Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/schema_salad/sourceline.py @ 4:79f47841a781 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 from __future__ import absolute_import
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2
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3 import itertools
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4 import os
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5 import re
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6 import traceback
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7 from typing import (
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8 Any,
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9 AnyStr,
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10 Dict,
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11 List,
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12 MutableMapping,
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13 MutableSequence,
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14 Optional,
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15 Pattern,
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16 Tuple,
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17 Type,
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18 Union,
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19 )
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20
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21 import six
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22 from future.utils import raise_from
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23 from typing_extensions import Text # pylint: disable=unused-import
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24
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25 import ruamel.yaml
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26 from ruamel.yaml.comments import CommentedBase, CommentedMap, CommentedSeq
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27
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28 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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29
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30
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31 lineno_re = re.compile(u"^(.*?:[0-9]+:[0-9]+: )(( *)(.*))")
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32
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33
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34 def regex_chunk(lines, regex):
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35 # type: (List[str], Pattern[str]) -> List[List[str]]
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36 lst = list(itertools.dropwhile(lambda x: not regex.match(x), lines))
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37 arr = []
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38 while lst:
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39 ret = [lst[0]] + list(
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40 itertools.takewhile(lambda x: not regex.match(x), lst[1:])
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41 )
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42 arr.append(ret)
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43 lst = list(itertools.dropwhile(lambda x: not regex.match(x), lst[1:]))
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44 return arr
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45
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46
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47 def chunk_messages(message): # type: (str) -> List[Tuple[int, str]]
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48 file_regex = re.compile(r"^(.+:\d+:\d+:)(\s+)(.+)$")
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49 item_regex = re.compile(r"^\s*\*\s+")
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50 arr = []
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51 for chun in regex_chunk(message.splitlines(), file_regex):
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52 fst = chun[0]
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53 mat = file_regex.match(fst)
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54 if mat:
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55 place = mat.group(1)
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56 indent = len(mat.group(2))
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57
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58 lst = [mat.group(3)] + chun[1:]
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59 if [x for x in lst if item_regex.match(x)]:
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60 for item in regex_chunk(lst, item_regex):
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61 msg = re.sub(item_regex, "", "\n".join(item))
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62 arr.append((indent, place + " " + re.sub(r"[\n\s]+", " ", msg)))
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63 else:
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64 msg = re.sub(item_regex, "", "\n".join(lst))
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65 arr.append((indent, place + " " + re.sub(r"[\n\s]+", " ", msg)))
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66 return arr
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67
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68
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69 def reformat_yaml_exception_message(message): # type: (str) -> str
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70 line_regex = re.compile(r'^\s+in "(.+)", line (\d+), column (\d+)$')
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71 fname_regex = re.compile(r"^file://" + re.escape(os.getcwd()) + "/")
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72 msgs = message.splitlines()
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73 ret = []
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74
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75 if len(msgs) == 3:
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76 msgs = msgs[1:]
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77 nblanks = 0
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78 elif len(msgs) == 4:
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79 c_msg = msgs[0]
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80 match = line_regex.match(msgs[1])
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81 if match:
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82 c_file, c_line, c_column = match.groups()
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83 c_file = re.sub(fname_regex, "", c_file)
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84 ret.append("{}:{}:{}: {}".format(c_file, c_line, c_column, c_msg))
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85
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86 msgs = msgs[2:]
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87 nblanks = 2
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88
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89 p_msg = msgs[0]
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90 match = line_regex.match(msgs[1])
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91 if match:
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92 p_file, p_line, p_column = match.groups()
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93 p_file = re.sub(fname_regex, "", p_file)
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94 ret.append(
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95 "{}:{}:{}:{} {}".format(p_file, p_line, p_column, " " * nblanks, p_msg)
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96 )
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97 return "\n".join(ret)
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98
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99
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100 def _add_lc_filename(
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101 r, source
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102 ): # type: (ruamel.yaml.comments.CommentedBase, AnyStr) -> None
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103 if isinstance(r, ruamel.yaml.comments.CommentedBase):
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104 r.lc.filename = source
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105 if isinstance(r, MutableSequence):
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106 for d in r:
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107 _add_lc_filename(d, source)
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108 elif isinstance(r, MutableMapping):
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109 for d in six.itervalues(r):
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110 _add_lc_filename(d, source)
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111
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112
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113 def relname(source): # type: (Text) -> Text
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114 if source.startswith("file://"):
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115 source = source[7:]
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116 source = os.path.relpath(source)
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117 return source
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118
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119
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120 def add_lc_filename(
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121 r, source
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122 ): # type: (ruamel.yaml.comments.CommentedBase, Text) -> None
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123 _add_lc_filename(r, relname(source))
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124
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125
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126 def reflow_all(text, maxline=None): # type: (Text, Optional[int]) -> Text
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127 if maxline is None:
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128 maxline = int(os.environ.get("COLUMNS", "100"))
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129 maxno = 0
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130 for l in text.splitlines():
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131 g = lineno_re.match(l)
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132 if not g:
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133 continue
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134 maxno = max(maxno, len(g.group(1)))
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135 maxno_text = maxline - maxno
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136 msg = []
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137 for l in text.splitlines():
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138 g = lineno_re.match(l)
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139 if not g:
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140 msg.append(l)
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141 continue
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142 pre = g.group(1)
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143 reflowed = reflow(g.group(2), maxno_text, g.group(3)).splitlines()
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144 msg.extend([pre.ljust(maxno, " ") + r for r in reflowed])
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145 return "\n".join(msg)
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146
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147
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148 def reflow(text, maxline, shift=""): # type: (Text, int, Text) -> Text
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149 if maxline < 20:
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150 maxline = 20
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151 if len(text) > maxline:
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152 sp = text.rfind(" ", 0, maxline)
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153 if sp < 1:
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154 sp = text.find(" ", sp + 1)
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155 if sp == -1:
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156 sp = len(text)
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157 if sp < len(text):
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158 return "{}\n{}{}".format(
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159 text[0:sp], shift, reflow(text[sp + 1 :], maxline, shift)
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160 )
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161 return text
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162
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163
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164 def indent(
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165 v, nolead=False, shift=u" ", bullet=u" "
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166 ): # type: (Text, bool, Text, Text) -> Text
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167 if nolead:
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168 return v.splitlines()[0] + u"\n".join([shift + l for l in v.splitlines()[1:]])
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169 else:
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170
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171 def lineno(i, l): # type: (int, Text) -> Text
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172 r = lineno_re.match(l)
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173 if r is not None:
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174 return r.group(1) + (bullet if i == 0 else shift) + r.group(2)
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175 else:
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176 return (bullet if i == 0 else shift) + l
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177
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178 return u"\n".join([lineno(i, l) for i, l in enumerate(v.splitlines())])
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179
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180
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181 def bullets(textlist, bul): # type: (List[Text], Text) -> Text
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182 if len(textlist) == 1:
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183 return textlist[0]
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184 else:
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185 return "\n".join(indent(t, bullet=bul) for t in textlist)
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186
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187
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188 def strip_duplicated_lineno(text): # type: (Text) -> Text
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189 """Same as `strip_dup_lineno` but without reflow"""
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190 pre = None
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191 msg = []
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192 for l in text.splitlines():
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193 g = lineno_re.match(l)
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194 if not g:
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195 msg.append(l)
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196 continue
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197 elif g.group(1) != pre:
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198 msg.append(l)
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199 pre = g.group(1)
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200 else:
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201 msg.append(" " * len(g.group(1)) + g.group(2))
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202 return "\n".join(msg)
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203
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204
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205 def strip_dup_lineno(text, maxline=None): # type: (Text, Optional[int]) -> Text
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206 if maxline is None:
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207 maxline = int(os.environ.get("COLUMNS", "100"))
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208 pre = None
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209 msg = []
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210 maxno = 0
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211 for l in text.splitlines():
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212 g = lineno_re.match(l)
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213 if not g:
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214 continue
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215 maxno = max(maxno, len(g.group(1)))
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216
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217 for l in text.splitlines():
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218 g = lineno_re.match(l)
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219 if not g:
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220 msg.append(l)
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221 continue
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222 if g.group(1) != pre:
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223 shift = maxno + len(g.group(3))
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224 g2 = reflow(g.group(2), maxline - shift, " " * shift)
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225 pre = g.group(1)
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226 msg.append(pre + " " * (maxno - len(g.group(1))) + g2)
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227 else:
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228 g2 = reflow(g.group(2), maxline - maxno, " " * (maxno + len(g.group(3))))
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229 msg.append(" " * maxno + g2)
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230 return "\n".join(msg)
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231
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232
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233 def cmap(
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234 d, # type: Union[int, float, str, Text, Dict[Text, Any], List[Dict[Text, Any]]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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235 lc=None, # type: Optional[List[int]]
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236 fn=None, # type: Optional[Text]
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237 ): # type: (...) -> Union[int, float, str, Text, CommentedMap, CommentedSeq]
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238 if lc is None:
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239 lc = [0, 0, 0, 0]
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240 if fn is None:
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241 fn = "test"
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242
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243 if isinstance(d, CommentedMap):
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244 fn = d.lc.filename if hasattr(d.lc, "filename") else fn
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245 for k, v in six.iteritems(d):
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246 if d.lc.data is not None and k in d.lc.data:
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247 d[k] = cmap(v, lc=d.lc.data[k], fn=fn)
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248 else:
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249 d[k] = cmap(v, lc, fn=fn)
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250 return d
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251 if isinstance(d, CommentedSeq):
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252 fn = d.lc.filename if hasattr(d.lc, "filename") else fn
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253 for k2, v2 in enumerate(d):
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254 if d.lc.data is not None and k2 in d.lc.data:
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255 d[k2] = cmap(v2, lc=d.lc.data[k2], fn=fn)
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256 else:
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257 d[k2] = cmap(v2, lc, fn=fn)
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258 return d
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259 if isinstance(d, MutableMapping):
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260 cm = CommentedMap()
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261 for k in sorted(d.keys()):
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262 v = d[k]
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263 if isinstance(v, CommentedBase):
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264 uselc = [v.lc.line, v.lc.col, v.lc.line, v.lc.col]
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265 vfn = v.lc.filename if hasattr(v.lc, "filename") else fn
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266 else:
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267 uselc = lc
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268 vfn = fn
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269 cm[k] = cmap(v, lc=uselc, fn=vfn)
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270 cm.lc.add_kv_line_col(k, uselc)
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271 cm.lc.filename = fn
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272 return cm
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273 if isinstance(d, MutableSequence):
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274 cs = CommentedSeq()
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275 for k3, v3 in enumerate(d):
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276 if isinstance(v3, CommentedBase):
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277 uselc = [v3.lc.line, v3.lc.col, v3.lc.line, v3.lc.col]
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278 vfn = v3.lc.filename if hasattr(v3.lc, "filename") else fn
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279 else:
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280 uselc = lc
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281 vfn = fn
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282 cs.append(cmap(v3, lc=uselc, fn=vfn))
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283 cs.lc.add_kv_line_col(k3, uselc)
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284 cs.lc.filename = fn
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285 return cs
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286 else:
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287 return d
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288
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289
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290 class SourceLine(object):
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291 def __init__(
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292 self,
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293 item, # type: Any
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294 key=None, # type: Optional[Any]
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295 raise_type=six.text_type, # type: Union[Type[six.text_type], Type[Exception]]
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296 include_traceback=False, # type: bool
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297 ): # type: (...) -> None
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298 self.item = item
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299 self.key = key
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300 self.raise_type = raise_type
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301 self.include_traceback = include_traceback
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302
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303 def __enter__(self): # type: () -> SourceLine
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304 return self
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305
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306 def __exit__(
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307 self,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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308 exc_type, # type: Any
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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309 exc_value, # type: Any
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310 tb, # type: Any
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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311 ): # type: (...) -> None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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312 if not exc_value:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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313 return
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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314 if self.include_traceback and six.PY2:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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315 # Python2 doesn't actually have chained exceptions, so
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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316 # fake it by injecting the backtrace into the message.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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317 raise_from(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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318 self.makeError(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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319 "\n".join(traceback.format_exception(exc_type, exc_value, tb))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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320 ),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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321 exc_value,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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322 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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323 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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324 raise_from(self.makeError(six.text_type(exc_value)), exc_value)
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325
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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326 def file(self): # type: () -> Optional[Text]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
327 if hasattr(self.item, "lc") and hasattr(self.item.lc, "filename"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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328 return Text(self.item.lc.filename)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
329 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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330 return None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
331
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
332 def start(self): # type: () -> Optional[Tuple[int, int]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
333 if self.file() is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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334 return None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
335 elif (
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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336 self.key is None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
337 or self.item.lc.data is None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
338 or self.key not in self.item.lc.data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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339 ):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
340 return ((self.item.lc.line or 0) + 1, (self.item.lc.col or 0) + 1)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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341 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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342 return (
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
343 (self.item.lc.data[self.key][0] or 0) + 1,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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344 (self.item.lc.data[self.key][1] or 0) + 1,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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345 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
346
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
347 def end(self): # type: () -> Optional[Tuple[int, int]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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348 return None
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349
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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350 def makeLead(self): # type: () -> Text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
351 if self.file():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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352 lcol = self.start()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
353 line, col = lcol if lcol else ("", "")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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354 return "{}:{}:{}:".format(self.file(), line, col)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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355 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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356 return ""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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357
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358 def makeError(self, msg): # type: (Text) -> Any
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
359 if not isinstance(self.item, ruamel.yaml.comments.CommentedBase):
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360 return self.raise_type(msg)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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361 errs = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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362 lead = self.makeLead()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
363 for m in msg.splitlines():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
364 if bool(lineno_re.match(m)):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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365 errs.append(m)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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366 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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367 errs.append("{} {}".format(lead, m))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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368 return self.raise_type("\n".join(errs))