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comparison planemo/lib/python3.7/site-packages/galaxy/tool_util/parser/stdio.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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0:d30785e31577 1:56ad4e20f292
1 class StdioErrorLevel(object):
2 """
3 These determine stdio-based error levels from matching on regular expressions
4 and exit codes. They are meant to be used comparatively, such as showing
5 that warning < fatal. This is really meant to just be an enum.
6 """
7 NO_ERROR = 0
8 LOG = 1
9 QC = 1.1
10 WARNING = 2
11 FATAL = 3
12 FATAL_OOM = 4
13 MAX = 4
14 descs = {
15 NO_ERROR: 'No error',
16 LOG: 'Log',
17 QC: 'QC',
18 WARNING: 'Warning',
19 FATAL: 'Fatal error',
20 FATAL_OOM: 'Out of memory error',
21 }
22
23 @staticmethod
24 def desc(error_level):
25 err_msg = "Unknown error"
26 if error_level > 0 and error_level <= StdioErrorLevel.MAX:
27 err_msg = StdioErrorLevel.descs[error_level]
28 return err_msg
29
30
31 class ToolStdioExitCode(object):
32 """
33 This is a container for the <stdio> element's <exit_code> subelement.
34 The exit_code element has a range of exit codes and the error level.
35 """
36
37 def __init__(self, as_dict=None):
38 as_dict = as_dict or {}
39 self.range_start = as_dict.get("range_start", float("-inf"))
40 self.range_end = as_dict.get("range_end", float("inf"))
41 self.error_level = as_dict.get("error_level", StdioErrorLevel.FATAL)
42 self.desc = as_dict.get("desc", "")
43
44 def to_dict(self):
45 return {
46 "class": "ToolStdioExitCode",
47 "range_start": self.range_start,
48 "range_end": self.range_end,
49 "error_level": self.error_level,
50 "desc": self.desc,
51 }
52
53
54 class ToolStdioRegex(object):
55 """
56 This is a container for the <stdio> element's regex subelement.
57 The regex subelement has a "match" attribute, a "sources"
58 attribute that contains "output" and/or "error", and a "level"
59 attribute that contains "warning" or "fatal".
60 """
61
62 def __init__(self, as_dict=None):
63 as_dict = as_dict or {}
64 self.match = as_dict.get("match", "")
65 self.stdout_match = as_dict.get("stdout_match", False)
66 self.stderr_match = as_dict.get("stderr_match", False)
67 self.error_level = as_dict.get("error_level", StdioErrorLevel.FATAL)
68 self.desc = as_dict.get("desc", "")
69
70 def to_dict(self):
71 return {
72 "class": "ToolStdioRegex",
73 "match": self.match,
74 "stdout_match": self.stdout_match,
75 "stderr_match": self.stderr_match,
76 "error_level": self.error_level,
77 "desc": self.desc,
78 }
79
80
81 def error_on_exit_code(out_of_memory_exit_code=None):
82 exit_codes = []
83
84 if out_of_memory_exit_code:
85 exit_code_oom = ToolStdioExitCode()
86 exit_code_oom.range_start = int(out_of_memory_exit_code)
87 exit_code_oom.range_end = int(out_of_memory_exit_code)
88 _set_oom(exit_code_oom)
89 exit_codes.append(exit_code_oom)
90
91 exit_code_lower = ToolStdioExitCode()
92 exit_code_lower.range_start = float("-inf")
93 exit_code_lower.range_end = -1
94 _set_fatal(exit_code_lower)
95 exit_codes.append(exit_code_lower)
96 exit_code_high = ToolStdioExitCode()
97 exit_code_high.range_start = 1
98 exit_code_high.range_end = float("inf")
99 _set_fatal(exit_code_high)
100 exit_codes.append(exit_code_high)
101 return exit_codes, []
102
103
104 def aggressive_error_checks():
105 exit_codes, _ = error_on_exit_code()
106 # these regexes are processed as case insensitive by default
107 regexes = [
108 _oom_regex("MemoryError"),
109 _oom_regex("std::bad_alloc"),
110 _oom_regex("java.lang.OutOfMemoryError"),
111 _oom_regex("Out of memory"),
112 _error_regex("exception:"),
113 _error_regex("error:")
114 ]
115 return exit_codes, regexes
116
117
118 def _oom_regex(match):
119 regex = ToolStdioRegex()
120 _set_oom(regex)
121 regex.match = match
122 regex.stdout_match = True
123 regex.stderr_match = True
124 return regex
125
126
127 def _error_regex(match):
128 regex = ToolStdioRegex()
129 _set_fatal(regex)
130 regex.match = match
131 regex.stdout_match = True
132 regex.stderr_match = True
133 return regex
134
135
136 def _set_oom(obj):
137 obj.error_level = StdioErrorLevel.FATAL_OOM
138
139
140 def _set_fatal(obj):
141 obj.error_level = StdioErrorLevel.FATAL