Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/util/__init__.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """ |
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2 Utility functions used systemwide. |
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3 |
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4 """ |
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5 |
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6 import binascii |
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7 import collections |
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8 import errno |
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9 import importlib |
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10 import json |
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11 import os |
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12 import random |
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13 import re |
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14 import shutil |
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15 import smtplib |
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16 import stat |
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17 import string |
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18 import sys |
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19 import tempfile |
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20 import textwrap |
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21 import threading |
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22 import time |
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23 import unicodedata |
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24 import xml.dom.minidom |
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25 from datetime import datetime |
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26 from email.mime.multipart import MIMEMultipart |
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27 from email.mime.text import MIMEText |
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28 from functools import partial |
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29 from hashlib import md5 |
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30 from os.path import relpath |
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31 from urllib.parse import ( |
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32 urlencode, |
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33 urlparse, |
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34 urlsplit, |
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35 urlunsplit, |
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36 ) |
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37 |
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38 import requests |
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39 try: |
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40 import grp |
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41 except ImportError: |
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42 # For Pulsar on Windows (which does not use the function that uses grp) |
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43 grp = None # type: ignore |
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44 from boltons.iterutils import ( |
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45 default_enter, |
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46 remap, |
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47 ) |
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48 LXML_AVAILABLE = True |
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49 try: |
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50 from lxml import etree |
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51 except ImportError: |
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52 LXML_AVAILABLE = False |
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53 import xml.etree.ElementTree as etree # type: ignore |
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54 from requests.adapters import HTTPAdapter |
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55 from requests.packages.urllib3.util.retry import Retry |
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56 |
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57 try: |
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58 import docutils.core as docutils_core |
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59 import docutils.writers.html4css1 as docutils_html4css1 |
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60 except ImportError: |
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61 docutils_core = None |
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62 docutils_html4css1 = None |
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63 |
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64 try: |
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65 import uwsgi |
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66 except ImportError: |
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67 uwsgi = None |
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68 |
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69 from .custom_logging import get_logger |
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70 from .inflection import Inflector |
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71 from .path import safe_contains, safe_makedirs, safe_relpath # noqa: F401 |
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72 |
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73 inflector = Inflector() |
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74 |
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75 log = get_logger(__name__) |
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76 _lock = threading.RLock() |
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77 |
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78 namedtuple = collections.namedtuple |
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79 |
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80 CHUNK_SIZE = 65536 # 64k |
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81 |
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82 DATABASE_MAX_STRING_SIZE = 32768 |
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83 DATABASE_MAX_STRING_SIZE_PRETTY = '32K' |
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84 |
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85 gzip_magic = b'\x1f\x8b' |
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86 bz2_magic = b'BZh' |
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87 DEFAULT_ENCODING = os.environ.get('GALAXY_DEFAULT_ENCODING', 'utf-8') |
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88 NULL_CHAR = b'\x00' |
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89 BINARY_CHARS = [NULL_CHAR] |
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90 FILENAME_VALID_CHARS = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' |
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91 |
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92 RW_R__R__ = stat.S_IRUSR | stat.S_IWUSR | stat.S_IRGRP | stat.S_IROTH |
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93 RWXR_XR_X = stat.S_IRWXU | stat.S_IRGRP | stat.S_IXGRP | stat.S_IROTH | stat.S_IXOTH |
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94 RWXRWXRWX = stat.S_IRWXU | stat.S_IRWXG | stat.S_IRWXO |
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95 |
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96 XML = etree.XML |
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97 |
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98 defaultdict = collections.defaultdict |
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99 |
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100 |
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101 def remove_protocol_from_url(url): |
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102 """ Supplied URL may be null, if not ensure http:// or https:// |
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103 etc... is stripped off. |
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104 """ |
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105 if url is None: |
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106 return url |
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107 |
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108 # We have a URL |
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109 if url.find('://') > 0: |
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110 new_url = url.split('://')[1] |
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111 else: |
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112 new_url = url |
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113 return new_url.rstrip('/') |
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114 |
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115 |
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116 def is_binary(value): |
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117 """ |
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118 File is binary if it contains a null-byte by default (e.g. behavior of grep, etc.). |
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119 This may fail for utf-16 files, but so would ASCII encoding. |
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120 >>> is_binary( string.printable ) |
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121 False |
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122 >>> is_binary( b'\\xce\\x94' ) |
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123 False |
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124 >>> is_binary( b'\\x00' ) |
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125 True |
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126 """ |
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127 value = smart_str(value) |
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128 for binary_char in BINARY_CHARS: |
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129 if binary_char in value: |
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130 return True |
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131 return False |
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132 |
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133 |
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134 def is_uuid(value): |
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135 """ |
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136 This method returns True if value is a UUID, otherwise False. |
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137 >>> is_uuid( "123e4567-e89b-12d3-a456-426655440000" ) |
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138 True |
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139 >>> is_uuid( "0x3242340298902834" ) |
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140 False |
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141 """ |
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142 uuid_re = re.compile("[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}") |
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143 if re.match(uuid_re, str(value)): |
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144 return True |
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145 else: |
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146 return False |
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147 |
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148 |
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149 def directory_hash_id(id): |
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150 """ |
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151 |
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152 >>> directory_hash_id( 100 ) |
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153 ['000'] |
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154 >>> directory_hash_id( "90000" ) |
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155 ['090'] |
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156 >>> directory_hash_id("777777777") |
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157 ['000', '777', '777'] |
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158 >>> directory_hash_id("135ee48a-4f51-470c-ae2f-ce8bd78799e6") |
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159 ['1', '3', '5'] |
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160 """ |
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161 s = str(id) |
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162 l = len(s) |
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163 # Shortcut -- ids 0-999 go under ../000/ |
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164 if l < 4: |
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165 return ["000"] |
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166 if not is_uuid(s): |
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167 # Pad with zeros until a multiple of three |
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168 padded = ((3 - len(s) % 3) * "0") + s |
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169 # Drop the last three digits -- 1000 files per directory |
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170 padded = padded[:-3] |
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171 # Break into chunks of three |
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172 return [padded[i * 3:(i + 1) * 3] for i in range(len(padded) // 3)] |
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173 else: |
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174 # assume it is a UUID |
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175 return list(iter(s[0:3])) |
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176 |
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177 |
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178 def get_charset_from_http_headers(headers, default=None): |
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179 rval = headers.get('content-type', None) |
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180 if rval and 'charset=' in rval: |
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181 rval = rval.split('charset=')[-1].split(';')[0].strip() |
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182 if rval: |
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183 return rval |
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184 return default |
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185 |
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186 |
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187 def synchronized(func): |
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188 """This wrapper will serialize access to 'func' to a single thread. Use it as a decorator.""" |
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189 def caller(*params, **kparams): |
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190 _lock.acquire(True) # Wait |
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191 try: |
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192 return func(*params, **kparams) |
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193 finally: |
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194 _lock.release() |
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195 return caller |
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196 |
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197 |
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198 def iter_start_of_line(fh, chunk_size=None): |
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199 """ |
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200 Iterate over fh and call readline(chunk_size) |
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201 """ |
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202 yield from iter(partial(fh.readline, chunk_size), "") |
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203 |
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204 |
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205 def file_reader(fp, chunk_size=CHUNK_SIZE): |
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206 """This generator yields the open fileobject in chunks (default 64k). Closes the file at the end""" |
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207 while 1: |
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208 data = fp.read(chunk_size) |
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209 if not data: |
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210 break |
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211 yield data |
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212 fp.close() |
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213 |
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214 |
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215 def unique_id(KEY_SIZE=128): |
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216 """ |
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217 Generates an unique id |
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218 |
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219 >>> ids = [ unique_id() for i in range(1000) ] |
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220 >>> len(set(ids)) |
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221 1000 |
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222 """ |
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223 random_bits = str(random.getrandbits(KEY_SIZE)).encode("UTF-8") |
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224 return md5(random_bits).hexdigest() |
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225 |
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226 |
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227 def parse_xml(fname, strip_whitespace=True, remove_comments=True): |
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228 """Returns a parsed xml tree""" |
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229 parser = None |
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230 if remove_comments and LXML_AVAILABLE: |
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231 # If using stdlib etree comments are always removed, |
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232 # but lxml doesn't do this by default |
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233 parser = etree.XMLParser(remove_comments=remove_comments) |
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234 try: |
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235 tree = etree.parse(fname, parser=parser) |
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236 root = tree.getroot() |
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237 if strip_whitespace: |
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238 for elem in root.iter('*'): |
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239 if elem.text is not None: |
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240 elem.text = elem.text.strip() |
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241 if elem.tail is not None: |
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242 elem.tail = elem.tail.strip() |
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243 except OSError as e: |
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244 if e.errno is None and not os.path.exists(fname): |
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245 # lxml doesn't set errno |
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246 e.errno = errno.ENOENT |
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247 raise |
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248 except etree.ParseError: |
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249 log.exception("Error parsing file %s", fname) |
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250 raise |
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251 return tree |
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252 |
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253 |
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254 def parse_xml_string(xml_string, strip_whitespace=True): |
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255 try: |
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256 tree = etree.fromstring(xml_string) |
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257 except ValueError as e: |
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258 if 'strings with encoding declaration are not supported' in unicodify(e): |
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259 tree = etree.fromstring(xml_string.encode('utf-8')) |
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260 else: |
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261 raise e |
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262 if strip_whitespace: |
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263 for elem in tree.iter('*'): |
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264 if elem.text is not None: |
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265 elem.text = elem.text.strip() |
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266 if elem.tail is not None: |
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267 elem.tail = elem.tail.strip() |
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268 return tree |
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269 |
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270 |
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271 def xml_to_string(elem, pretty=False): |
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272 """ |
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273 Returns a string from an xml tree. |
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274 """ |
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275 try: |
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276 if elem is not None: |
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277 xml_str = etree.tostring(elem, encoding='unicode') |
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278 else: |
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279 xml_str = '' |
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280 except TypeError as e: |
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281 # we assume this is a comment |
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282 if hasattr(elem, 'text'): |
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283 return "<!-- %s -->\n" % elem.text |
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284 else: |
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285 raise e |
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286 if xml_str and pretty: |
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287 pretty_string = xml.dom.minidom.parseString(xml_str).toprettyxml(indent=' ') |
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288 return "\n".join(line for line in pretty_string.split('\n') if not re.match(r'^[\s\\nb\']*$', line)) |
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289 return xml_str |
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290 |
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291 |
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292 def xml_element_compare(elem1, elem2): |
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293 if not isinstance(elem1, dict): |
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294 elem1 = xml_element_to_dict(elem1) |
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295 if not isinstance(elem2, dict): |
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296 elem2 = xml_element_to_dict(elem2) |
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297 return elem1 == elem2 |
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298 |
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299 |
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300 def xml_element_list_compare(elem_list1, elem_list2): |
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301 return [xml_element_to_dict(elem) for elem in elem_list1] == [xml_element_to_dict(elem) for elem in elem_list2] |
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302 |
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303 |
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304 def xml_element_to_dict(elem): |
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305 rval = {} |
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306 if elem.attrib: |
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307 rval[elem.tag] = {} |
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308 else: |
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309 rval[elem.tag] = None |
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310 |
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311 sub_elems = list(elem) |
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312 if sub_elems: |
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313 sub_elem_dict = dict() |
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314 for sub_sub_elem_dict in map(xml_element_to_dict, sub_elems): |
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315 for key, value in sub_sub_elem_dict.items(): |
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316 if key not in sub_elem_dict: |
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317 sub_elem_dict[key] = [] |
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318 sub_elem_dict[key].append(value) |
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319 for key, value in sub_elem_dict.items(): |
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320 if len(value) == 1: |
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321 rval[elem.tag][key] = value[0] |
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322 else: |
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323 rval[elem.tag][key] = value |
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324 if elem.attrib: |
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325 for key, value in elem.attrib.items(): |
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326 rval[elem.tag]["@%s" % key] = value |
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327 |
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328 if elem.text: |
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329 text = elem.text.strip() |
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330 if text and sub_elems or elem.attrib: |
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331 rval[elem.tag]['#text'] = text |
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332 else: |
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333 rval[elem.tag] = text |
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334 |
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335 return rval |
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336 |
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337 |
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338 def pretty_print_xml(elem, level=0): |
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339 pad = ' ' |
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340 i = "\n" + level * pad |
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341 if len(elem): |
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342 if not elem.text or not elem.text.strip(): |
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343 elem.text = i + pad + pad |
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344 if not elem.tail or not elem.tail.strip(): |
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345 elem.tail = i |
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346 for e in elem: |
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347 pretty_print_xml(e, level + 1) |
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348 if not elem.tail or not elem.tail.strip(): |
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349 elem.tail = i |
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350 else: |
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351 if level and (not elem.tail or not elem.tail.strip()): |
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352 elem.tail = i + pad |
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353 return elem |
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354 |
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355 |
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356 def get_file_size(value, default=None): |
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357 try: |
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358 # try built-in |
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359 return os.path.getsize(value) |
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360 except Exception: |
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361 try: |
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362 # try built-in one name attribute |
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363 return os.path.getsize(value.name) |
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364 except Exception: |
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365 try: |
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366 # try tell() of end of object |
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367 offset = value.tell() |
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368 value.seek(0, 2) |
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369 rval = value.tell() |
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370 value.seek(offset) |
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371 return rval |
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372 except Exception: |
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373 # return default value |
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374 return default |
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375 |
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376 |
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377 def shrink_stream_by_size(value, size, join_by=b"..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False): |
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378 """ |
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379 Shrinks bytes read from `value` to `size`. |
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380 |
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381 `value` needs to implement tell/seek, so files need to be opened in binary mode. |
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382 Returns unicode text with invalid characters replaced. |
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383 """ |
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384 rval = b'' |
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385 join_by = smart_str(join_by) |
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386 if get_file_size(value) > size: |
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387 start = value.tell() |
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388 len_join_by = len(join_by) |
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389 min_size = len_join_by + 2 |
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390 if size < min_size: |
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391 if beginning_on_size_error: |
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392 rval = value.read(size) |
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393 value.seek(start) |
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394 return rval |
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395 elif end_on_size_error: |
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396 value.seek(-size, 2) |
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397 rval = value.read(size) |
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398 value.seek(start) |
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399 return rval |
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400 raise ValueError('With the provided join_by value (%s), the minimum size value is %i.' % (join_by, min_size)) |
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401 left_index = right_index = int((size - len_join_by) / 2) |
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402 if left_index + right_index + len_join_by < size: |
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403 if left_larger: |
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404 left_index += 1 |
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405 else: |
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406 right_index += 1 |
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407 rval = value.read(left_index) + join_by |
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408 value.seek(-right_index, 2) |
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409 rval += value.read(right_index) |
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410 else: |
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411 while True: |
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412 data = value.read(CHUNK_SIZE) |
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413 if not data: |
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414 break |
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415 rval += data |
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416 return unicodify(rval) |
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417 |
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418 |
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419 def shrink_and_unicodify(stream): |
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420 stream = unicodify(stream, strip_null=True) or '' |
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421 if (len(stream) > DATABASE_MAX_STRING_SIZE): |
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422 stream = shrink_string_by_size(stream, |
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423 DATABASE_MAX_STRING_SIZE, |
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424 join_by="\n..\n", |
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425 left_larger=True, |
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426 beginning_on_size_error=True) |
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427 return stream |
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428 |
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429 |
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430 def shrink_string_by_size(value, size, join_by="..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False): |
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431 if len(value) > size: |
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432 len_join_by = len(join_by) |
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433 min_size = len_join_by + 2 |
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434 if size < min_size: |
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435 if beginning_on_size_error: |
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436 return value[:size] |
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437 elif end_on_size_error: |
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438 return value[-size:] |
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439 raise ValueError('With the provided join_by value (%s), the minimum size value is %i.' % (join_by, min_size)) |
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440 left_index = right_index = int((size - len_join_by) / 2) |
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441 if left_index + right_index + len_join_by < size: |
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442 if left_larger: |
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443 left_index += 1 |
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444 else: |
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445 right_index += 1 |
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446 value = "{}{}{}".format(value[:left_index], join_by, value[-right_index:]) |
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447 return value |
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448 |
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449 |
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450 def pretty_print_time_interval(time=False, precise=False, utc=False): |
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451 """ |
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452 Get a datetime object or a int() Epoch timestamp and return a |
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453 pretty string like 'an hour ago', 'Yesterday', '3 months ago', |
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shellac
parents:
diff
changeset
|
454 'just now', etc |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
455 credit: http://stackoverflow.com/questions/1551382/user-friendly-time-format-in-python |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
456 """ |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
457 if utc: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
458 now = datetime.utcnow() |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
459 else: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
460 now = datetime.now() |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
461 if type(time) is int: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
462 diff = now - datetime.fromtimestamp(time) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
463 elif isinstance(time, datetime): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
464 diff = now - time |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
465 elif isinstance(time, str): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
466 try: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
467 time = datetime.strptime(time, "%Y-%m-%dT%H:%M:%S.%f") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
468 except ValueError: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
469 # MySQL may not support microseconds precision |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
470 time = datetime.strptime(time, "%Y-%m-%dT%H:%M:%S") |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
471 diff = now - time |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
472 else: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
473 diff = now - now |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
474 second_diff = diff.seconds |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
475 day_diff = diff.days |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
476 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
477 if day_diff < 0: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
478 return '' |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
479 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
480 if precise: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
481 if day_diff == 0: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
482 if second_diff < 10: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
483 return "just now" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
484 if second_diff < 60: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
485 return str(second_diff) + " seconds ago" |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
486 if second_diff < 120: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
487 return "a minute ago" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
488 if second_diff < 3600: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
489 return str(second_diff / 60) + " minutes ago" |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
490 if second_diff < 7200: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
491 return "an hour ago" |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
492 if second_diff < 86400: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
493 return str(second_diff / 3600) + " hours ago" |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
494 if day_diff == 1: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
495 return "yesterday" |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
496 if day_diff < 7: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
497 return str(day_diff) + " days ago" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
498 if day_diff < 31: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
499 return str(day_diff / 7) + " weeks ago" |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
500 if day_diff < 365: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
501 return str(day_diff / 30) + " months ago" |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
502 return str(day_diff / 365) + " years ago" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
503 else: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
504 if day_diff == 0: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
505 return "today" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
506 if day_diff == 1: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
507 return "yesterday" |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
508 if day_diff < 7: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
509 return "less than a week" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
510 if day_diff < 31: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
511 return "less than a month" |
4f3585e2f14b
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shellac
parents:
diff
changeset
|
512 if day_diff < 365: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
513 return "less than a year" |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
514 return "a few years ago" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
515 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
516 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
517 def pretty_print_json(json_data, is_json_string=False): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
518 if is_json_string: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
519 json_data = json.loads(json_data) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
520 return json.dumps(json_data, sort_keys=True, indent=4) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
521 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
522 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
523 # characters that are valid |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
524 valid_chars = set(string.ascii_letters + string.digits + " -=_.()/+*^,:?!") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
525 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
526 # characters that are allowed but need to be escaped |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
527 mapped_chars = {'>': '__gt__', |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
528 '<': '__lt__', |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
529 "'": '__sq__', |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
530 '"': '__dq__', |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
531 '[': '__ob__', |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
532 ']': '__cb__', |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
533 '{': '__oc__', |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
534 '}': '__cc__', |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
535 '@': '__at__', |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
536 '\n': '__cn__', |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
537 '\r': '__cr__', |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
538 '\t': '__tc__', |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
539 '#': '__pd__'} |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
540 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
541 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
542 def restore_text(text, character_map=mapped_chars): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
543 """Restores sanitized text""" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
544 if not text: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
545 return text |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
546 for key, value in character_map.items(): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
547 text = text.replace(value, key) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
548 return text |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
549 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
550 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
551 def sanitize_text(text, valid_characters=valid_chars, character_map=mapped_chars, invalid_character='X'): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
552 """ |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
553 Restricts the characters that are allowed in text; accepts both strings |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
554 and lists of strings; non-string entities will be cast to strings. |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
555 """ |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
556 if isinstance(text, list): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
557 return [sanitize_text(x, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character) for x in text] |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
558 if not isinstance(text, str): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
559 text = smart_str(text) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
560 return _sanitize_text_helper(text, valid_characters=valid_characters, character_map=character_map) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
561 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
562 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
563 def _sanitize_text_helper(text, valid_characters=valid_chars, character_map=mapped_chars, invalid_character='X'): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
564 """Restricts the characters that are allowed in a string""" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
565 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
566 out = [] |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
567 for c in text: |
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568 if c in valid_characters: |
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569 out.append(c) |
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570 elif c in character_map: |
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571 out.append(character_map[c]) |
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572 else: |
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573 out.append(invalid_character) # makes debugging easier |
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574 return ''.join(out) |
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575 |
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576 |
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577 def sanitize_lists_to_string(values, valid_characters=valid_chars, character_map=mapped_chars, invalid_character='X'): |
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578 if isinstance(values, list): |
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579 rval = [] |
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580 for value in values: |
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581 rval.append(sanitize_lists_to_string(value, |
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582 valid_characters=valid_characters, |
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583 character_map=character_map, |
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584 invalid_character=invalid_character)) |
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585 values = ",".join(rval) |
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586 else: |
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587 values = sanitize_text(values, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character) |
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588 return values |
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589 |
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590 |
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591 def sanitize_param(value, valid_characters=valid_chars, character_map=mapped_chars, invalid_character='X'): |
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592 """Clean incoming parameters (strings or lists)""" |
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593 if isinstance(value, str): |
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594 return sanitize_text(value, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character) |
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595 elif isinstance(value, list): |
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596 return [sanitize_text(x, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character) for x in value] |
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597 else: |
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598 raise Exception('Unknown parameter type (%s)' % (type(value))) |
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599 |
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600 |
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601 valid_filename_chars = set(string.ascii_letters + string.digits + '_.') |
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602 invalid_filenames = ['', '.', '..'] |
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603 |
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604 |
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605 def sanitize_for_filename(text, default=None): |
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606 """ |
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607 Restricts the characters that are allowed in a filename portion; Returns default value or a unique id string if result is not a valid name. |
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608 Method is overly aggressive to minimize possible complications, but a maximum length is not considered. |
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609 """ |
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610 out = [] |
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611 for c in text: |
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612 if c in valid_filename_chars: |
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613 out.append(c) |
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614 else: |
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615 out.append('_') |
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616 out = ''.join(out) |
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617 if out in invalid_filenames: |
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618 if default is None: |
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619 return sanitize_for_filename(str(unique_id())) |
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620 return default |
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621 return out |
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622 |
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623 |
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624 def find_instance_nested(item, instances, match_key=None): |
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625 """ |
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626 Recursively find instances from lists, dicts, tuples. |
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627 |
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628 `instances` should be a tuple of valid instances |
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629 If match_key is given the key must match for an instance to be added to the list of found instances. |
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630 """ |
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631 |
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632 matches = [] |
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633 |
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634 def visit(path, key, value): |
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635 if isinstance(value, instances): |
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636 if match_key is None or match_key == key: |
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637 matches.append(value) |
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638 return key, value |
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639 |
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640 def enter(path, key, value): |
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641 if isinstance(value, instances): |
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642 return None, False |
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643 return default_enter(path, key, value) |
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644 |
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645 remap(item, visit, reraise_visit=False, enter=enter) |
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646 |
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647 return matches |
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648 |
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649 |
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650 def mask_password_from_url(url): |
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651 """ |
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652 Masks out passwords from connection urls like the database connection in galaxy.ini |
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653 |
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654 >>> mask_password_from_url( 'sqlite+postgresql://user:password@localhost/' ) |
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655 'sqlite+postgresql://user:********@localhost/' |
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656 >>> mask_password_from_url( 'amqp://user:amqp@localhost' ) |
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657 'amqp://user:********@localhost' |
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658 >>> mask_password_from_url( 'amqp://localhost') |
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659 'amqp://localhost' |
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660 """ |
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661 split = urlsplit(url) |
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662 if split.password: |
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663 if url.count(split.password) == 1: |
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664 url = url.replace(split.password, "********") |
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665 else: |
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666 # This can manipulate the input other than just masking password, |
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667 # so the previous string replace method is preferred when the |
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668 # password doesn't appear twice in the url |
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669 split = split._replace(netloc=split.netloc.replace(f"{split.username}:{split.password}", '%s:********' % split.username)) |
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670 url = urlunsplit(split) |
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671 return url |
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672 |
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673 |
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674 def ready_name_for_url(raw_name): |
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675 """ General method to convert a string (i.e. object name) to a URL-ready |
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676 slug. |
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677 |
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678 >>> ready_name_for_url( "My Cool Object" ) |
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679 'My-Cool-Object' |
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680 >>> ready_name_for_url( "!My Cool Object!" ) |
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681 'My-Cool-Object' |
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|
682 >>> ready_name_for_url( "Hello₩◎ґʟⅾ" ) |
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683 'Hello' |
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|
684 """ |
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|
685 |
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|
686 # Replace whitespace with '-' |
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687 slug_base = re.sub(r"\s+", "-", raw_name) |
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688 # Remove all non-alphanumeric characters. |
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689 slug_base = re.sub(r"[^a-zA-Z0-9\-]", "", slug_base) |
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690 # Remove trailing '-'. |
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691 if slug_base.endswith('-'): |
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692 slug_base = slug_base[:-1] |
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693 return slug_base |
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|
694 |
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parents:
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|
695 |
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696 def which(file): |
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697 # http://stackoverflow.com/questions/5226958/which-equivalent-function-in-python |
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698 for path in os.environ["PATH"].split(":"): |
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699 if os.path.exists(path + "/" + file): |
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700 return path + "/" + file |
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701 |
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702 return None |
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|
703 |
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parents:
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|
704 |
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705 def in_directory(file, directory, local_path_module=os.path): |
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706 """ |
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|
707 Return true, if the common prefix of both is equal to directory |
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708 e.g. /a/b/c/d.rst and directory is /a/b, the common prefix is /a/b. |
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709 This function isn't used exclusively for security checks, but if it is |
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|
710 used for such checks it is assumed that ``directory`` is a "trusted" path - |
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711 supplied by Galaxy or by the admin and ``file`` is something generated by |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
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|
712 a tool, configuration, external web server, or user supplied input. |
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parents:
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|
713 |
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|
714 local_path_module is used by Pulsar to check Windows paths while running on |
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|
715 a POSIX-like system. |
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|
716 |
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|
717 >>> base_dir = tempfile.mkdtemp() |
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718 >>> safe_dir = os.path.join(base_dir, "user") |
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|
719 >>> os.mkdir(safe_dir) |
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|
720 >>> good_file = os.path.join(safe_dir, "1") |
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721 >>> with open(good_file, "w") as f: _ = f.write("hello") |
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|
722 >>> in_directory(good_file, safe_dir) |
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parents:
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723 True |
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724 >>> in_directory("/other/file/is/here.txt", safe_dir) |
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725 False |
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|
726 >>> unsafe_link = os.path.join(safe_dir, "2") |
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|
727 >>> os.symlink("/other/file/bad.fasta", unsafe_link) |
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|
728 >>> in_directory(unsafe_link, safe_dir) |
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|
729 False |
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shellac
parents:
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changeset
|
730 """ |
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parents:
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|
731 if local_path_module != os.path: |
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|
732 _safe_contains = importlib.import_module('galaxy.util.path.%s' % local_path_module.__name__).safe_contains |
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|
733 else: |
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|
734 directory = os.path.realpath(directory) |
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|
735 _safe_contains = safe_contains |
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parents:
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|
736 return _safe_contains(directory, file) |
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parents:
diff
changeset
|
737 |
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shellac
parents:
diff
changeset
|
738 |
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shellac
parents:
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|
739 def merge_sorted_iterables(operator, *iterables): |
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shellac
parents:
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|
740 """ |
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shellac
parents:
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|
741 |
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parents:
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|
742 >>> operator = lambda x: x |
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|
743 >>> list( merge_sorted_iterables( operator, [1,2,3], [4,5] ) ) |
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|
744 [1, 2, 3, 4, 5] |
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|
745 >>> list( merge_sorted_iterables( operator, [4, 5], [1,2,3] ) ) |
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shellac
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|
746 [1, 2, 3, 4, 5] |
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shellac
parents:
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|
747 >>> list( merge_sorted_iterables( operator, [1, 4, 5], [2], [3] ) ) |
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shellac
parents:
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|
748 [1, 2, 3, 4, 5] |
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shellac
parents:
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|
749 """ |
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parents:
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|
750 first_iterable = iterables[0] |
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parents:
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|
751 if len(iterables) == 1: |
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parents:
diff
changeset
|
752 yield from first_iterable |
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shellac
parents:
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|
753 else: |
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shellac
parents:
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|
754 yield from __merge_two_sorted_iterables( |
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shellac
parents:
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changeset
|
755 operator, |
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shellac
parents:
diff
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|
756 iter(first_iterable), |
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parents:
diff
changeset
|
757 merge_sorted_iterables(operator, *iterables[1:]) |
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shellac
parents:
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changeset
|
758 ) |
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shellac
parents:
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changeset
|
759 |
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shellac
parents:
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changeset
|
760 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
761 def __merge_two_sorted_iterables(operator, iterable1, iterable2): |
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shellac
parents:
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|
762 unset = object() |
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shellac
parents:
diff
changeset
|
763 continue_merge = True |
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shellac
parents:
diff
changeset
|
764 next_1 = unset |
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shellac
parents:
diff
changeset
|
765 next_2 = unset |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
766 while continue_merge: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
767 try: |
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shellac
parents:
diff
changeset
|
768 if next_1 is unset: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
769 next_1 = next(iterable1) |
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shellac
parents:
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changeset
|
770 if next_2 is unset: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
771 next_2 = next(iterable2) |
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shellac
parents:
diff
changeset
|
772 if operator(next_2) < operator(next_1): |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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|
773 yield next_2 |
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shellac
parents:
diff
changeset
|
774 next_2 = unset |
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shellac
parents:
diff
changeset
|
775 else: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
776 yield next_1 |
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shellac
parents:
diff
changeset
|
777 next_1 = unset |
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shellac
parents:
diff
changeset
|
778 except StopIteration: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
779 continue_merge = False |
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shellac
parents:
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changeset
|
780 if next_1 is not unset: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
781 yield next_1 |
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shellac
parents:
diff
changeset
|
782 if next_2 is not unset: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
783 yield next_2 |
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shellac
parents:
diff
changeset
|
784 yield from iterable1 |
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shellac
parents:
diff
changeset
|
785 yield from iterable2 |
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shellac
parents:
diff
changeset
|
786 |
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shellac
parents:
diff
changeset
|
787 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
788 class Params: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
789 """ |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
790 Stores and 'sanitizes' parameters. Alphanumeric characters and the |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
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791 non-alphanumeric ones that are deemed safe are let to pass through (see L{valid_chars}). |
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792 Some non-safe characters are escaped to safe forms for example C{>} becomes C{__lt__} |
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|
793 (see L{mapped_chars}). All other characters are replaced with C{X}. |
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794 |
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795 Operates on string or list values only (HTTP parameters). |
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796 |
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797 >>> values = { 'status':'on', 'symbols':[ 'alpha', '<>', '$rm&#!' ] } |
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798 >>> par = Params(values) |
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799 >>> par.status |
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800 'on' |
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801 >>> par.value == None # missing attributes return None |
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802 True |
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803 >>> par.get('price', 0) |
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804 0 |
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805 >>> par.symbols # replaces unknown symbols with X |
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806 ['alpha', '__lt____gt__', 'XrmX__pd__!'] |
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807 >>> sorted(par.flatten()) # flattening to a list |
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808 [('status', 'on'), ('symbols', 'XrmX__pd__!'), ('symbols', '__lt____gt__'), ('symbols', 'alpha')] |
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809 """ |
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810 |
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811 # is NEVER_SANITIZE required now that sanitizing for tool parameters can be controlled on a per parameter basis and occurs via InputValueWrappers? |
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812 NEVER_SANITIZE = ['file_data', 'url_paste', 'URL', 'filesystem_paths'] |
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813 |
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814 def __init__(self, params, sanitize=True): |
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815 if sanitize: |
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816 for key, value in params.items(): |
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817 # sanitize check both ungrouped and grouped parameters by |
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818 # name. Anything relying on NEVER_SANITIZE should be |
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819 # changed to not require this and NEVER_SANITIZE should be |
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820 # removed. |
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821 if (value is not None and key not in self.NEVER_SANITIZE |
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822 and True not in [key.endswith("|%s" % nonsanitize_parameter) for |
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823 nonsanitize_parameter in self.NEVER_SANITIZE]): |
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824 self.__dict__[key] = sanitize_param(value) |
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825 else: |
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826 self.__dict__[key] = value |
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827 else: |
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828 self.__dict__.update(params) |
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829 |
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830 def flatten(self): |
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831 """ |
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832 Creates a tuple list from a dict with a tuple/value pair for every value that is a list |
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833 """ |
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834 flat = [] |
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835 for key, value in self.__dict__.items(): |
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836 if isinstance(value, list): |
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837 for v in value: |
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838 flat.append((key, v)) |
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839 else: |
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840 flat.append((key, value)) |
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841 return flat |
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842 |
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843 def __getattr__(self, name): |
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844 """This is here to ensure that we get None for non existing parameters""" |
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845 return None |
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846 |
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847 def get(self, key, default): |
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848 return self.__dict__.get(key, default) |
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849 |
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850 def __str__(self): |
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851 return '%s' % self.__dict__ |
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852 |
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853 def __len__(self): |
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854 return len(self.__dict__) |
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855 |
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856 def __iter__(self): |
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857 return iter(self.__dict__) |
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858 |
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859 def update(self, values): |
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860 self.__dict__.update(values) |
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861 |
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862 |
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863 def rst_to_html(s, error=False): |
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864 """Convert a blob of reStructuredText to HTML""" |
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865 log = get_logger("docutils") |
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866 |
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867 if docutils_core is None: |
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868 raise Exception("Attempted to use rst_to_html but docutils unavailable.") |
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869 |
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870 class FakeStream: |
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871 def write(self, str): |
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872 if len(str) > 0 and not str.isspace(): |
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873 if error: |
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874 raise Exception(str) |
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875 log.warning(str) |
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|
876 |
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877 settings_overrides = { |
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878 "embed_stylesheet": False, |
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879 "template": os.path.join(os.path.dirname(__file__), "docutils_template.txt"), |
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880 "warning_stream": FakeStream(), |
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881 "doctitle_xform": False, # without option, very different rendering depending on |
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882 # number of sections in help content. |
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883 } |
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884 |
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885 return unicodify(docutils_core.publish_string( |
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886 s, writer=docutils_html4css1.Writer(), |
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887 settings_overrides=settings_overrides)) |
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888 |
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889 |
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890 def xml_text(root, name=None): |
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891 """Returns the text inside an element""" |
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892 if name is not None: |
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893 # Try attribute first |
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894 val = root.get(name) |
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895 if val: |
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896 return val |
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897 # Then try as element |
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898 elem = root.find(name) |
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899 else: |
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900 elem = root |
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901 if elem is not None and elem.text: |
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902 text = ''.join(elem.text.splitlines()) |
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903 return text.strip() |
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parents:
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|
904 # No luck, return empty string |
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parents:
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|
905 return '' |
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parents:
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|
906 |
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parents:
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|
907 |
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parents:
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|
908 def parse_resource_parameters(resource_param_file): |
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parents:
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|
909 """Code shared between jobs and workflows for reading resource parameter configuration files. |
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parents:
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|
910 |
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parents:
diff
changeset
|
911 TODO: Allow YAML in addition to XML. |
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parents:
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|
912 """ |
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parents:
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|
913 resource_parameters = {} |
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parents:
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|
914 if os.path.exists(resource_param_file): |
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parents:
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|
915 resource_definitions = parse_xml(resource_param_file) |
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parents:
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|
916 resource_definitions_root = resource_definitions.getroot() |
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parents:
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|
917 for parameter_elem in resource_definitions_root.findall("param"): |
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parents:
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|
918 name = parameter_elem.get("name") |
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parents:
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|
919 resource_parameters[name] = parameter_elem |
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parents:
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|
920 |
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parents:
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|
921 return resource_parameters |
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parents:
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|
922 |
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|
923 |
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|
924 # asbool implementation pulled from PasteDeploy |
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|
925 truthy = frozenset({'true', 'yes', 'on', 'y', 't', '1'}) |
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|
926 falsy = frozenset({'false', 'no', 'off', 'n', 'f', '0'}) |
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|
927 |
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|
928 |
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|
929 def asbool(obj): |
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|
930 if isinstance(obj, str): |
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|
931 obj = obj.strip().lower() |
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|
932 if obj in truthy: |
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|
933 return True |
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|
934 elif obj in falsy: |
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|
935 return False |
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|
936 else: |
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|
937 raise ValueError("String is not true/false: %r" % obj) |
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|
938 return bool(obj) |
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|
939 |
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|
940 |
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parents:
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|
941 def string_as_bool(string): |
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|
942 if str(string).lower() in ('true', 'yes', 'on', '1'): |
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|
943 return True |
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|
944 else: |
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|
945 return False |
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|
946 |
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|
947 |
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parents:
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|
948 def string_as_bool_or_none(string): |
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|
949 """ |
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|
950 Returns True, None or False based on the argument: |
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|
951 True if passed True, 'True', 'Yes', or 'On' |
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|
952 None if passed None or 'None' |
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|
953 False otherwise |
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parents:
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|
954 |
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parents:
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|
955 Note: string comparison is case-insensitive so lowecase versions of those |
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parents:
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|
956 function equivalently. |
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|
957 """ |
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|
958 string = str(string).lower() |
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parents:
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|
959 if string in ('true', 'yes', 'on'): |
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shellac
parents:
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|
960 return True |
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parents:
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|
961 elif string in ['none', 'null']: |
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parents:
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|
962 return None |
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parents:
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|
963 else: |
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|
964 return False |
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parents:
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|
965 |
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parents:
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|
966 |
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parents:
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|
967 def listify(item, do_strip=False): |
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shellac
parents:
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|
968 """ |
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parents:
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|
969 Make a single item a single item list. |
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parents:
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|
970 |
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shellac
parents:
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|
971 If *item* is a string, it is split on comma (``,``) characters to produce the list. Optionally, if *do_strip* is |
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shellac
parents:
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|
972 true, any extra whitespace around the split items is stripped. |
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parents:
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|
973 |
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shellac
parents:
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|
974 If *item* is a list it is returned unchanged. If *item* is a tuple, it is converted to a list and returned. If |
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shellac
parents:
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|
975 *item* evaluates to False, an empty list is returned. |
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shellac
parents:
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|
976 |
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parents:
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|
977 :type item: object |
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shellac
parents:
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|
978 :param item: object to make a list from |
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shellac
parents:
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|
979 :type do_strip: bool |
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shellac
parents:
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|
980 :param do_strip: strip whitespaces from around split items, if set to ``True`` |
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shellac
parents:
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|
981 :rtype: list |
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shellac
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|
982 :returns: The input as a list |
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|
983 """ |
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parents:
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|
984 if not item: |
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parents:
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|
985 return [] |
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parents:
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|
986 elif isinstance(item, list): |
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parents:
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|
987 return item |
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parents:
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|
988 elif isinstance(item, tuple): |
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parents:
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|
989 return list(item) |
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shellac
parents:
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|
990 elif isinstance(item, str) and item.count(','): |
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parents:
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|
991 if do_strip: |
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parents:
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|
992 return [token.strip() for token in item.split(',')] |
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shellac
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|
993 else: |
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parents:
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|
994 return item.split(',') |
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shellac
parents:
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|
995 else: |
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parents:
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|
996 return [item] |
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shellac
parents:
diff
changeset
|
997 |
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shellac
parents:
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|
998 |
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shellac
parents:
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|
999 def commaify(amount): |
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parents:
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|
1000 orig = amount |
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shellac
parents:
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|
1001 new = re.sub(r"^(-?\d+)(\d{3})", r'\g<1>,\g<2>', amount) |
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parents:
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changeset
|
1002 if orig == new: |
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parents:
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|
1003 return new |
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parents:
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changeset
|
1004 else: |
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shellac
parents:
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|
1005 return commaify(new) |
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shellac
parents:
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changeset
|
1006 |
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shellac
parents:
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changeset
|
1007 |
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shellac
parents:
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|
1008 def roundify(amount, sfs=2): |
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|
1009 """ |
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1010 Take a number in string form and truncate to 'sfs' significant figures. |
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parents:
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|
1011 """ |
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|
1012 if len(amount) <= sfs: |
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parents:
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1013 return amount |
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1014 else: |
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parents:
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|
1015 return amount[0:sfs] + '0' * (len(amount) - sfs) |
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|
1016 |
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parents:
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|
1017 |
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1018 def unicodify(value, encoding=DEFAULT_ENCODING, error='replace', strip_null=False, log_exception=True): |
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1019 """ |
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1020 Returns a Unicode string or None. |
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1021 |
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1022 >>> assert unicodify(None) is None |
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1023 >>> assert unicodify('simple string') == 'simple string' |
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1024 >>> assert unicodify(3) == '3' |
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1025 >>> assert unicodify(bytearray([115, 116, 114, 196, 169, 195, 177, 103])) == 'strĩñg' |
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1026 >>> assert unicodify(Exception('strĩñg')) == 'strĩñg' |
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1027 >>> assert unicodify('cómplǐcḁtëd strĩñg') == 'cómplǐcḁtëd strĩñg' |
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1028 >>> s = 'cómplǐcḁtëd strĩñg'; assert unicodify(s) == s |
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1029 >>> s = 'lâtín strìñg'; assert unicodify(s.encode('latin-1'), 'latin-1') == s |
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1030 >>> s = 'lâtín strìñg'; assert unicodify(s.encode('latin-1')) == 'l\ufffdt\ufffdn str\ufffd\ufffdg' |
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1031 >>> s = 'lâtín strìñg'; assert unicodify(s.encode('latin-1'), error='ignore') == 'ltn strg' |
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1032 """ |
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1033 if value is None: |
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1034 return value |
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1035 try: |
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1036 if isinstance(value, bytearray): |
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1037 value = bytes(value) |
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1038 elif not isinstance(value, (str, bytes)): |
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1039 value = str(value) |
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1040 # Now value is an instance of bytes or str |
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1041 if not isinstance(value, str): |
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1042 value = str(value, encoding, error) |
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1043 except Exception as e: |
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1044 if log_exception: |
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1045 msg = "Value '{}' could not be coerced to Unicode: {}('{}')".format(repr(value), type(e).__name__, e) |
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1046 log.exception(msg) |
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1047 raise |
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1048 if strip_null: |
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1049 return value.replace('\0', '') |
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1050 return value |
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1051 |
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1052 |
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1053 def smart_str(s, encoding=DEFAULT_ENCODING, strings_only=False, errors='strict'): |
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1054 """ |
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1055 Returns a bytestring version of 's', encoded as specified in 'encoding'. |
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1056 |
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1057 If strings_only is True, don't convert (some) non-string-like objects. |
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1058 |
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1059 Adapted from an older, simpler version of django.utils.encoding.smart_str. |
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1060 |
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1061 >>> assert smart_str(None) == b'None' |
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1062 >>> assert smart_str(None, strings_only=True) is None |
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1063 >>> assert smart_str(3) == b'3' |
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1064 >>> assert smart_str(3, strings_only=True) == 3 |
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1065 >>> s = b'a bytes string'; assert smart_str(s) == s |
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1066 >>> s = bytearray(b'a bytes string'); assert smart_str(s) == s |
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1067 >>> assert smart_str('a simple unicode string') == b'a simple unicode string' |
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1068 >>> assert smart_str('à strange ünicode ڃtring') == b'\\xc3\\xa0 strange \\xc3\\xbcnicode \\xda\\x83tring' |
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1069 >>> assert smart_str(b'\\xc3\\xa0n \\xc3\\xabncoded utf-8 string', encoding='latin-1') == b'\\xe0n \\xebncoded utf-8 string' |
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1070 >>> assert smart_str(bytearray(b'\\xc3\\xa0n \\xc3\\xabncoded utf-8 string'), encoding='latin-1') == b'\\xe0n \\xebncoded utf-8 string' |
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1071 """ |
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1072 if strings_only and isinstance(s, (type(None), int)): |
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1073 return s |
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1074 if not isinstance(s, (str, bytes, bytearray)): |
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1075 s = str(s) |
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1076 # Now s is an instance of str, bytes or bytearray |
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1077 if not isinstance(s, (bytes, bytearray)): |
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1078 return s.encode(encoding, errors) |
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1079 elif s and encoding != DEFAULT_ENCODING: |
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1080 return s.decode(DEFAULT_ENCODING, errors).encode(encoding, errors) |
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1081 else: |
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1082 return s |
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1083 |
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1084 |
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1085 def strip_control_characters(s): |
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1086 """Strip unicode control characters from a string.""" |
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1087 return "".join(c for c in unicodify(s) if unicodedata.category(c) != "Cc") |
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1088 |
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1089 |
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1090 def object_to_string(obj): |
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1091 return binascii.hexlify(obj) |
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1092 |
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1093 |
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1094 def string_to_object(s): |
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1095 return binascii.unhexlify(s) |
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1096 |
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1097 |
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1098 def clean_multiline_string(multiline_string, sep='\n'): |
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1099 """ |
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1100 Dedent, split, remove first and last empty lines, rejoin. |
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1101 """ |
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1102 multiline_string = textwrap.dedent(multiline_string) |
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1103 string_list = multiline_string.split(sep) |
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1104 if not string_list[0]: |
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1105 string_list = string_list[1:] |
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1106 if not string_list[-1]: |
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1107 string_list = string_list[:-1] |
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1108 return '\n'.join(string_list) + '\n' |
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1109 |
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1110 |
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1111 class ParamsWithSpecs(collections.defaultdict): |
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1112 """ |
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1113 """ |
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1114 |
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1115 def __init__(self, specs=None, params=None): |
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1116 self.specs = specs or dict() |
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1117 self.params = params or dict() |
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1118 for name, value in self.params.items(): |
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1119 if name not in self.specs: |
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1120 self._param_unknown_error(name) |
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1121 if 'map' in self.specs[name]: |
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1122 try: |
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1123 self.params[name] = self.specs[name]['map'](value) |
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1124 except Exception: |
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|
1125 self._param_map_error(name, value) |
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|
1126 if 'valid' in self.specs[name]: |
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|
1127 if not self.specs[name]['valid'](value): |
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|
1128 self._param_vaildation_error(name, value) |
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|
1129 |
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|
1130 self.update(self.params) |
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1131 |
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|
1132 def __missing__(self, name): |
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|
1133 return self.specs[name]['default'] |
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1134 |
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|
1135 def __getattr__(self, name): |
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1136 return self[name] |
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|
1137 |
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|
1138 def _param_unknown_error(self, name): |
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1139 raise NotImplementedError() |
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|
1140 |
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1141 def _param_map_error(self, name, value): |
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|
1142 raise NotImplementedError() |
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|
1143 |
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1144 def _param_vaildation_error(self, name, value): |
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|
1145 raise NotImplementedError() |
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1146 |
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1147 |
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1148 def compare_urls(url1, url2, compare_scheme=True, compare_hostname=True, compare_path=True): |
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1149 url1 = urlparse(url1) |
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1150 url2 = urlparse(url2) |
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1151 if compare_scheme and url1.scheme and url2.scheme and url1.scheme != url2.scheme: |
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1152 return False |
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1153 if compare_hostname and url1.hostname and url2.hostname and url1.hostname != url2.hostname: |
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1154 return False |
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1155 if compare_path and url1.path and url2.path and url1.path != url2.path: |
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1156 return False |
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1157 return True |
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1158 |
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1159 |
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1160 def read_build_sites(filename, check_builds=True): |
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1161 """ read db names to ucsc mappings from file, this file should probably be merged with the one above """ |
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1162 build_sites = [] |
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1163 try: |
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1164 for line in open(filename): |
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1165 try: |
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1166 if line[0:1] == "#": |
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1167 continue |
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1168 fields = line.replace("\r", "").replace("\n", "").split("\t") |
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1169 site_name = fields[0] |
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1170 site = fields[1] |
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1171 if check_builds: |
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1172 site_builds = fields[2].split(",") |
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1173 site_dict = {'name': site_name, 'url': site, 'builds': site_builds} |
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1174 else: |
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1175 site_dict = {'name': site_name, 'url': site} |
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1176 build_sites.append(site_dict) |
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1177 except Exception: |
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1178 continue |
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1179 except Exception: |
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1180 log.error("ERROR: Unable to read builds for site file %s", filename) |
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1181 return build_sites |
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|
1182 |
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1183 |
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1184 def relativize_symlinks(path, start=None, followlinks=False): |
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1185 for root, _, files in os.walk(path, followlinks=followlinks): |
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1186 rel_start = None |
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|
1187 for file_name in files: |
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1188 symlink_file_name = os.path.join(root, file_name) |
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|
1189 if os.path.islink(symlink_file_name): |
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1190 symlink_target = os.readlink(symlink_file_name) |
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1191 if rel_start is None: |
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1192 if start is None: |
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1193 rel_start = root |
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1194 else: |
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1195 rel_start = start |
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1196 rel_path = relpath(symlink_target, rel_start) |
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1197 os.remove(symlink_file_name) |
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|
1198 os.symlink(rel_path, symlink_file_name) |
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|
1199 |
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|
1200 |
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|
1201 def stringify_dictionary_keys(in_dict): |
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1202 # returns a new dictionary |
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1203 # changes unicode keys into strings, only works on top level (does not recurse) |
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1204 # unicode keys are not valid for expansion into keyword arguments on method calls |
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1205 out_dict = {} |
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1206 for key, value in in_dict.items(): |
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|
1207 out_dict[str(key)] = value |
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1208 return out_dict |
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|
1209 |
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|
1210 |
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1211 def mkstemp_ln(src, prefix='mkstemp_ln_'): |
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|
1212 """ |
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1213 From tempfile._mkstemp_inner, generate a hard link in the same dir with a |
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1214 random name. Created so we can persist the underlying file of a |
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1215 NamedTemporaryFile upon its closure. |
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|
1216 """ |
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1217 dir = os.path.dirname(src) |
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1218 names = tempfile._get_candidate_names() |
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1219 for _ in range(tempfile.TMP_MAX): |
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1220 name = next(names) |
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1221 file = os.path.join(dir, prefix + name) |
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1222 try: |
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1223 os.link(src, file) |
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1224 return (os.path.abspath(file)) |
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1225 except OSError as e: |
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1226 if e.errno == errno.EEXIST: |
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1227 continue # try again |
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|
1228 raise |
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|
1229 raise OSError(errno.EEXIST, "No usable temporary file name found") |
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|
1230 |
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1231 |
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1232 def umask_fix_perms(path, umask, unmasked_perms, gid=None): |
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1233 """ |
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1234 umask-friendly permissions fixing |
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parents:
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1235 """ |
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parents:
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changeset
|
1236 perms = unmasked_perms & ~umask |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1237 try: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1238 st = os.stat(path) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1239 except OSError: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1240 log.exception('Unable to set permissions or group on %s', path) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1241 return |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1242 # fix modes |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1243 if stat.S_IMODE(st.st_mode) != perms: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1244 try: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1245 os.chmod(path, perms) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1246 except Exception as e: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1247 log.warning('Unable to honor umask ({}) for {}, tried to set: {} but mode remains {}, error was: {}'.format(oct(umask), |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1248 path, |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1249 oct(perms), |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1250 oct(stat.S_IMODE(st.st_mode)), |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1251 unicodify(e))) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1252 # fix group |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1253 if gid is not None and st.st_gid != gid: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1254 try: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1255 os.chown(path, -1, gid) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1256 except Exception as e: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1257 try: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1258 desired_group = grp.getgrgid(gid) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1259 current_group = grp.getgrgid(st.st_gid) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1260 except Exception: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1261 desired_group = gid |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1262 current_group = st.st_gid |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1263 log.warning('Unable to honor primary group ({}) for {}, group remains {}, error was: {}'.format(desired_group, |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1264 path, |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1265 current_group, |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1266 unicodify(e))) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1267 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1268 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1269 def docstring_trim(docstring): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1270 """Trimming python doc strings. Taken from: http://www.python.org/dev/peps/pep-0257/""" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1271 if not docstring: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1272 return '' |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1273 # Convert tabs to spaces (following the normal Python rules) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1274 # and split into a list of lines: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1275 lines = docstring.expandtabs().splitlines() |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1276 # Determine minimum indentation (first line doesn't count): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1277 indent = sys.maxsize |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1278 for line in lines[1:]: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1279 stripped = line.lstrip() |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1280 if stripped: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1281 indent = min(indent, len(line) - len(stripped)) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1282 # Remove indentation (first line is special): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1283 trimmed = [lines[0].strip()] |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1284 if indent < sys.maxsize: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1285 for line in lines[1:]: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1286 trimmed.append(line[indent:].rstrip()) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1287 # Strip off trailing and leading blank lines: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1288 while trimmed and not trimmed[-1]: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1289 trimmed.pop() |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1290 while trimmed and not trimmed[0]: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1291 trimmed.pop(0) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1292 # Return a single string: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1293 return '\n'.join(trimmed) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1294 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1295 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1296 def nice_size(size): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1297 """ |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1298 Returns a readably formatted string with the size |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1299 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1300 >>> nice_size(100) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1301 '100 bytes' |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1302 >>> nice_size(10000) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1303 '9.8 KB' |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1304 >>> nice_size(1000000) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1305 '976.6 KB' |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1306 >>> nice_size(100000000) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1307 '95.4 MB' |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1308 """ |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1309 words = ['bytes', 'KB', 'MB', 'GB', 'TB', 'PB', 'EB'] |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1310 prefix = '' |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1311 try: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1312 size = float(size) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1313 if size < 0: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1314 size = abs(size) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1315 prefix = '-' |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1316 except Exception: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1317 return '??? bytes' |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1318 for ind, word in enumerate(words): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1319 step = 1024 ** (ind + 1) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1320 if step > size: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1321 size = size / float(1024 ** ind) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1322 if word == 'bytes': # No decimals for bytes |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1323 return "%s%d bytes" % (prefix, size) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1324 return f"{prefix}{size:.1f} {word}" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1325 return '??? bytes' |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1326 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1327 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1328 def size_to_bytes(size): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1329 """ |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1330 Returns a number of bytes (as integer) if given a reasonably formatted string with the size |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1331 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1332 >>> size_to_bytes('1024') |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1333 1024 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1334 >>> size_to_bytes('1.0') |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1335 1 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1336 >>> size_to_bytes('10 bytes') |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1337 10 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1338 >>> size_to_bytes('4k') |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1339 4096 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1340 >>> size_to_bytes('2.2 TB') |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1341 2418925581107 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1342 >>> size_to_bytes('.01 TB') |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1343 10995116277 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1344 >>> size_to_bytes('1.b') |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1345 1 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1346 >>> size_to_bytes('1.2E2k') |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1347 122880 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1348 """ |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1349 # The following number regexp is based on https://stackoverflow.com/questions/385558/extract-float-double-value/385597#385597 |
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shellac
parents:
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changeset
|
1350 size_re = re.compile(r'(?P<number>(\d+(\.\d*)?|\.\d+)(e[+-]?\d+)?)\s*(?P<multiple>[eptgmk]?(b|bytes?)?)?$') |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1351 size_match = size_re.match(size.lower()) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1352 if size_match is None: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1353 raise ValueError("Could not parse string '%s'" % size) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1354 number = float(size_match.group("number")) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1355 multiple = size_match.group("multiple") |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1356 if multiple == "" or multiple.startswith('b'): |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
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|
1357 return int(number) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1358 elif multiple.startswith('k'): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1359 return int(number * 1024) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1360 elif multiple.startswith('m'): |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1361 return int(number * 1024 ** 2) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1362 elif multiple.startswith('g'): |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1363 return int(number * 1024 ** 3) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1364 elif multiple.startswith('t'): |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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|
1365 return int(number * 1024 ** 4) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1366 elif multiple.startswith('p'): |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1367 return int(number * 1024 ** 5) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1368 elif multiple.startswith('e'): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1369 return int(number * 1024 ** 6) |
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shellac
parents:
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changeset
|
1370 else: |
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shellac
parents:
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changeset
|
1371 raise ValueError(f"Unknown multiplier '{multiple}' in '{size}'") |
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shellac
parents:
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changeset
|
1372 |
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shellac
parents:
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changeset
|
1373 |
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shellac
parents:
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changeset
|
1374 def send_mail(frm, to, subject, body, config, html=None): |
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shellac
parents:
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|
1375 """ |
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shellac
parents:
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changeset
|
1376 Sends an email. |
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shellac
parents:
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changeset
|
1377 |
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shellac
parents:
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changeset
|
1378 :type frm: str |
4f3585e2f14b
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shellac
parents:
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|
1379 :param frm: from address |
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shellac
parents:
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changeset
|
1380 |
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shellac
parents:
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changeset
|
1381 :type to: str |
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shellac
parents:
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changeset
|
1382 :param to: to address |
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shellac
parents:
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changeset
|
1383 |
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shellac
parents:
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changeset
|
1384 :type subject: str |
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shellac
parents:
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changeset
|
1385 :param subject: Subject line |
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shellac
parents:
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changeset
|
1386 |
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shellac
parents:
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changeset
|
1387 :type body: str |
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shellac
parents:
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changeset
|
1388 :param body: Body text (should be plain text) |
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shellac
parents:
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changeset
|
1389 |
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shellac
parents:
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changeset
|
1390 :type config: object |
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shellac
parents:
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changeset
|
1391 :param config: Galaxy configuration object |
4f3585e2f14b
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shellac
parents:
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changeset
|
1392 |
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shellac
parents:
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changeset
|
1393 :type html: str |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1394 :param html: Alternative HTML representation of the body content. If |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1395 provided will convert the message to a MIMEMultipart. (Default 'None') |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1396 """ |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1397 |
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shellac
parents:
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changeset
|
1398 to = listify(to) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1399 if html: |
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shellac
parents:
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changeset
|
1400 msg = MIMEMultipart('alternative') |
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shellac
parents:
diff
changeset
|
1401 else: |
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shellac
parents:
diff
changeset
|
1402 msg = MIMEText(body, 'plain', 'utf-8') |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1403 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1404 msg['To'] = ', '.join(to) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1405 msg['From'] = frm |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1406 msg['Subject'] = subject |
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shellac
parents:
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changeset
|
1407 |
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shellac
parents:
diff
changeset
|
1408 if config.smtp_server is None: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1409 log.error("Mail is not configured for this Galaxy instance.") |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
1410 log.info(msg) |
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shellac
parents:
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changeset
|
1411 return |
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shellac
parents:
diff
changeset
|
1412 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1413 if html: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1414 mp_text = MIMEText(body, 'plain', 'utf-8') |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1415 mp_html = MIMEText(html, 'html', 'utf-8') |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1416 msg.attach(mp_text) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1417 msg.attach(mp_html) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1418 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1419 smtp_ssl = asbool(getattr(config, 'smtp_ssl', False)) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1420 if smtp_ssl: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1421 s = smtplib.SMTP_SSL(config.smtp_server) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1422 else: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1423 s = smtplib.SMTP(config.smtp_server) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1424 if not smtp_ssl: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1425 try: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1426 s.starttls() |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1427 log.debug('Initiated SSL/TLS connection to SMTP server: %s', config.smtp_server) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1428 except RuntimeError as e: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1429 log.warning('SSL/TLS support is not available to your Python interpreter: %s', unicodify(e)) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1430 except smtplib.SMTPHeloError as e: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1431 log.error("The server didn't reply properly to the HELO greeting: %s", unicodify(e)) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1432 s.close() |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1433 raise |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1434 except smtplib.SMTPException as e: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1435 log.warning('The server does not support the STARTTLS extension: %s', unicodify(e)) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1436 if config.smtp_username and config.smtp_password: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1437 try: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1438 s.login(config.smtp_username, config.smtp_password) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1439 except smtplib.SMTPHeloError as e: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1440 log.error("The server didn't reply properly to the HELO greeting: %s", unicodify(e)) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1441 s.close() |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1442 raise |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1443 except smtplib.SMTPAuthenticationError as e: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1444 log.error("The server didn't accept the username/password combination: %s", unicodify(e)) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1445 s.close() |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1446 raise |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1447 except smtplib.SMTPException as e: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1448 log.error("No suitable authentication method was found: %s", unicodify(e)) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1449 s.close() |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1450 raise |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1451 s.sendmail(frm, to, msg.as_string()) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1452 s.quit() |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1453 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1454 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1455 def force_symlink(source, link_name): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1456 try: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1457 os.symlink(source, link_name) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1458 except OSError as e: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1459 if e.errno == errno.EEXIST: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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|
1460 os.remove(link_name) |
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|
1461 os.symlink(source, link_name) |
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|
1462 else: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff
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|
1463 raise e |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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|
1464 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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|
1465 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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|
1466 def move_merge(source, target): |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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|
1467 # when using shutil and moving a directory, if the target exists, |
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|
1468 # then the directory is placed inside of it |
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|
1469 # if the target doesn't exist, then the target is made into the directory |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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|
1470 # this makes it so that the target is always the target, and if it exists, |
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|
1471 # the source contents are moved into the target |
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parents:
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|
1472 if os.path.isdir(source) and os.path.exists(target) and os.path.isdir(target): |
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|
1473 for name in os.listdir(source): |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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|
1474 move_merge(os.path.join(source, name), os.path.join(target, name)) |
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|
1475 else: |
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|
1476 return shutil.move(source, target) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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|
1477 |
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|
1478 |
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|
1479 def safe_str_cmp(a, b): |
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|
1480 """safely compare two strings in a timing-attack-resistant manner |
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|
1481 """ |
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|
1482 if len(a) != len(b): |
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|
1483 return False |
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|
1484 rv = 0 |
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|
1485 for x, y in zip(a, b): |
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|
1486 rv |= ord(x) ^ ord(y) |
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|
1487 return rv == 0 |
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|
1488 |
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|
1489 |
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|
1490 galaxy_root_path = os.path.join(__path__[0], os.pardir, os.pardir, os.pardir) # type: ignore |
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|
1491 galaxy_samples_path = os.path.join(__path__[0], os.pardir, 'config', 'sample') # type: ignore |
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|
1492 |
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|
1493 |
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|
1494 def galaxy_directory(): |
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|
1495 root_path = os.path.abspath(galaxy_root_path) |
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|
1496 if os.path.basename(root_path) == "packages": |
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|
1497 root_path = os.path.abspath(os.path.join(root_path, "..")) |
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|
1498 return root_path |
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|
1499 |
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|
1500 |
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|
1501 def galaxy_samples_directory(): |
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|
1502 return os.path.abspath(galaxy_samples_path) |
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|
1503 |
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|
1504 |
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|
1505 def config_directories_from_setting(directories_setting, galaxy_root=galaxy_root_path): |
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|
1506 """ |
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|
1507 Parse the ``directories_setting`` into a list of relative or absolute |
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|
1508 filesystem paths that will be searched to discover plugins. |
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|
1509 |
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shellac
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|
1510 :type galaxy_root: string |
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|
1511 :param galaxy_root: the root path of this galaxy installation |
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|
1512 :type directories_setting: string (default: None) |
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|
1513 :param directories_setting: the filesystem path (or paths) |
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|
1514 to search for plugins. Can be CSV string of paths. Will be treated as |
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|
1515 absolute if a path starts with '/', relative otherwise. |
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|
1516 :rtype: list of strings |
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|
1517 :returns: list of filesystem paths |
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|
1518 """ |
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|
1519 directories = [] |
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|
1520 if not directories_setting: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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|
1521 return directories |
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parents:
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|
1522 |
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shellac
parents:
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|
1523 for directory in listify(directories_setting): |
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shellac
parents:
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|
1524 directory = directory.strip() |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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|
1525 if not directory.startswith('/'): |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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|
1526 directory = os.path.join(galaxy_root, directory) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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|
1527 if not os.path.exists(directory): |
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shellac
parents:
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|
1528 log.warning('directory not found: %s', directory) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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|
1529 continue |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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|
1530 directories.append(directory) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
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|
1531 return directories |
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shellac
parents:
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|
1532 |
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shellac
parents:
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|
1533 |
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shellac
parents:
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|
1534 def parse_int(value, min_val=None, max_val=None, default=None, allow_none=False): |
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|
1535 try: |
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parents:
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|
1536 value = int(value) |
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shellac
parents:
diff
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|
1537 if min_val is not None and value < min_val: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff
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|
1538 return min_val |
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shellac
parents:
diff
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|
1539 if max_val is not None and value > max_val: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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|
1540 return max_val |
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parents:
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|
1541 return value |
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parents:
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|
1542 except ValueError: |
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parents:
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|
1543 if allow_none: |
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parents:
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|
1544 if default is None or value == "None": |
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parents:
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|
1545 return None |
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parents:
diff
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|
1546 if default: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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|
1547 return default |
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|
1548 else: |
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shellac
parents:
diff
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|
1549 raise |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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|
1550 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
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|
1551 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff
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|
1552 def parse_non_hex_float(s): |
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shellac
parents:
diff
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|
1553 r""" |
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parents:
diff
changeset
|
1554 Parse string `s` into a float but throw a `ValueError` if the string is in |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff
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|
1555 the otherwise acceptable format `\d+e\d+` (e.g. 40000000000000e5.) |
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parents:
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|
1556 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1557 This can be passed into `json.loads` to prevent a hex string in the above |
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parents:
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|
1558 format from being incorrectly parsed as a float in scientific notation. |
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parents:
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|
1559 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
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|
1560 >>> parse_non_hex_float( '123.4' ) |
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shellac
parents:
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|
1561 123.4 |
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shellac
parents:
diff
changeset
|
1562 >>> parse_non_hex_float( '2.45e+3' ) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1563 2450.0 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1564 >>> parse_non_hex_float( '2.45e-3' ) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
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|
1565 0.00245 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
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|
1566 >>> parse_non_hex_float( '40000000000000e5' ) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
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|
1567 Traceback (most recent call last): |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
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|
1568 ... |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
1569 ValueError: could not convert string to float: 40000000000000e5 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
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|
1570 """ |
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|
1571 f = float(s) |
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|
1572 # successfully parsed as float if here - check for format in original string |
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|
1573 if 'e' in s and not ('+' in s or '-' in s): |
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|
1574 raise ValueError('could not convert string to float: ' + s) |
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|
1575 return f |
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|
1576 |
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|
1577 |
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1578 def build_url(base_url, port=80, scheme='http', pathspec=None, params=None, doseq=False): |
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|
1579 if params is None: |
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1580 params = dict() |
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1581 if pathspec is None: |
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1582 pathspec = [] |
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1583 parsed_url = urlparse(base_url) |
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1584 if scheme != 'http': |
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1585 parsed_url.scheme = scheme |
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1586 assert parsed_url.scheme in ('http', 'https', 'ftp'), 'Invalid URL scheme: %s' % scheme |
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1587 if port != 80: |
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1588 url = '%s://%s:%d/%s' % (parsed_url.scheme, parsed_url.netloc.rstrip('/'), int(port), parsed_url.path) |
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1589 else: |
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1590 url = '{}://{}/{}'.format(parsed_url.scheme, parsed_url.netloc.rstrip('/'), parsed_url.path.lstrip('/')) |
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1591 if len(pathspec) > 0: |
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1592 url = '{}/{}'.format(url.rstrip('/'), '/'.join(pathspec)) |
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1593 if parsed_url.query: |
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1594 for query_parameter in parsed_url.query.split('&'): |
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1595 key, value = query_parameter.split('=') |
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1596 params[key] = value |
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1597 if params: |
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1598 url += '?%s' % urlencode(params, doseq=doseq) |
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1599 return url |
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1600 |
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1601 |
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1602 def url_get(base_url, auth=None, pathspec=None, params=None, max_retries=5, backoff_factor=1): |
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1603 """Make contact with the uri provided and return any contents.""" |
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1604 full_url = build_url(base_url, pathspec=pathspec, params=params) |
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1605 s = requests.Session() |
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1606 retries = Retry(total=max_retries, backoff_factor=backoff_factor, status_forcelist=[429]) |
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1607 s.mount(base_url, HTTPAdapter(max_retries=retries)) |
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1608 response = s.get(full_url, auth=auth) |
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1609 response.raise_for_status() |
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1610 return response.text |
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1611 |
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1612 |
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1613 def download_to_file(url, dest_file_path, timeout=30, chunk_size=2 ** 20): |
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1614 """Download a URL to a file in chunks.""" |
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1615 with requests.get(url, timeout=timeout, stream=True) as r, open(dest_file_path, 'wb') as f: |
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1616 for chunk in r.iter_content(chunk_size): |
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1617 if chunk: |
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1618 f.write(chunk) |
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1619 |
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1620 |
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1621 class classproperty: |
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1622 |
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1623 def __init__(self, f): |
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1624 self.f = f |
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1625 |
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1626 def __get__(self, obj, owner): |
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1627 return self.f(owner) |
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1628 |
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1629 |
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1630 def get_executable(): |
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1631 exe = sys.executable |
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1632 if exe.endswith('uwsgi'): |
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1633 virtualenv = None |
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1634 if uwsgi is not None: |
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1635 for name in ('home', 'virtualenv', 'venv', 'pyhome'): |
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|
1636 if name in uwsgi.opt: |
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|
1637 virtualenv = unicodify(uwsgi.opt[name]) |
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|
1638 break |
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|
1639 if virtualenv is None and 'VIRTUAL_ENV' in os.environ: |
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1640 virtualenv = os.environ['VIRTUAL_ENV'] |
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1641 if virtualenv is not None: |
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1642 exe = os.path.join(virtualenv, 'bin', 'python') |
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1643 else: |
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1644 exe = os.path.join(os.path.dirname(exe), 'python') |
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|
1645 if not os.path.exists(exe): |
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|
1646 exe = 'python' |
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|
1647 return exe |
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|
1648 |
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|
1649 |
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|
1650 class ExecutionTimer: |
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|
1651 |
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|
1652 def __init__(self): |
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1653 self.begin = time.time() |
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1654 |
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|
1655 def __str__(self): |
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1656 return "(%0.3f ms)" % (self.elapsed * 1000) |
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|
1657 |
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|
1658 @property |
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|
1659 def elapsed(self): |
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|
1660 return (time.time() - self.begin) |
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|
1661 |
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|
1662 |
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|
1663 class StructuredExecutionTimer: |
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|
1664 |
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|
1665 def __init__(self, timer_id, template, **tags): |
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|
1666 self.begin = time.time() |
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1667 self.timer_id = timer_id |
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1668 self.template = template |
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1669 self.tags = tags |
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|
1670 |
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|
1671 def __str__(self): |
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1672 return self.to_str() |
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1673 |
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|
1674 def to_str(self, **kwd): |
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1675 if kwd: |
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|
1676 message = string.Template(self.template).safe_substitute(kwd) |
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1677 else: |
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|
1678 message = self.template |
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|
1679 log_message = message + " (%0.3f ms)" % (self.elapsed * 1000) |
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|
1680 return log_message |
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1681 |
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1682 @property |
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1683 def elapsed(self): |
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1684 return (time.time() - self.begin) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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1685 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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1686 |
4f3585e2f14b
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1687 if __name__ == '__main__': |
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1688 import doctest |
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1689 doctest.testmod(sys.modules[__name__], verbose=False) |