import autotranslate
autotranslate(['pkipplib'])
from pkipplib import pkipplib
TRAVIS_USER = os.getenv('TRAVIS_USER', 'travis')
TRAVIS_BUILD_DIR = os.getenv('TRAVIS_BUILD_DIR')
@pytest.mark.skipif(sys.version_info > (3,),
reason='pkipplib is only python2 compatible')
class AsyncSubprocessTestCase(tornado.testing.AsyncTestCase):
ipptool_path = ('%s/ipptool-20130731/ipptool' % TRAVIS_BUILD_DIR if
TRAVIS_BUILD_DIR else '/usr/bin/ipptool')
config = {'ipptool_path': ipptool_path,
'login': TRAVIS_USER,
:Author: Arthur Goldberg <*****@*****.**>
:Date: 2016-07-12
:Copyright: 2016-2018, Karr Lab
:License: MIT
"""
import sys
import math
import argparse
from matplotlib import pyplot
from matplotlib.backends.backend_pdf import PdfPages
from past import autotranslate
autotranslate(['recordtype'])
from recordtype import recordtype
'''
Steps:
read and parse log
plot parameters:
line weight
color, shape, size of symbols
location legend
x is time, and y is copy number
'''
# A population adjustment event
event_fields = 'time adjustment_type population flux'
Adjustment_event = recordtype('Adjustment_event', event_fields)
import os
import sys
import typing
import six
from .utils import onWindows
__author__ = '*****@*****.**'
_logger = logging.getLogger("salad")
_logger.addHandler(logging.StreamHandler())
_logger.setLevel(logging.INFO)
if six.PY3:
if onWindows:
# create '/tmp' folder if not present
# required by autotranslate module
# TODO: remove when https://github.com/PythonCharmers/python-future/issues/295
# is fixed
if not os.path.exists("/tmp"):
try:
os.makedirs("/tmp")
except OSError as exception:
_logger.error(u"Cannot create '\\tmp' folder in root needed for",
"'cwltool' Python 3 installation.")
exit(1)
from past import autotranslate # type: ignore
autotranslate(['avro', 'avro.schema'])
from builtins import object
import os.path
from django.contrib.auth.models import User
from django.db import models
from calisphere.cache_retry import SOLR_select, SOLR_raw, json_loads_url
from django.urls import reverse
from django.utils.encoding import python_2_unicode_compatible
from calisphere.constants import getCollectionData, getRepositoryData
from django.conf import settings
from exhibits.custom_fields import HeroField
from past import autotranslate
autotranslate(['md5s3stash'])
from md5s3stash import md5s3stash
RENDERING_OPTIONS = (
('H', 'HTML'),
('T', 'Plain Text'),
('M', 'Markdown')
)
# class ImageArk(models.Model):
# hero = models.ImageField(blank=True, verbose_name='Hero Image', upload_to='uploads/')
# lockup_derivative = models.ImageField(blank=True, verbose_name='Lockup Image', upload_to='uploads/')
# alternate_lockup_derivative = models.ImageField(blank=True, verbose_name='Alternate Lockup Image', upload_to='uploads/')
# item_id = models.CharField(blank=True, max_length=200)
#
# def __str__(self):
# return self.item_id
from __future__ import unicode_literals
from builtins import object
import os.path
from django.contrib.auth.models import User
from django.db import models
from positions.fields import PositionField
from calisphere.cache_retry import SOLR_select, SOLR_raw, json_loads_url
from django.core.urlresolvers import reverse
from django.utils.encoding import python_2_unicode_compatible
from calisphere.constants import getCollectionData, getRepositoryData
from django.conf import settings
from exhibits.custom_fields import HeroField
from past import autotranslate
autotranslate(['md5s3stash'])
from md5s3stash import md5s3stash
RENDERING_OPTIONS = (('H', 'HTML'), ('T', 'Plain Text'), ('M', 'Markdown'))
# class ImageArk(models.Model):
# hero = models.ImageField(blank=True, verbose_name='Hero Image', upload_to='uploads/')
# lockup_derivative = models.ImageField(blank=True, verbose_name='Lockup Image', upload_to='uploads/')
# alternate_lockup_derivative = models.ImageField(blank=True, verbose_name='Alternate Lockup Image', upload_to='uploads/')
# item_id = models.CharField(blank=True, max_length=200)
#
# def __str__(self):
# return self.item_id
class PublishedExhibitManager(models.Manager):
# coding=utf-8
import pdb
import pybedtools
from past import autotranslate
autotranslate(['swalign'])
import swalign
def revcomp(seq):
return "".join(
[{
"A": "T",
"C": "G",
"G": "C",
"T": "A",
"N": "N"
}[lett] for lett in
[seq[i] for i in [len(seq) - idx - 1 for idx in range(len(seq))]]])
def getMatchSize(tup):
if tup[1] == "M":
return tup[0]
else:
return 0
def getAlign(ref_seq, query_seq):
match = 1
mismatch = -5
scoring = swalign.NucleotideScoringMatrix(match, mismatch)
from past import autotranslate
autotranslate(['fanficfare.adapters'])
autotranslate(['fanficfare.configurable'])
import fanficfare.adapters
from fanficfare import adapters
from fanficfare.configurable import Configuration
class FFFOverides(object):
def getNormalStoryURLSite(url):
# print("getNormalStoryURLSite:%s"%url)
if not adapters.gerNormalStoryURL.__dummyconfig:
adapters.getNormalStoryURL.__dummyconfig = Configuration(
["test1.com"], "EPUB", lightweight=True)
# pulling up an adapter is pretty low over-head. If
# it fails, it's a bad url.
try:
adapter = adapters.getAdapter(
adapters.getNormalStoryURL.__dummyconfig, url)
url = adapter.url
site = adapter.getSiteDomain()
storyid = adapter.story.getMetadata('storyId')
del adapter
return (url, site, storyid)
except:
return None
# $ pip3 install mypackagename --no-compile # to ignore SyntaxErrors from past import autotranslate autotranslate(['mypackagename']) import mypackagename
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation; either version 2 of the License, or #
# (at your option) any later version. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
#*******************************************************************************#
# Functions for converting between ascii and gadget format
import sys
import time
from past import autotranslate
autotranslate(['glio'])
import glio
import numpy as np
from astropy.units import solMass, Mpc, m, s
def ascii2gadget(infile, outfile, Lbox, H0, UNITLENGTH_IN_CM):
'''
Function to convert a StePS ascii file to Gadget format.
infile: input StePS ascii file
outfile: output Gadget file
'''
#Setting up the units of distance and time
UNIT_T = 47.14829951063323 #Unit time in Gy
UNIT_V = 20.738652969925447 #Unit velocity in km/s
UNIT_D = 3.0856775814671917e24 #=1Mpc Unit distance in cm (in the StePS code)
# http://python-future.org/translation.html
from past import autotranslate
autotranslate(['MouseConnectivityCache'])
# Path to Allen SDK
import sys
sys.path.append('../git3/')
from allensdk.core.mouse_connectivity_cache import MouseConnectivityCache
# The manifest file is a simple JSON file that keeps track of all of
# the data that has already been downloaded onto the hard drives.
# If you supply a relative path, it is assumed to be relative to your
# current working directory.
mcc = MouseConnectivityCache(
manifest_file='connectivity/mouse_connectivity_manifest.json')
# open up a list of all of the experiments
all_experiments = mcc.get_experiments(dataframe=True)
# take a look at what we know about an experiment with a primary motor injection
#all_experiments.loc[122642490]
# grab the StructureTree instance
structure_tree = mcc.get_structure_tree()
from allensdk.api.queries.ontologies_api import OntologiesApi
oapi = OntologiesApi()
# get the ids of all the structure sets in the tree
# Remote Academy LabBox Environment
# Webcam Wrapper
from past import autotranslate
autotranslate(['v4l2'])
import v4l2
import fcntl
import os
import mmap
import time
from io import StringIO
class Webcam:
def __init__(self):
self.available = False
self.cp = None
self.device = None
self.fmt = None
self.reqbuf = None
self.imagebuffers = []
try:
fd = os.open('/dev/video0', os.O_RDWR)
self.device = open(fd, 'wb+', buffering=0)
self.available = True
self.cp = v4l2.v4l2_capability()
fcntl.ioctl(self.device, v4l2.VIDIOC_QUERYCAP, self.cp)
except:
pass