text stringlengths 0 1.05M | meta dict |
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__author__ = 'bkeroack'
from types import FunctionType
import functools
import logging
import collections
import type_check
def log_wrapper(func):
@functools.wraps(func)
def log(*args, **kwargs):
logging.debug("CALLING: {} (args: {}, kwargs: {}".format(func.__name__, args, kwargs))
ret = func... | {
"repo_name": "bkeroack/elita",
"path": "elita/util/__init__.py",
"copies": "1",
"size": "3592",
"license": "apache-2.0",
"hash": 2348633151828624000,
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"autogenerated": false,
"ratio": 3.617321248741188,
"config_test": fals... |
__author__ = 'bkeroack'
import deployment.salt_control
import deployment.sshconfig
def setup_new_server(datasvc, name):
'''
Do any initial server setup so it works for elita.
Initially we just check if it's a Windows server and if so set up the git wrapper. At some point maybe we should
verify that g... | {
"repo_name": "bkeroack/elita",
"path": "elita/servers.py",
"copies": "1",
"size": "2777",
"license": "apache-2.0",
"hash": -5600264720181478000,
"line_mean": 38.6714285714,
"line_max": 120,
"alpha_frac": 0.5819229384,
"autogenerated": false,
"ratio": 3.9785100286532953,
"config_test": false,
... |
__author__ = 'bkeroack'
import fnmatch
import logging
import elita.util
from elita.dataservice.models import User
class ValidatePermissionsObject:
__metaclass__ = elita.util.LoggingMetaClass
def __init__(self, permissions):
self.permissions = permissions
def verify_top_dict(self):
retur... | {
"repo_name": "bkeroack/elita",
"path": "elita/auth.py",
"copies": "1",
"size": "7103",
"license": "apache-2.0",
"hash": -6390413687966621000,
"line_mean": 39.1299435028,
"line_max": 107,
"alpha_frac": 0.570322399,
"autogenerated": false,
"ratio": 4.495569620253165,
"config_test": false,
"has... |
__author__ = 'bkeroack'
import logging
import bson
import collections
import elita.util
import models
DEFAULT_ADMIN_USERNAME = 'admin'
DEFAULT_ADMIN_PASSWORD = 'elita'
DEFAULT_ADMIN_PERMISSIONS = {
'apps': {
'*': 'read/write',
'_global': 'read/write'
},
'actions': {
'*': {
... | {
"repo_name": "bkeroack/elita",
"path": "elita/dataservice/datavalidator.py",
"copies": "1",
"size": "27790",
"license": "apache-2.0",
"hash": 1252719993124415200,
"line_mean": 45.8634064081,
"line_max": 132,
"alpha_frac": 0.4686577906,
"autogenerated": false,
"ratio": 4.38743290179981,
"config... |
__author__ = 'bkeroack'
import logging
import collections
import pprint
class RootTree(collections.MutableMapping):
def __init__(self, db, updater, tree, doc, *args, **kwargs):
self.pp = pprint.PrettyPrinter(indent=4)
self.db = db
self.tree = tree
self.doc = doc
self.updat... | {
"repo_name": "bkeroack/elita",
"path": "elita/dataservice/root_tree.py",
"copies": "1",
"size": "2449",
"license": "apache-2.0",
"hash": -8585424347718574000,
"line_mean": 30.3974358974,
"line_max": 109,
"alpha_frac": 0.5300122499,
"autogenerated": false,
"ratio": 3.9756493506493507,
"config_t... |
__author__ = 'bkeroack'
import logging
import elita.util
import bson
class MongoService:
# logspam
#__metaclass__ = elita.util.LoggingMetaClass
def __init__(self, db):
'''
@type db = pymongo.database.Database
'''
assert db
self.db = db
def create_new(self, col... | {
"repo_name": "bkeroack/elita",
"path": "elita/dataservice/mongo_service.py",
"copies": "1",
"size": "6422",
"license": "apache-2.0",
"hash": 7265936299309052000,
"line_mean": 39.1375,
"line_max": 125,
"alpha_frac": 0.5879788228,
"autogenerated": false,
"ratio": 4.167423750811162,
"config_test"... |
__author__ = 'bkeroack'
import logging
import os
import shutil
import bson
import datetime
import pytz
import copy
import sys
import jsonpatch
import traceback
import elita.util
import elita.elita_exceptions
import models
from root_tree import RootTree
from mongo_service import MongoService
from elita.deployment.gits... | {
"repo_name": "bkeroack/elita",
"path": "elita/dataservice/__init__.py",
"copies": "1",
"size": "69752",
"license": "apache-2.0",
"hash": 7504837548507160000,
"line_mean": 41.2483343428,
"line_max": 289,
"alpha_frac": 0.5893164354,
"autogenerated": false,
"ratio": 3.9407909604519773,
"config_te... |
__author__ = 'bkeroack'
import os
import pkg_resources
from clint.arguments import Args
from clint.textui import puts, colored
import subcommands
config = {
'host': 'localhost' if 'ELITA_HOST' not in os.environ else os.environ['ELITA_HOST'],
'port': 2718 if 'ELITA_PORT' not in os.environ else os.environ['EL... | {
"repo_name": "bkeroack/elita",
"path": "elita_cli/__init__.py",
"copies": "1",
"size": "1066",
"license": "apache-2.0",
"hash": -6089715625281243000,
"line_mean": 23.25,
"line_max": 108,
"alpha_frac": 0.6181988743,
"autogenerated": false,
"ratio": 3.182089552238806,
"config_test": false,
"ha... |
__author__ = 'bkeroack'
import os
import platform
from clint.textui import puts, indent, colored
import linux
import darwin
# Autodetect platform, perform correct installation routine
def Install():
os_name = os.name
p_name = platform.system()
puts("Installing Elita")
with indent(4, quote=colored.... | {
"repo_name": "bkeroack/elita",
"path": "elita_install/__init__.py",
"copies": "1",
"size": "1058",
"license": "apache-2.0",
"hash": 2948814902095085000,
"line_mean": 30.1470588235,
"line_max": 104,
"alpha_frac": 0.5746691871,
"autogenerated": false,
"ratio": 3.9185185185185185,
"config_test": ... |
__author__ = 'bkeroack'
import os
import shutil
import requests
import zipfile
import tarfile
import tempfile
import logging
import glob2
import billiard
import elita.util
class SupportedFileType:
TarGz = 'tar.gz'
TarBz2 = 'tar.bz2'
Zip = 'zip'
types = [TarBz2, TarGz, Zip]
class UnsupportedFileType(... | {
"repo_name": "bkeroack/elita",
"path": "elita/builds.py",
"copies": "1",
"size": "13088",
"license": "apache-2.0",
"hash": 1384370331425454600,
"line_mean": 36.3942857143,
"line_max": 119,
"alpha_frac": 0.6101772616,
"autogenerated": false,
"ratio": 3.86989946777055,
"config_test": false,
"h... |
__author__ = 'bkeroack'
import pymongo
import bson
import multiprocessing
import copy
import time
import random
import elita.dataservice.mongo_service
def setup_db():
mc = pymongo.MongoClient(host='localhost', port=27017)
db = mc['elita_testing']
return mc, db
def clear_mocks(db):
db['mock_objs'].re... | {
"repo_name": "bkeroack/elita",
"path": "test/test_mongo.py",
"copies": "1",
"size": "6847",
"license": "apache-2.0",
"hash": -6909328713277020000,
"line_mean": 26.0632411067,
"line_max": 105,
"alpha_frac": 0.5764568424,
"autogenerated": false,
"ratio": 3.2918269230769233,
"config_test": true,
... |
__author__ = 'bkeroack'
import shutil
import os
import os.path
import sys
import stat
import sh
from sh import useradd, chown, chmod
import logging
from clint.textui import puts, colored, indent
ELITA_HOME = "/home/elita"
ELITA_LOG_DIR = "/var/log/elita"
ELITA_ETC = "/etc/elita"
ELITA_INITD = "/etc/init.d/elita"
ELI... | {
"repo_name": "bkeroack/elita",
"path": "elita_install/linux.py",
"copies": "1",
"size": "5930",
"license": "apache-2.0",
"hash": 3686449027852783600,
"line_mean": 32.1340782123,
"line_max": 116,
"alpha_frac": 0.6507588533,
"autogenerated": false,
"ratio": 3.028600612870276,
"config_test": fals... |
__author__ = 'bkeroack'
import sys
import logging
import traceback
import time
import billiard
import itertools
import pprint
pp = pprint.PrettyPrinter(indent=4)
import elita.util
import elita.util.type_check
import gitservice
import salt_control
from elita.actions.action import regen_datasvc
class FatalDeploymentEr... | {
"repo_name": "bkeroack/elita",
"path": "elita/deployment/deploy.py",
"copies": "1",
"size": "43499",
"license": "apache-2.0",
"hash": 4793380084265116000,
"line_mean": 51.9184914842,
"line_max": 179,
"alpha_frac": 0.5557139245,
"autogenerated": false,
"ratio": 4.2554294658579535,
"config_test"... |
__author__ = 'bk'
from typecheck import typecheck
import typecheck as tc
import collections.abc as abc
import collections
@typecheck
def flatten(list_obj: abc.MutableSequence):
'''
Iterate through n-dimensional list yielding items
'''
for item in list_obj:
if isinstance(item, collections.Iter... | {
"repo_name": "bkeroack/py-extlib",
"path": "extlib/seq_tools/__init__.py",
"copies": "1",
"size": "1796",
"license": "apache-2.0",
"hash": 4003092329899896000,
"line_mean": 23.2702702703,
"line_max": 80,
"alpha_frac": 0.5189309577,
"autogenerated": false,
"ratio": 3.5776892430278884,
"config_t... |
__author__ = 'bk'
from typecheck import typecheck
import typecheck as tc
import collections.abc as abc
@typecheck
def filter_dict_keys(obj: abc.MutableMapping, char: str, rep: str):
'''
Recursively replaces char in nested dict keys with rep (for sanitizing input to mongo, for example)
'''
new_obj = ob... | {
"repo_name": "bkeroack/py-extlib",
"path": "extlib/tree_tools/__init__.py",
"copies": "1",
"size": "3312",
"license": "apache-2.0",
"hash": -1787854337991367700,
"line_mean": 30.8557692308,
"line_max": 103,
"alpha_frac": 0.5495169082,
"autogenerated": false,
"ratio": 3.576673866090713,
"config... |
__author__ = 'bk'
from typecheck import typecheck
import typecheck as tc
import zipfile
import os
import logging
@typecheck
def zipfolder(path: str, zipname: str, subpath: tc.optional(str)=""):
'''
Create zip of a folder, prepending subpath to all archive paths if supplied
'''
assert os.path.isdir(pat... | {
"repo_name": "bkeroack/py-extlib",
"path": "extlib/zip/__init__.py",
"copies": "1",
"size": "1141",
"license": "apache-2.0",
"hash": 1253618606030430500,
"line_mean": 35.8387096774,
"line_max": 96,
"alpha_frac": 0.6354075372,
"autogenerated": false,
"ratio": 3.4264264264264264,
"config_test": ... |
__author__ = 'bkovacev'
import os
import json
import urllib
from uuid import uuid1
from collections import OrderedDict
from google.appengine.ext import blobstore
from google.appengine.ext.webapp import blobstore_handlers
from google.appengine.ext.webapp import template
from handlers import user_required, BaseHandler... | {
"repo_name": "bkovacev/gae-student-portal",
"path": "views.py",
"copies": "1",
"size": "20149",
"license": "mit",
"hash": 1683300293784673300,
"line_mean": 30.8309636651,
"line_max": 112,
"alpha_frac": 0.5783909871,
"autogenerated": false,
"ratio": 3.7086324314375116,
"config_test": false,
"... |
__author__ = 'bkovacev'
import time
import webapp2_extras.appengine.auth.models
from google.appengine.ext import ndb
from webapp2_extras import security
from google.appengine.api import images
class Activity(ndb.Model):
"""
#TODO Remodel.
"""
user = ndb.KeyProperty(kind='User', required=True)
ty... | {
"repo_name": "bkovacev/gae-student-portal",
"path": "models.py",
"copies": "1",
"size": "12387",
"license": "mit",
"hash": -4557605148718367000,
"line_mean": 34.8005780347,
"line_max": 110,
"alpha_frac": 0.6393799952,
"autogenerated": false,
"ratio": 3.761615548132402,
"config_test": false,
... |
__author__ = 'blackmesa'
# coding=utf-8
__author__ = 'sudo'
from configparser import ConfigParser
import requests
import bs4
session = requests.Session()
session.headers.update({'User-Agent': 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/17.0 Firefox/17.0'})
def login():
LOGIN_URL = "http://de.ogame.ga... | {
"repo_name": "erstis-go-botting/sexy-bot",
"path": "examples/easy_build_something.py",
"copies": "1",
"size": "1385",
"license": "mit",
"hash": -3293300163620382000,
"line_mean": 25.1320754717,
"line_max": 110,
"alpha_frac": 0.6758122744,
"autogenerated": false,
"ratio": 3.1986143187066975,
"c... |
__author__ = 'blackthorne'
import call
import logging
import cStringIO
import unittest
import datetime
def hexdump(src, length=16, sep='.'):
FILTER = ''.join([(len(repr(chr(x))) == 3) and chr(x) or sep for x in range(256)])
lines = []
for c in xrange(0, len(src), length):
chars = src[c:c+length]
... | {
"repo_name": "blackthorne/Libcall",
"path": "libcall/tests/tests.py",
"copies": "1",
"size": "4441",
"license": "apache-2.0",
"hash": 7139044174125079000,
"line_mean": 30.0629370629,
"line_max": 96,
"alpha_frac": 0.5904075659,
"autogenerated": false,
"ratio": 3.4968503937007873,
"config_test":... |
__author__ = 'akoziol'
# Import the necessary modules
# OS is used for file/folder manipulations
import os
# Subprocess->call is used for making system calls
import subprocess
# Errno is used in the file creation command - I think it's similar to the $! variable in Perl
import errno
# Glob finds all the path names ma... | {
"repo_name": "adamkoziol/SipprModeling",
"path": "SipprModellingMultiprocessingMultifile.py",
"copies": "1",
"size": "23959",
"license": "mit",
"hash": -3824011015604236300,
"line_mean": 45.4321705426,
"line_max": 125,
"alpha_frac": 0.547143036,
"autogenerated": false,
"ratio": 3.991171081126103... |
__author__ = 'blais'
__author__ = 'akoziol'
# Import the necessary modules
# OS is used for file/folder manipulations
import os
# Subprocess->call is used for making system calls
import subprocess
# Errno is used in the file creation command - I think it's similar to the $! variable in Perl
import errno
# Glob finds ... | {
"repo_name": "adamkoziol/SipprModeling",
"path": "modellingClasses.py",
"copies": "1",
"size": "9269",
"license": "mit",
"hash": 3818036614657197000,
"line_mean": 34.5172413793,
"line_max": 117,
"alpha_frac": 0.6295177473,
"autogenerated": false,
"ratio": 3.5256751616584254,
"config_test": fal... |
__author__ = 'blais'
import multiprocessing
import os
import sys
import subprocess
import errno
import glob
from multiprocessing import Pool
# Define the variables for the read length and fold coverage, respectively
readLength = [21, 22, 23, 24]
foldCoverage = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
kmer = [5, 7, 9]
os.chdi... | {
"repo_name": "adamkoziol/SipprModeling",
"path": "test.py",
"copies": "1",
"size": "2331",
"license": "mit",
"hash": -5624553209837212000,
"line_mean": 34.3333333333,
"line_max": 117,
"alpha_frac": 0.6735306735,
"autogenerated": false,
"ratio": 3.1246648793565686,
"config_test": false,
"has_... |
__author__ = 'Blake'
import copy
from functools import partial
from synpost.fn.helpers import min_max
class PluginMeta(type):
def __new__(cls, name, parents, dct):
if not 'name' in dct:
dct['name'] = name.lower().replace('plugin', '').replace('site', '')
if not 'action' in dct:
... | {
"repo_name": "blakev/synpost",
"path": "synpost/plugins/core.py",
"copies": "1",
"size": "1275",
"license": "mit",
"hash": -3715593717965198000,
"line_mean": 20.9827586207,
"line_max": 80,
"alpha_frac": 0.5796078431,
"autogenerated": false,
"ratio": 3.8871951219512195,
"config_test": false,
... |
__author__ = 'Blake'
from synpost.plugins.core import PluginMeta as PluginType
class Action(object):
def __init__(self, plugins = None, pipeline = None):
if not plugins:
plugins = []
if not pipeline:
pipeline = []
self.description = 'DefaultAction'
self.g... | {
"repo_name": "blakev/synpost",
"path": "synpost/objects/action.py",
"copies": "1",
"size": "1630",
"license": "mit",
"hash": 3046031050051586000,
"line_mean": 28.125,
"line_max": 79,
"alpha_frac": 0.5809815951,
"autogenerated": false,
"ratio": 4.190231362467866,
"config_test": false,
"has_no... |
__author__ = 'Blake'
from synpost.plugins.core import SitePluginCore
class AssetByUuidSitePlugin(SitePluginCore):
priority = 50
action = 'site'
@staticmethod
def execute(Site):
if not Site.is_available('uuid_map'):
return Site
uuid_chain = {}
for article in Sit... | {
"repo_name": "blakev/synpost",
"path": "synpost/plugins/siteplugin_prevnext.py",
"copies": "1",
"size": "1297",
"license": "mit",
"hash": 7759951492744031000,
"line_mean": 22.1607142857,
"line_max": 81,
"alpha_frac": 0.599074788,
"autogenerated": false,
"ratio": 4.157051282051282,
"config_test... |
__author__ = 'Blake'
import os
import re
from collections import namedtuple
from jinja2 import Environment as JinjaEnvironment, FileSystemLoader as JinjaLoader
from synpost.globals import Values as Globals
from synpost.fn.io import generic_collect
ThemeFile = namedtuple('ThemeFile', 'filename valiname filepath ext... | {
"repo_name": "blakev/synpost",
"path": "synpost/objects/theme.py",
"copies": "1",
"size": "4114",
"license": "mit",
"hash": 7507073140990266000,
"line_mean": 37.4485981308,
"line_max": 130,
"alpha_frac": 0.6550802139,
"autogenerated": false,
"ratio": 3.709648331830478,
"config_test": false,
... |
__author__ = 'Blake'
import os
import re
from collections import namedtuple
SiteFile = namedtuple('SiteFile', 'filename valiname filepath extension type')
# coerce all files from collect_files_from into objects with properties
def generic_collect(path, regex, ftype, nametuple = None):
if nametuple is None:
... | {
"repo_name": "blakev/synpost",
"path": "synpost/fn/io.py",
"copies": "1",
"size": "2521",
"license": "mit",
"hash": 6480167290787344000,
"line_mean": 24.4646464646,
"line_max": 87,
"alpha_frac": 0.6255454185,
"autogenerated": false,
"ratio": 3.762686567164179,
"config_test": false,
"has_no_k... |
__author__ = 'Blake'
import os
import re
import json
import shutil
from synpost.globals import Values as Globals
import synpost.objects.content as Content
from synpost.objects.action import Action
from synpost.fn.io import collect_files_from, create_folders_from_dict
from synpost.fn.conversions import path_to_asset
... | {
"repo_name": "blakev/synpost",
"path": "synpost/build.py",
"copies": "1",
"size": "3715",
"license": "mit",
"hash": 7454657811869437000,
"line_mean": 29.7024793388,
"line_max": 85,
"alpha_frac": 0.5819650067,
"autogenerated": false,
"ratio": 3.861746361746362,
"config_test": false,
"has_no_k... |
__author__ = 'Blake'
import os
import shutil
from synpost.plugins.core import PluginCore
class MovePagesPlugin(PluginCore):
action = 'build'
priority = 100
@staticmethod
def execute(Action):
page_files_in_root = Action.config.get('page_files_in_root', True)
assets_as_pages = Action.c... | {
"repo_name": "blakev/synpost",
"path": "synpost/plugins/plugin_movepages.py",
"copies": "1",
"size": "2076",
"license": "mit",
"hash": -9083565942894766000,
"line_mean": 35.4210526316,
"line_max": 111,
"alpha_frac": 0.6045279383,
"autogenerated": false,
"ratio": 3.579310344827586,
"config_test... |
__author__ = 'Blake'
import os
from synpost.extensions.metaextension import MetaExtension
# root folders/categories for all items to go inside
STATIC_CATEGORIES = ['articles', 'pages']
class Category(MetaExtension):
def __init__(self, asset, attribute):
super(Category, self).__init__(asset, attribute)
... | {
"repo_name": "blakev/synpost",
"path": "synpost/extensions/categories.py",
"copies": "1",
"size": "1717",
"license": "mit",
"hash": -8163497288748322000,
"line_mean": 34.0408163265,
"line_max": 115,
"alpha_frac": 0.6144437973,
"autogenerated": false,
"ratio": 4.068720379146919,
"config_test": ... |
__author__ = 'blastron'
sass_lines = [
"Apologize to your audio software.",
"I hope you realize that what you are doing is wrong.",
"Prepare yourself for the consequences.",
"Every bit you crush is a callous waste of sound.",
"You are a 1-bit monster.",
"Octo might forgive you, but I never will... | {
"repo_name": "whoozle/Octo",
"path": "tools/Chipify/chipify.py",
"copies": "4",
"size": "4585",
"license": "mit",
"hash": 85802641558327620,
"line_mean": 30.404109589,
"line_max": 111,
"alpha_frac": 0.6763358779,
"autogenerated": false,
"ratio": 3.2152875175315567,
"config_test": false,
"has... |
__author__ = 'blaz'
import sys
import os
import time
import threading
import select
import sys
import pybonjour
import settings
import socket
import serial
import datetime, time
from logger import *
class BrowseService(threading.Thread):
"""
Class for browsing services advertised using Bonjour (MDNS) It runs ... | {
"repo_name": "blazdivjak/rzpproject",
"path": "VirtualInstrument.py",
"copies": "1",
"size": "6164",
"license": "mit",
"hash": 3192977577192329000,
"line_mean": 33.2444444444,
"line_max": 112,
"alpha_frac": 0.5663530175,
"autogenerated": false,
"ratio": 4.176151761517615,
"config_test": false,... |
__author__ = 'bloomj'
from OPLCollector import *
from Optimizer import *
try:
from pyspark import SparkConf, SparkContext
from pyspark.sql import SparkSession, Row, functions
from pyspark.sql.types import StructType, StructField, StringType, IntegerType, DoubleType
except ImportError as e:
p... | {
"repo_name": "JeremyBloom/Optimization-Examples",
"path": "Tableau.py",
"copies": "1",
"size": "20854",
"license": "mit",
"hash": 2056460358115131400,
"line_mean": 53.0237467018,
"line_max": 166,
"alpha_frac": 0.5891435696,
"autogenerated": false,
"ratio": 4.429481733220051,
"config_test": fal... |
__author__ = 'bloomj'
try:
import folium
except:
if hasattr(sys, 'real_prefix'):
# we are in a virtual env.
!pip install folium
else:
!pip install - -user folium
import folium
from pyspark.sql.types import StringType, IntegerType, DoubleType
class Maps(object... | {
"repo_name": "JeremyBloom/Optimization-Examples",
"path": "Maps.py",
"copies": "1",
"size": "9331",
"license": "mit",
"hash": -6601105806906867000,
"line_mean": 49.2692307692,
"line_max": 187,
"alpha_frac": 0.624477548,
"autogenerated": false,
"ratio": 4.434885931558935,
"config_test": true,
... |
import os
import argparse
import sys
import warnings
def quants_to_dict(quantFiles, tpm_index):
tpmD = {}
for q in quantFiles:
with open(q, 'r') as f:
for line in f:
if (line.startswith('Name') or line.startswith('#')):
continue
line = li... | {
"repo_name": "bluegenes/MakeMyTranscriptome",
"path": "scripts/util/filter_contigs_by_tpm.py",
"copies": "1",
"size": "1985",
"license": "bsd-3-clause",
"hash": 4465984347683032000,
"line_mean": 37.1730769231,
"line_max": 110,
"alpha_frac": 0.5370277078,
"autogenerated": false,
"ratio": 3.780952... |
from time import strftime
import tarfile
import zipfile
from mmt_defaults import PATH_TOOLS, PATH_ROOT
from external_tools import TOOLS_DICT
import os
from os.path import exists, join, split
import json
import argparse
import sys
import functools
import subprocess
import platform
from tasks_v2 import Sup... | {
"repo_name": "bluegenes/MakeMyTranscriptome",
"path": "scripts/manage_tools.py",
"copies": "1",
"size": "5926",
"license": "bsd-3-clause",
"hash": -376996449616382140,
"line_mean": 33.6987951807,
"line_max": 153,
"alpha_frac": 0.6012487344,
"autogenerated": false,
"ratio": 3.6068167985392576,
... |
from tools_class import ext_tool as tc
from mmt_defaults import PATH_TOOLS
from os.path import join,dirname,abspath
import platform
#samtools --> need to either add here, or make sure user has downloaded somehow..
TOOL_LIST = []
### Trinity ###
trinity_source_url = 'https://github.com/trinityrnaseq/trinit... | {
"repo_name": "bluegenes/MakeMyTranscriptome",
"path": "scripts/external_tools.py",
"copies": "1",
"size": "20538",
"license": "bsd-3-clause",
"hash": -397815896911887900,
"line_mean": 61.7826086957,
"line_max": 313,
"alpha_frac": 0.6840003895,
"autogenerated": false,
"ratio": 2.6555469356089993,... |
import os
from os.path import join, exists, dirname
from tasks_v2 import Task
class ext_tool:
def __init__(self,name,url,target,executables, instructions, web='',urltype='tar.gz',dependencies = [], folder_name = '', install=True, executeable_flags=None):
self.name = name
self.url = url
... | {
"repo_name": "bluegenes/MakeMyTranscriptome",
"path": "scripts/tools_class.py",
"copies": "1",
"size": "2198",
"license": "bsd-3-clause",
"hash": 8358604300291748000,
"line_mean": 41.0980392157,
"line_max": 164,
"alpha_frac": 0.6251137398,
"autogenerated": false,
"ratio": 3.445141065830721,
"c... |
__author__ = 'bmiller'
import os, shutil
mymodules = ['document', 'math', 'operator', 'processing', 'random', 're', 'time', 'test', 'turtle', 'unittest', 'urllib', 'webgl']
p26root = '/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/'
def make_stub(fname,fpath):
modname = fname.replace('.p... | {
"repo_name": "ArcherSys/ArcherSys",
"path": "skulpt/stdlibstubs.py",
"copies": "1",
"size": "1151",
"license": "mit",
"hash": 4704379083999486000,
"line_mean": 35,
"line_max": 131,
"alpha_frac": 0.5977410947,
"autogenerated": false,
"ratio": 3.336231884057971,
"config_test": false,
"has_no_k... |
__author__ = 'bms'
import logging
from django.test import TestCase
import django.forms as djforms
import django.forms.widgets as djwidgets
import django_forms_bootstrapped as forms
import django_forms_bootstrapped.widgets as widgets
log = logging.getLogger(__name__)
class FormTestCase(TestCase):
def setUp(s... | {
"repo_name": "bmsilva/django-forms-bootstrapped",
"path": "django_forms_bootstrapped/tests/test_forms.py",
"copies": "1",
"size": "11079",
"license": "mit",
"hash": 4167612409363470000,
"line_mean": 34.854368932,
"line_max": 131,
"alpha_frac": 0.5075367813,
"autogenerated": false,
"ratio": 3.726... |
__author__ = 'bms'
import sys
from django.conf import settings
def main():
settings.configure(
DEBUG=True,
DATABASES={'default': {'ENGINE': 'django.db.backends.sqlite3'}},
#ROOT_URLCONF='myapp.urls',
INSTALLED_APPS=(
# 'django.contrib.auth',
# 'django.cont... | {
"repo_name": "bmsilva/django-forms-bootstrapped",
"path": "run_tests.py",
"copies": "1",
"size": "1564",
"license": "mit",
"hash": -5155171105587350000,
"line_mean": 26.9285714286,
"line_max": 80,
"alpha_frac": 0.439258312,
"autogenerated": false,
"ratio": 4.520231213872832,
"config_test": fal... |
__author__ = 'bmustafa'
import numpy as np
import warnings
import matplotlib.pyplot as plt
from skimage.segmentation import random_walker
def rw_segment(image, seeds, threshold=0.95, beta=90, bg_label=-1, return_bg_label = False, debug=False):
# Uses scikit-image's implementation of Leo Grady's Random Walker algor... | {
"repo_name": "Basil-M/AMGEN-Summer-Project-2017",
"path": "python/code/Random walker/rw_segmenter.py",
"copies": "1",
"size": "4387",
"license": "mit",
"hash": 7968893898825929000,
"line_mean": 42.4356435644,
"line_max": 132,
"alpha_frac": 0.580123091,
"autogenerated": false,
"ratio": 4.02108157... |
__author__ = 'bnelson'
from SIDServer import Objects
import io
import yaml
import datetime as dt
import math
import numpy as np
from matplotlib.mlab import psd
import h5py
import os
import zipfile
import bz2
class PrintHelper:
def __init__(self):
"""
"""
@staticmethod
def print_level():
... | {
"repo_name": "SidWatch/pySIDServerDataProcessor",
"path": "source/SIDServer/Utilities.py",
"copies": "1",
"size": "6570",
"license": "mit",
"hash": 7018871561048283000,
"line_mean": 31.2058823529,
"line_max": 100,
"alpha_frac": 0.5736681887,
"autogenerated": false,
"ratio": 4.05305367057372,
"... |
__author__ = 'bnelson'
import datetime as dt
import dateutil.parser
import os
import time as threadtime
import numpy as np
from boto.s3.connection import S3Connection
from boto.s3.key import Key
from boto.s3.connection import OrdinaryCallingFormat
from SIDServer.Objects import File
from SIDServer.Objects import Stati... | {
"repo_name": "SidWatch/pySIDServerDataProcessor",
"path": "source/SIDServer/Controllers.py",
"copies": "1",
"size": "12201",
"license": "mit",
"hash": -3010909326260304000,
"line_mean": 39.4006622517,
"line_max": 107,
"alpha_frac": 0.5500368822,
"autogenerated": false,
"ratio": 4.602414183327046... |
"""
nimsdata.medimg.nimsmontage
===========================
NIMSMontage provides montage writing capabilities for MR datasets read by any subclass of NIMSMRReader.
Provides a NIMSMRWriter subclass for creating image pyramids.
"""
import os
import math
import logging
import sqlite3
import cStringIO
import numpy as ... | {
"repo_name": "cni/nimsdata",
"path": "medimg/nimsmontage.py",
"copies": "1",
"size": "15269",
"license": "mit",
"hash": -3379602223019705000,
"line_mean": 43.7771260997,
"line_max": 210,
"alpha_frac": 0.6011526623,
"autogenerated": false,
"ratio": 3.452181777074384,
"config_test": false,
"ha... |
"""
scitran.data.medimg.montage
===========================
Montage provides montage writing capabilities for MR datasets read by any subclass of MedImgReader.
Provides a MedImgWriter subclass for creating image pyramids.
"""
import os
import json
import math
import logging
import zipfile
import cStringIO
import n... | {
"repo_name": "scitran/data",
"path": "scitran/data/medimg/montage.py",
"copies": "1",
"size": "11335",
"license": "mit",
"hash": 8649182239321435000,
"line_mean": 39.9205776173,
"line_max": 132,
"alpha_frac": 0.6120864579,
"autogenerated": false,
"ratio": 3.482334869431644,
"config_test": fals... |
import sys
from code import InteractiveConsole
from gevent import socket
from gevent.greenlet import Greenlet
from gevent.server import StreamServer
__all__ = ['BackdoorServer']
try:
sys.ps1
except AttributeError:
sys.ps1 = '>>> '
try:
sys.ps2
except AttributeError:
sys.ps2 = '... '
class SocketCo... | {
"repo_name": "wangyou/XX-Net",
"path": "code/default/python27/1.0/lib/linux/gevent/backdoor.py",
"copies": "10",
"size": "3181",
"license": "bsd-2-clause",
"hash": 287806789964393730,
"line_mean": 29.2952380952,
"line_max": 83,
"alpha_frac": 0.6633134235,
"autogenerated": false,
"ratio": 3.85108... |
__author__ = 'bobwhite'
"""
This example shows how to create a mGui window with menus and submenus using the new mGui 2.1 submenu syntax
"""
from mGui import gui
def food_selected(*_, **kwargs):
print "order " + kwargs['sender'].label
def pizza_selected(*_, **kwargs):
pizza = kwargs['sender'].parent
... | {
"repo_name": "theodox/mGui",
"path": "mGui/examples/menus.py",
"copies": "1",
"size": "2203",
"license": "mit",
"hash": -5057149350408243000,
"line_mean": 35.7166666667,
"line_max": 108,
"alpha_frac": 0.6382206083,
"autogenerated": false,
"ratio": 3.8246527777777777,
"config_test": false,
"h... |
__author__ = 'Bohdan Mushkevych'
from bson import ObjectId
from threading import RLock
from db.model.raw_data import *
from db.model.site_statistics import SiteStatistics
from synergy.db.manager import ds_manager
from synergy.system.decorator import thread_safe
class SiteDao(object):
""" Thread-safe Data Access... | {
"repo_name": "eggsandbeer/scheduler",
"path": "db/dao/site_dao.py",
"copies": "1",
"size": "1526",
"license": "bsd-3-clause",
"hash": -9145484630527294000,
"line_mean": 36.2195121951,
"line_max": 83,
"alpha_frac": 0.6553079948,
"autogenerated": false,
"ratio": 4.037037037037037,
"config_test":... |
__author__ = 'Bohdan Mushkevych'
from bson import ObjectId
from threading import RLock
from synergy.db.manager import ds_manager
from synergy.system.decorator import thread_safe
class BaseDao(object):
""" Thread-safe base Data Access Object """
def __init__(self, logger, model_class, primary_key, collectio... | {
"repo_name": "eggsandbeer/scheduler",
"path": "synergy/db/dao/base_dao.py",
"copies": "1",
"size": "2636",
"license": "bsd-3-clause",
"hash": -6725759968638984000,
"line_mean": 34.6216216216,
"line_max": 103,
"alpha_frac": 0.6297420334,
"autogenerated": false,
"ratio": 3.952023988005997,
"conf... |
__author__ = 'Bohdan Mushkevych'
from collections import OrderedDict, defaultdict
from threading import RLock
from werkzeug.utils import cached_property
from synergy.db.dao import job_dao
from synergy.db.dao.job_dao import JobDao
from synergy.db.dao import unit_of_work_dao
from synergy.db.dao.unit_of_work_dao import... | {
"repo_name": "mushkevych/scheduler",
"path": "synergy/mx/dashboard_handler.py",
"copies": "1",
"size": "7454",
"license": "bsd-3-clause",
"hash": -7140851055054475000,
"line_mean": 48.3642384106,
"line_max": 119,
"alpha_frac": 0.635229407,
"autogenerated": false,
"ratio": 4.033549783549783,
"c... |
__author__ = 'Bohdan Mushkevych'
from collections import OrderedDict
from threading import RLock
from werkzeug.utils import cached_property
from synergy.db.dao import job_dao
from synergy.db.dao.job_dao import JobDao
from synergy.db.dao import unit_of_work_dao
from synergy.db.dao.unit_of_work_dao import UnitOfWorkDa... | {
"repo_name": "eggsandbeer/scheduler",
"path": "synergy/mx/dashboard_handler.py",
"copies": "1",
"size": "4960",
"license": "bsd-3-clause",
"hash": -6348352276310111000,
"line_mean": 40.3333333333,
"line_max": 110,
"alpha_frac": 0.6796370968,
"autogenerated": false,
"ratio": 3.6336996336996337,
... |
__author__ = 'Bohdan Mushkevych'
from collections import OrderedDict
from synergy.conf import context
from synergy.db.model.managed_process_entry import ManagedProcessEntry
from synergy.system.time_qualifier import *
from synergy.system.time_helper import cast_to_time_qualifier
from synergy.system.timeperiod_dict imp... | {
"repo_name": "mushkevych/scheduler",
"path": "synergy/scheduler/process_hierarchy.py",
"copies": "1",
"size": "4220",
"license": "bsd-3-clause",
"hash": -207520052219369060,
"line_mean": 38.4392523364,
"line_max": 118,
"alpha_frac": 0.6630331754,
"autogenerated": false,
"ratio": 4.32377049180327... |
__author__ = 'Bohdan Mushkevych'
from constants import COLLECTION_SITE_DAILY
from db.model.site_statistics import SiteStatistics
from db.dao.site_dao import SiteDao
from synergy.conf import settings
from workers.abstract_vertical_worker import AbstractVerticalWorker
from synergy.system import time_helper
from synergy.... | {
"repo_name": "eggsandbeer/scheduler",
"path": "workers/alert_daily_worker.py",
"copies": "1",
"size": "2702",
"license": "bsd-3-clause",
"hash": -4291066537242268700,
"line_mean": 44.0333333333,
"line_max": 116,
"alpha_frac": 0.6617320503,
"autogenerated": false,
"ratio": 3.541284403669725,
"c... |
__author__ = 'Bohdan Mushkevych'
from constants import COLLECTION_SITE_DAILY
from db.model.site_statistics import SiteStatistics
from db.model.alert import Alert, DOMAIN_NAME, TIMEPERIOD
from db.dao.site_dao import SiteDao
from workers.abstract_mongo_worker import AbstractMongoWorker
from synergy.system import time_he... | {
"repo_name": "mushkevych/scheduler",
"path": "workers/alert_daily_worker.py",
"copies": "1",
"size": "2760",
"license": "bsd-3-clause",
"hash": -625608595574918500,
"line_mean": 44.2459016393,
"line_max": 116,
"alpha_frac": 0.6565217391,
"autogenerated": false,
"ratio": 3.5114503816793894,
"co... |
__author__ = 'Bohdan Mushkevych'
from constants import COLLECTION_SITE_YEARLY
from tests import base_fixtures
from synergy.system.time_qualifier import QUALIFIER_YEARLY
# pylint: disable=C0301
EXPECTED_SITE_YEARLY_00 = {
'stat': {'screen_resolution': {u'(320, 240)': 9, u'(640, 480)': 15, u'(1024, 960)': 21, u'(1280,... | {
"repo_name": "eggsandbeer/scheduler",
"path": "tests/yearly_fixtures.py",
"copies": "1",
"size": "20835",
"license": "bsd-3-clause",
"hash": -1394630649565285000,
"line_mean": 81.6825396825,
"line_max": 117,
"alpha_frac": 0.5444204464,
"autogenerated": false,
"ratio": 2.3420638489208634,
"conf... |
__author__ = 'Bohdan Mushkevych'
from constants import *
from settings import ENVIRONMENT
from synergy.system.time_qualifier import *
from synergy.scheduler.scheduler_constants import *
from synergy.workers.worker_constants import *
from synergy.db.model.queue_context_entry import queue_context_entry
from synergy.db.m... | {
"repo_name": "eggsandbeer/scheduler",
"path": "context.py",
"copies": "1",
"size": "6679",
"license": "bsd-3-clause",
"hash": -465940350792028000,
"line_mean": 37.1657142857,
"line_max": 112,
"alpha_frac": 0.6779458003,
"autogenerated": false,
"ratio": 3.543236074270557,
"config_test": false,
... |
__author__ = 'Bohdan Mushkevych'
from datetime import datetime
from logging import ERROR, WARNING, INFO
from synergy.conf import context
from synergy.db.dao.freerun_process_dao import FreerunProcessDao
from synergy.db.dao.unit_of_work_dao import UnitOfWorkDao
from synergy.db.error import DuplicateKeyError
from synerg... | {
"repo_name": "mushkevych/scheduler",
"path": "synergy/scheduler/state_machine_freerun.py",
"copies": "1",
"size": "8423",
"license": "bsd-3-clause",
"hash": -5388459291552159000,
"line_mean": 44.777173913,
"line_max": 120,
"alpha_frac": 0.660216075,
"autogenerated": false,
"ratio": 3.46198109330... |
__author__ = 'Bohdan Mushkevych'
from datetime import datetime
from logging import ERROR, WARNING, INFO
from synergy.conf import context
from synergy.db.error import DuplicateKeyError
from synergy.db.model import unit_of_work
from synergy.db.model.unit_of_work import UnitOfWork
from synergy.db.model.synergy_mq_transm... | {
"repo_name": "eggsandbeer/scheduler",
"path": "synergy/scheduler/state_machine_freerun.py",
"copies": "1",
"size": "6635",
"license": "bsd-3-clause",
"hash": -1499173110432158000,
"line_mean": 43.5302013423,
"line_max": 119,
"alpha_frac": 0.6532027129,
"autogenerated": false,
"ratio": 3.46113719... |
__author__ = 'Bohdan Mushkevych'
from datetime import datetime
from logging import ERROR, WARNING, INFO
from synergy.db.model import job
from synergy.db.model.job import Job
from synergy.db.model.unit_of_work import UnitOfWork
from synergy.db.manager import ds_manager
from synergy.conf import context
from synergy.sys... | {
"repo_name": "eggsandbeer/scheduler",
"path": "synergy/scheduler/state_machine_continuous.py",
"copies": "1",
"size": "8717",
"license": "bsd-3-clause",
"hash": 6394817306943148000,
"line_mean": 57.8986486486,
"line_max": 116,
"alpha_frac": 0.6425375703,
"autogenerated": false,
"ratio": 3.933664... |
__author__ = 'Bohdan Mushkevych'
from datetime import datetime
from logging import ERROR, WARNING, INFO
from synergy.db.model import job
from synergy.scheduler.scheduler_constants import STATE_MACHINE_DISCRETE
from synergy.scheduler.abstract_state_machine import AbstractStateMachine
from synergy.system import time_he... | {
"repo_name": "eggsandbeer/scheduler",
"path": "synergy/scheduler/state_machine_dicrete.py",
"copies": "1",
"size": "5655",
"license": "bsd-3-clause",
"hash": 8304448557221240000,
"line_mean": 53.9029126214,
"line_max": 111,
"alpha_frac": 0.6183908046,
"autogenerated": false,
"ratio": 4.042172980... |
__author__ = 'Bohdan Mushkevych'
from datetime import datetime
from logging import INFO, WARNING, ERROR
from synergy.db.model import job
from synergy.db.model.job import Job
from synergy.db.error import DuplicateKeyError
from synergy.db.dao.unit_of_work_dao import UnitOfWorkDao
from synergy.db.dao.job_dao import JobD... | {
"repo_name": "eggsandbeer/scheduler",
"path": "synergy/scheduler/abstract_state_machine.py",
"copies": "1",
"size": "9642",
"license": "bsd-3-clause",
"hash": 3454144652146593300,
"line_mean": 46.9701492537,
"line_max": 119,
"alpha_frac": 0.6610661688,
"autogenerated": false,
"ratio": 3.81257413... |
__author__ = 'Bohdan Mushkevych'
from datetime import datetime
from threading import RLock
from synergy.db.dao.unit_of_work_dao import UnitOfWorkDao
from synergy.db.dao.job_dao import JobDao
from synergy.db.model.job import Job
from synergy.db.model import job, unit_of_work
from synergy.conf import context
from syner... | {
"repo_name": "eggsandbeer/scheduler",
"path": "synergy/scheduler/timetable.py",
"copies": "1",
"size": "14130",
"license": "bsd-3-clause",
"hash": -5386719221785159000,
"line_mean": 44.1437699681,
"line_max": 117,
"alpha_frac": 0.6246992215,
"autogenerated": false,
"ratio": 3.782119914346895,
... |
__author__ = 'Bohdan Mushkevych'
from datetime import datetime
from flow.core.execution_context import ContextDriven, get_step_logger, valid_context
from synergy.system.log_recording_handler import LogRecordingHandler
from flow.db.model.step import Step, STATE_EMBRYO, STATE_INVALID, STATE_PROCESSED, STATE_IN_PROGRES... | {
"repo_name": "mushkevych/synergy_flow",
"path": "flow/core/flow_graph_node.py",
"copies": "1",
"size": "3064",
"license": "bsd-3-clause",
"hash": -1284216443896132900,
"line_mean": 35.4761904762,
"line_max": 100,
"alpha_frac": 0.6475195822,
"autogenerated": false,
"ratio": 3.858942065491184,
"... |
__author__ = 'Bohdan Mushkevych'
from datetime import datetime
from synergy.db.model import unit_of_work
from synergy.db.model.mq_transmission import MqTransmission
from synergy.db.dao.unit_of_work_dao import UnitOfWorkDao
from synergy.system.mq_transmitter import MqTransmitter
from synergy.system.performance_tracker... | {
"repo_name": "mushkevych/scheduler",
"path": "synergy/workers/abstract_uow_aware_worker.py",
"copies": "1",
"size": "4991",
"license": "bsd-3-clause",
"hash": -4788686773611804000,
"line_mean": 43.963963964,
"line_max": 118,
"alpha_frac": 0.6203165698,
"autogenerated": false,
"ratio": 3.83627978... |
__author__ = 'Bohdan Mushkevych'
from datetime import datetime
from synergy.db.model import unit_of_work
from synergy.db.model.synergy_mq_transmission import SynergyMqTransmission
from synergy.db.dao.unit_of_work_dao import UnitOfWorkDao
from synergy.mq.flopsy import PublishersPool
from synergy.workers.abstract_mq_wo... | {
"repo_name": "eggsandbeer/scheduler",
"path": "synergy/workers/abstract_uow_aware_worker.py",
"copies": "1",
"size": "4651",
"license": "bsd-3-clause",
"hash": 4145579758013639000,
"line_mean": 44.5980392157,
"line_max": 116,
"alpha_frac": 0.6200817029,
"autogenerated": false,
"ratio": 3.8823038... |
__author__ = 'Bohdan Mushkevych'
from datetime import datetime
from synergy.scheduler.process_hierarchy import ProcessHierarchy
from synergy.scheduler.tree_node import TreeNode, RootNode, AbstractTreeNode
from synergy.conf import settings
from synergy.system import time_helper
from synergy.system.time_helper import c... | {
"repo_name": "mushkevych/scheduler",
"path": "synergy/scheduler/tree.py",
"copies": "1",
"size": "10217",
"license": "bsd-3-clause",
"hash": 8327217932241422000,
"line_mean": 45.2307692308,
"line_max": 119,
"alpha_frac": 0.6581188216,
"autogenerated": false,
"ratio": 4.27668480535789,
"config_... |
__author__ = 'Bohdan Mushkevych'
from datetime import datetime, timedelta
from synergy.system.repeat_timer import RepeatTimer
TRIGGER_INTERVAL = 30 # half a minute
EVERY_DAY = '*' # marks every day as suitable to trigger the event
TIME_OF_DAY_FORMAT = "%H:%M"
TRIGGER_PREAMBLE_AT = 'at '
TRIGGER_PREAMBLE_EVERY... | {
"repo_name": "eggsandbeer/scheduler",
"path": "synergy/system/event_clock.py",
"copies": "1",
"size": "7018",
"license": "bsd-3-clause",
"hash": 89917818426944600,
"line_mean": 37.349726776,
"line_max": 114,
"alpha_frac": 0.6208321459,
"autogenerated": false,
"ratio": 3.809989142236699,
"confi... |
__author__ = 'Bohdan Mushkevych'
from datetime import datetime, timedelta
from threading import Lock
from amqp import AMQPError
from synergy.conf import context
from synergy.mq.flopsy import PublishersPool
from synergy.mx.synergy_mx import MX
from synergy.db.manager import db_manager
from synergy.db.model.synergy_mq... | {
"repo_name": "eggsandbeer/scheduler",
"path": "synergy/scheduler/synergy_scheduler.py",
"copies": "1",
"size": "11280",
"license": "bsd-3-clause",
"hash": -6493068878860936000,
"line_mean": 45.8049792531,
"line_max": 112,
"alpha_frac": 0.6340425532,
"autogenerated": false,
"ratio": 4.16851441241... |
__author__ = 'Bohdan Mushkevych'
from datetime import datetime, timedelta
from threading import Lock
from synergy.conf import context
from synergy.mx.synergy_mx import MX
from synergy.db.manager import db_manager
from synergy.db.model.managed_process_entry import ManagedProcessEntry
from synergy.db.model.freerun_proc... | {
"repo_name": "mushkevych/scheduler",
"path": "synergy/scheduler/synergy_scheduler.py",
"copies": "1",
"size": "9886",
"license": "bsd-3-clause",
"hash": -5053138936638035000,
"line_mean": 45.1962616822,
"line_max": 113,
"alpha_frac": 0.6369613595,
"autogenerated": false,
"ratio": 4.1854360711261... |
__author__ = 'Bohdan Mushkevych'
from datetime import datetime, timedelta
from synergy.scheduler.process_hierarchy import ProcessHierarchy
from synergy.scheduler.tree_node import TreeNode
from synergy.conf import settings
from synergy.system import time_helper
from synergy.system.time_helper import cast_to_time_quali... | {
"repo_name": "eggsandbeer/scheduler",
"path": "synergy/scheduler/tree.py",
"copies": "1",
"size": "11943",
"license": "bsd-3-clause",
"hash": -3035589669388636700,
"line_mean": 44.4106463878,
"line_max": 119,
"alpha_frac": 0.6562002847,
"autogenerated": false,
"ratio": 4.266881028938907,
"conf... |
__author__ = 'Bohdan Mushkevych'
from datetime import datetime, timedelta
from synergy.system.repeat_timer import RepeatTimer
TIME_OF_DAY_FORMAT = "%H:%M"
EVERY_DAY = '*' # marks every day as suitable to trigger the event
TRIGGER_INTERVAL = 30 # half a minute
class EventTime(object):
def __init__(self,... | {
"repo_name": "mushkevych/scheduler",
"path": "synergy/system/event_clock.py",
"copies": "1",
"size": "5191",
"license": "bsd-3-clause",
"hash": -5935195343356679000,
"line_mean": 36.0785714286,
"line_max": 114,
"alpha_frac": 0.6018108264,
"autogenerated": false,
"ratio": 3.839497041420118,
"co... |
__author__ = 'Bohdan Mushkevych'
from db.model.client_statistics import ClientStatistics
from synergy.system.utils import copy_and_sum_families
from synergy.system import time_helper
from workers.client_daily_aggregator import ClientDailyAggregator
class ClientMonthlyAggregator(ClientDailyAggregator):
""" class ... | {
"repo_name": "eggsandbeer/scheduler",
"path": "workers/client_monthly_aggregator.py",
"copies": "1",
"size": "1844",
"license": "bsd-3-clause",
"hash": 6276059106931069000,
"line_mean": 39.9777777778,
"line_max": 108,
"alpha_frac": 0.7071583514,
"autogenerated": false,
"ratio": 3.566731141199226... |
__author__ = 'Bohdan Mushkevych'
from db.model.raw_data import DOMAIN_NAME
from db.model.site_statistics import SiteStatistics
from db.model.client_statistics import ClientStatistics
from synergy.system.utils import copy_and_sum_families
from synergy.conf import settings
from synergy.system import time_helper
from syn... | {
"repo_name": "eggsandbeer/scheduler",
"path": "workers/client_daily_aggregator.py",
"copies": "1",
"size": "2625",
"license": "bsd-3-clause",
"hash": -706293630090908700,
"line_mean": 41.3387096774,
"line_max": 100,
"alpha_frac": 0.675047619,
"autogenerated": false,
"ratio": 3.723404255319149,
... |
__author__ = 'Bohdan Mushkevych'
from db.model.single_session import SingleSession, DOMAIN_NAME, TIMEPERIOD
from db.model.site_statistics import SiteStatistics
from synergy.system.utils import increment_family_property
from workers.abstract_mongo_worker import AbstractMongoWorker
class SiteHourlyAggregator(AbstractM... | {
"repo_name": "mushkevych/scheduler",
"path": "workers/site_hourly_aggregator.py",
"copies": "1",
"size": "2284",
"license": "bsd-3-clause",
"hash": -2254821314411407000,
"line_mean": 42.9230769231,
"line_max": 111,
"alpha_frac": 0.715849387,
"autogenerated": false,
"ratio": 3.7198697068403908,
... |
__author__ = 'Bohdan Mushkevych'
from db.model.single_session import SingleSession
from db.model.site_statistics import SiteStatistics
from synergy.system.utils import increment_family_property
from synergy.system import time_helper
from synergy.conf import settings
from workers.abstract_vertical_worker import Abstrac... | {
"repo_name": "eggsandbeer/scheduler",
"path": "workers/site_hourly_aggregator.py",
"copies": "1",
"size": "2326",
"license": "bsd-3-clause",
"hash": -2648299537357980000,
"line_mean": 42.0740740741,
"line_max": 115,
"alpha_frac": 0.7252794497,
"autogenerated": false,
"ratio": 3.7156549520766773,... |
__author__ = 'Bohdan Mushkevych'
from db.model.site_statistics import SiteStatistics, DOMAIN_NAME, TIMEPERIOD
from synergy.system.utils import copy_and_sum_families
from synergy.system import time_helper
from workers.abstract_mongo_worker import AbstractMongoWorker
class SiteDailyAggregator(AbstractMongoWorker):
... | {
"repo_name": "mushkevych/scheduler",
"path": "workers/site_daily_aggregator.py",
"copies": "1",
"size": "1999",
"license": "bsd-3-clause",
"hash": 7854702936228471000,
"line_mean": 39.7959183673,
"line_max": 99,
"alpha_frac": 0.7013506753,
"autogenerated": false,
"ratio": 3.452504317789292,
"c... |
__author__ = 'Bohdan Mushkevych'
from db.model.site_statistics import SiteStatistics
from synergy.system.utils import copy_and_sum_families
from synergy.conf import settings
from synergy.system import time_helper
from workers.abstract_vertical_worker import AbstractVerticalWorker
class SiteDailyAggregator(AbstractVe... | {
"repo_name": "eggsandbeer/scheduler",
"path": "workers/site_daily_aggregator.py",
"copies": "1",
"size": "1977",
"license": "bsd-3-clause",
"hash": 6794603272468982000,
"line_mean": 39.3469387755,
"line_max": 90,
"alpha_frac": 0.708143652,
"autogenerated": false,
"ratio": 3.4806338028169015,
"... |
__author__ = 'Bohdan Mushkevych'
from flow.core.abstract_action import AbstractAction
class MkdirAction(AbstractAction):
""" Filesystem action: make the target directory and all folders along the path if needed """
def __init__(self, uri_path, bucket_name=None):
super(MkdirAction, self).__init__('mkd... | {
"repo_name": "mushkevych/synergy_flow",
"path": "flow/core/filesystem_actions.py",
"copies": "1",
"size": "4448",
"license": "bsd-3-clause",
"hash": -5862026090865802000,
"line_mean": 43.9292929293,
"line_max": 120,
"alpha_frac": 0.6785071942,
"autogenerated": false,
"ratio": 3.827882960413081,
... |
__author__ = 'Bohdan Mushkevych'
from flow.core.abstract_cluster import AbstractCluster
from flow.core.execution_context import ContextDriven, get_action_logger, valid_context
class AbstractAction(ContextDriven):
""" abstraction for action
API sequence:
1. *set_context*
2. *do*
3.... | {
"repo_name": "mushkevych/synergy_flow",
"path": "flow/core/abstract_action.py",
"copies": "1",
"size": "1897",
"license": "bsd-3-clause",
"hash": -4694522191198998000,
"line_mean": 35.4807692308,
"line_max": 109,
"alpha_frac": 0.6299420137,
"autogenerated": false,
"ratio": 3.911340206185567,
"... |
__author__ = 'Bohdan Mushkevych'
from flow.core.execution_context import ExecutionContext, get_cluster_logger
class ClusterError(Exception):
pass
class AbstractCluster(object):
""" abstraction for action execution environment
API sequence is to launch the cluster, perform one or more steps/commands... | {
"repo_name": "mushkevych/synergy_flow",
"path": "flow/core/abstract_cluster.py",
"copies": "1",
"size": "1187",
"license": "bsd-3-clause",
"hash": 5495472388559978000,
"line_mean": 27.2619047619,
"line_max": 99,
"alpha_frac": 0.6368997473,
"autogenerated": false,
"ratio": 4.254480286738351,
"c... |
__author__ = 'Bohdan Mushkevych'
from http import HTTPStatus
import json
from werkzeug.wrappers import Response
from werkzeug.utils import redirect
from synergy.mx.gc_action_handler import GcActionHandler
from synergy.mx.freerun_action_handler import FreerunActionHandler
from synergy.mx.managed_action_handler import... | {
"repo_name": "mushkevych/scheduler",
"path": "synergy/mx/views.py",
"copies": "1",
"size": "9947",
"license": "bsd-3-clause",
"hash": -705303144000122600,
"line_mean": 33.4186851211,
"line_max": 102,
"alpha_frac": 0.7381119936,
"autogenerated": false,
"ratio": 3.652956298200514,
"config_test":... |
__author__ = 'Bohdan Mushkevych'
from logging import ERROR, INFO
from synergy.db.model import job
from synergy.db.manager import ds_manager
from synergy.conf import context
from synergy.system.decorator import with_reconnect
from synergy.system import time_helper
from synergy.scheduler.scheduler_constants import STAT... | {
"repo_name": "mushkevych/scheduler",
"path": "synergy/scheduler/state_machine_recomputing.py",
"copies": "1",
"size": "6626",
"license": "bsd-3-clause",
"hash": -6055053112663943000,
"line_mean": 57.6371681416,
"line_max": 114,
"alpha_frac": 0.6817084214,
"autogenerated": false,
"ratio": 3.76049... |
__author__ = 'Bohdan Mushkevych'
from logging import ERROR, INFO
from synergy.db.model import job
from synergy.scheduler.scheduler_constants import STATE_MACHINE_DISCRETE
from synergy.scheduler.abstract_state_machine import AbstractStateMachine
from synergy.system import time_helper
from synergy.conf import context
... | {
"repo_name": "mushkevych/scheduler",
"path": "synergy/scheduler/state_machine_discrete.py",
"copies": "1",
"size": "6216",
"license": "bsd-3-clause",
"hash": 7253418096692521000,
"line_mean": 52.1282051282,
"line_max": 115,
"alpha_frac": 0.6549227799,
"autogenerated": false,
"ratio": 3.731092436... |
__author__ = 'Bohdan Mushkevych'
from logging import ERROR, INFO
from synergy.db.model import job
from synergy.scheduler.scheduler_constants import STATE_MACHINE_SIMPLE_DISCRETE
from synergy.scheduler.state_machine_dicrete import StateMachineDiscrete
from synergy.system import time_helper
from synergy.conf import con... | {
"repo_name": "eggsandbeer/scheduler",
"path": "synergy/scheduler/state_machine_simple_dicrete.py",
"copies": "1",
"size": "5844",
"license": "bsd-3-clause",
"hash": 6921274129728505000,
"line_mean": 54.6571428571,
"line_max": 118,
"alpha_frac": 0.6461327858,
"autogenerated": false,
"ratio": 3.95... |
__author__ = 'Bohdan Mushkevych'
from logging import ERROR
from synergy.db.model import job
from synergy.scheduler.scheduler_constants import STATE_MACHINE_CONTINUOUS
from synergy.scheduler.abstract_state_machine import AbstractStateMachine
from synergy.system import time_helper
from synergy.conf import context
cla... | {
"repo_name": "mushkevych/scheduler",
"path": "synergy/scheduler/state_machine_continuous.py",
"copies": "1",
"size": "3754",
"license": "bsd-3-clause",
"hash": -3075468334046331000,
"line_mean": 44.7804878049,
"line_max": 107,
"alpha_frac": 0.6574320725,
"autogenerated": false,
"ratio": 3.906347... |
__author__ = 'Bohdan Mushkevych'
from logging import INFO
from synergy.db.model import job
from synergy.system import time_helper
from synergy.system.immutable_dict import ImmutableDict
from synergy.conf import context
class DependentOnSummary(object):
""" This structure is compiled to represent a composite sta... | {
"repo_name": "mushkevych/scheduler",
"path": "synergy/scheduler/tree_node.py",
"copies": "1",
"size": "9847",
"license": "bsd-3-clause",
"hash": 5602275472174949000,
"line_mean": 41.4439655172,
"line_max": 118,
"alpha_frac": 0.6525845435,
"autogenerated": false,
"ratio": 4.065648224607762,
"co... |
__author__ = 'Bohdan Mushkevych'
from odm.document import BaseDocument
from odm.fields import StringField, DictField, ListField
from synergy.scheduler.scheduler_constants import EXCHANGE_UTILS
class DaemonProcessEntry(BaseDocument):
""" Non-persistent model. This class presents Process Context Entry record """
... | {
"repo_name": "mushkevych/scheduler",
"path": "synergy/db/model/daemon_process_entry.py",
"copies": "1",
"size": "2032",
"license": "bsd-3-clause",
"hash": 6181570959778046000,
"line_mean": 34.649122807,
"line_max": 110,
"alpha_frac": 0.6146653543,
"autogenerated": false,
"ratio": 4.3605150214592... |
__author__ = 'Bohdan Mushkevych'
from odm.document import BaseDocument
from odm.fields import StringField, IntegerField, BooleanField, DateTimeField
TIMEPERIOD = 'timeperiod'
TIMESTAMP = 'timestamp'
CREATION_TIME = 'creation_time'
SESSION_ID = 'session_id'
IP = 'ip'
OS = 'os'
BROWSER = 'browser'
USER_ID = 'user_id'
L... | {
"repo_name": "eggsandbeer/scheduler",
"path": "db/model/raw_data.py",
"copies": "1",
"size": "2161",
"license": "bsd-3-clause",
"hash": -5514135305181858000,
"line_mean": 26.0125,
"line_max": 107,
"alpha_frac": 0.6992133272,
"autogenerated": false,
"ratio": 2.9765840220385673,
"config_test": f... |
__author__ = 'Bohdan Mushkevych'
from odm.document import BaseDocument
from odm.fields import StringField, ListField
class TimetableTreeEntry(BaseDocument):
""" Non-persistent model. Class presents single process tree (an atomic entry for the Timetable) """
tree_name = StringField()
dependent_on = ListF... | {
"repo_name": "mushkevych/scheduler",
"path": "synergy/db/model/timetable_tree_entry.py",
"copies": "1",
"size": "1261",
"license": "bsd-3-clause",
"hash": -5698079545335060000,
"line_mean": 35.0285714286,
"line_max": 104,
"alpha_frac": 0.5804916733,
"autogenerated": false,
"ratio": 4.60218978102... |
__author__ = 'Bohdan Mushkevych'
from odm.document import BaseDocument
from odm.fields import StringField, ListField
TREE_NAME = 'tree_name'
DEPENDENT_ON = 'dependent_on'
ENCLOSED_PROCESSES = 'enclosed_processes'
MX_PAGE = 'mx_page'
MX_NAME = 'mx_name'
class TimetableTreeEntry(BaseDocument):
""" Non-persistent ... | {
"repo_name": "eggsandbeer/scheduler",
"path": "synergy/db/model/timetable_tree_entry.py",
"copies": "1",
"size": "1527",
"license": "bsd-3-clause",
"hash": 5522360935908390000,
"line_mean": 32.9333333333,
"line_max": 104,
"alpha_frac": 0.6018336608,
"autogenerated": false,
"ratio": 4.06117021276... |
__author__ = 'Bohdan Mushkevych'
from odm.document import BaseDocument
from odm.fields import StringField
MQ_QUEUE = 'mq_queue'
MQ_EXCHANGE = 'mq_exchange'
MQ_ROUTING_KEY = 'mq_routing_key'
class QueueContextEntry(BaseDocument):
""" Non-persistent model. This class presents Queue Context Entry record """
m... | {
"repo_name": "eggsandbeer/scheduler",
"path": "synergy/db/model/queue_context_entry.py",
"copies": "1",
"size": "1049",
"license": "bsd-3-clause",
"hash": -8475873796806015000,
"line_mean": 26.6052631579,
"line_max": 80,
"alpha_frac": 0.6081982841,
"autogenerated": false,
"ratio": 3.914179104477... |
__author__ = 'Bohdan Mushkevych'
from odm.document import BaseDocument
from odm.fields import StringField, ObjectIdField, DateTimeField
# Step record created in the DB
# Next valid states: STATE_IN_PROGRESS
STATE_EMBRYO = 'state_embryo'
# Step execution started by a worker
STATE_IN_PROGRESS = 'state_in_progress'
#... | {
"repo_name": "mushkevych/synergy_flow",
"path": "flow/db/model/step.py",
"copies": "1",
"size": "1800",
"license": "bsd-3-clause",
"hash": -7769299203127902000,
"line_mean": 27.5714285714,
"line_max": 80,
"alpha_frac": 0.7066666667,
"autogenerated": false,
"ratio": 3.592814371257485,
"config_t... |
__author__ = 'Bohdan Mushkevych'
from odm.document import BaseDocument
from odm.fields import StringField, ObjectIdField, DateTimeField
RUN_MODE_NOMINAL = 'run_mode_nominal'
RUN_MODE_RECOVERY = 'run_mode_recovery'
# Flow can get into STATE_INVALID if:
# a. related Job was marked for reprocessing via MX
# b. have fai... | {
"repo_name": "mushkevych/synergy_flow",
"path": "flow/db/model/flow.py",
"copies": "1",
"size": "1967",
"license": "bsd-3-clause",
"hash": -7517891078223204000,
"line_mean": 32.3389830508,
"line_max": 110,
"alpha_frac": 0.7269954245,
"autogenerated": false,
"ratio": 3.4691358024691357,
"config... |
__author__ = 'Bohdan Mushkevych'
from odm.document import BaseDocument
from odm.fields import StringField, ObjectIdField, IntegerField, DictField, DateTimeField
from synergy.scheduler.scheduler_constants import TYPE_FREERUN, TYPE_MANAGED
TIMEPERIOD = 'timeperiod'
START_TIMEPERIOD = 'start_timeperiod' # lower boundar... | {
"repo_name": "eggsandbeer/scheduler",
"path": "synergy/db/model/unit_of_work.py",
"copies": "1",
"size": "4693",
"license": "bsd-3-clause",
"hash": -7704751275372359000,
"line_mean": 40.1666666667,
"line_max": 114,
"alpha_frac": 0.7048796079,
"autogenerated": false,
"ratio": 3.663544106167057,
... |
__author__ = 'Bohdan Mushkevych'
from odm.document import BaseDocument
from odm.fields import StringField, ObjectIdField, IntegerField, DictField, DateTimeField
TYPE_MANAGED = 'type_managed' # identifies UOW created by Abstract State Machine child for Managed Process
TYPE_FREERUN = 'type_freerun' ... | {
"repo_name": "mushkevych/scheduler",
"path": "synergy/db/model/unit_of_work.py",
"copies": "1",
"size": "4120",
"license": "bsd-3-clause",
"hash": -3814641550784682000,
"line_mean": 37.1481481481,
"line_max": 120,
"alpha_frac": 0.7065533981,
"autogenerated": false,
"ratio": 3.7694419030192132,
... |
__author__ = 'Bohdan Mushkevych'
from odm.document import BaseDocument
from odm.fields import StringField, ObjectIdField, ListField, IntegerField
MAX_NUMBER_OF_LOG_ENTRIES = 32
TIMEPERIOD = 'timeperiod'
PROCESS_NAME = 'process_name'
START_OBJ_ID = 'start_obj_id'
END_OBJ_ID = 'end_obj_id'
STATE = 'state'
RELATED_UNIT_... | {
"repo_name": "eggsandbeer/scheduler",
"path": "synergy/db/model/job.py",
"copies": "1",
"size": "3409",
"license": "bsd-3-clause",
"hash": -6139948443617114000,
"line_mean": 33.4343434343,
"line_max": 116,
"alpha_frac": 0.7095922558,
"autogenerated": false,
"ratio": 3.5180598555211557,
"config... |
__author__ = 'Bohdan Mushkevych'
from odm.document import BaseDocument
from odm.fields import StringField, ObjectIdField, ListField, IntegerField
# number of job events to be stored in Job.event_log, such as emission of the UOW
EVENT_LOG_MAX_SIZE = 128
# given Job was _not_ processed by aggregator because of multipl... | {
"repo_name": "mushkevych/scheduler",
"path": "synergy/db/model/job.py",
"copies": "1",
"size": "2896",
"license": "bsd-3-clause",
"hash": -7586497326456092000,
"line_mean": 31.9090909091,
"line_max": 116,
"alpha_frac": 0.716160221,
"autogenerated": false,
"ratio": 3.6751269035532994,
"config_t... |
__author__ = 'Bohdan Mushkevych'
from odm.document import BaseDocument
from odm.fields import StringField, ObjectIdField
class MqTransmission(BaseDocument):
""" Non-persistent model. Instance of this class presents either:
- single request from Synergy Scheduler to any worker
- response/report from the... | {
"repo_name": "mushkevych/scheduler",
"path": "synergy/db/model/mq_transmission.py",
"copies": "1",
"size": "1083",
"license": "bsd-3-clause",
"hash": -7772328595199005000,
"line_mean": 35.1,
"line_max": 92,
"alpha_frac": 0.6528162512,
"autogenerated": false,
"ratio": 3.8268551236749118,
"confi... |
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