diff env/lib/python3.9/site-packages/galaxy/tool_util/parser/stdio.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/galaxy/tool_util/parser/stdio.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,141 @@
+class StdioErrorLevel:
+    """
+    These determine stdio-based error levels from matching on regular expressions
+    and exit codes. They are meant to be used comparatively, such as showing
+    that warning < fatal. This is really meant to just be an enum.
+    """
+    NO_ERROR = 0
+    LOG = 1
+    QC = 1.1
+    WARNING = 2
+    FATAL = 3
+    FATAL_OOM = 4
+    MAX = 4
+    descs = {
+        NO_ERROR: 'No error',
+        LOG: 'Log',
+        QC: 'QC',
+        WARNING: 'Warning',
+        FATAL: 'Fatal error',
+        FATAL_OOM: 'Out of memory error',
+    }
+
+    @staticmethod
+    def desc(error_level):
+        err_msg = "Unknown error"
+        if error_level > 0 and error_level <= StdioErrorLevel.MAX:
+            err_msg = StdioErrorLevel.descs[error_level]
+        return err_msg
+
+
+class ToolStdioExitCode:
+    """
+    This is a container for the <stdio> element's <exit_code> subelement.
+    The exit_code element has a range of exit codes and the error level.
+    """
+
+    def __init__(self, as_dict=None):
+        as_dict = as_dict or {}
+        self.range_start = as_dict.get("range_start", float("-inf"))
+        self.range_end = as_dict.get("range_end", float("inf"))
+        self.error_level = as_dict.get("error_level", StdioErrorLevel.FATAL)
+        self.desc = as_dict.get("desc", "")
+
+    def to_dict(self):
+        return {
+            "class": "ToolStdioExitCode",
+            "range_start": self.range_start,
+            "range_end": self.range_end,
+            "error_level": self.error_level,
+            "desc": self.desc,
+        }
+
+
+class ToolStdioRegex:
+    """
+    This is a container for the <stdio> element's regex subelement.
+    The regex subelement has a "match" attribute, a "sources"
+    attribute that contains "output" and/or "error", and a "level"
+    attribute that contains "warning" or "fatal".
+    """
+
+    def __init__(self, as_dict=None):
+        as_dict = as_dict or {}
+        self.match = as_dict.get("match", "")
+        self.stdout_match = as_dict.get("stdout_match", False)
+        self.stderr_match = as_dict.get("stderr_match", False)
+        self.error_level = as_dict.get("error_level", StdioErrorLevel.FATAL)
+        self.desc = as_dict.get("desc", "")
+
+    def to_dict(self):
+        return {
+            "class": "ToolStdioRegex",
+            "match": self.match,
+            "stdout_match": self.stdout_match,
+            "stderr_match": self.stderr_match,
+            "error_level": self.error_level,
+            "desc": self.desc,
+        }
+
+
+def error_on_exit_code(out_of_memory_exit_code=None):
+    exit_codes = []
+
+    if out_of_memory_exit_code:
+        exit_code_oom = ToolStdioExitCode()
+        exit_code_oom.range_start = int(out_of_memory_exit_code)
+        exit_code_oom.range_end = int(out_of_memory_exit_code)
+        _set_oom(exit_code_oom)
+        exit_codes.append(exit_code_oom)
+
+    exit_code_lower = ToolStdioExitCode()
+    exit_code_lower.range_start = float("-inf")
+    exit_code_lower.range_end = -1
+    _set_fatal(exit_code_lower)
+    exit_codes.append(exit_code_lower)
+    exit_code_high = ToolStdioExitCode()
+    exit_code_high.range_start = 1
+    exit_code_high.range_end = float("inf")
+    _set_fatal(exit_code_high)
+    exit_codes.append(exit_code_high)
+    return exit_codes, []
+
+
+def aggressive_error_checks():
+    exit_codes, _ = error_on_exit_code()
+    # these regexes are processed as case insensitive by default
+    regexes = [
+        _oom_regex("MemoryError"),
+        _oom_regex("std::bad_alloc"),
+        _oom_regex("java.lang.OutOfMemoryError"),
+        _oom_regex("Out of memory"),
+        _error_regex("exception:"),
+        _error_regex("error:")
+    ]
+    return exit_codes, regexes
+
+
+def _oom_regex(match):
+    regex = ToolStdioRegex()
+    _set_oom(regex)
+    regex.match = match
+    regex.stdout_match = True
+    regex.stderr_match = True
+    return regex
+
+
+def _error_regex(match):
+    regex = ToolStdioRegex()
+    _set_fatal(regex)
+    regex.match = match
+    regex.stdout_match = True
+    regex.stderr_match = True
+    return regex
+
+
+def _set_oom(obj):
+    obj.error_level = StdioErrorLevel.FATAL_OOM
+
+
+def _set_fatal(obj):
+    obj.error_level = StdioErrorLevel.FATAL