diff env/lib/python3.9/site-packages/galaxy/tool_util/linters/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/linters/stdio.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,43 @@
+"""This module contains a linting functions for tool error detection."""
+from .command import get_command
+
+
+def lint_stdio(tool_source, lint_ctx):
+    tool_xml = getattr(tool_source, "xml_tree", None)
+    stdios = tool_xml.findall("./stdio") if tool_xml else []
+
+    if not stdios:
+        command = get_command(tool_xml) if tool_xml else None
+        if command is None or not command.get("detect_errors"):
+            if tool_source.parse_profile() <= "16.01":
+                lint_ctx.info("No stdio definition found, tool indicates error conditions with output written to stderr.")
+            else:
+                lint_ctx.info("No stdio definition found, tool indicates error conditions with non-zero exit codes.")
+        return
+
+    if len(stdios) > 1:
+        lint_ctx.error("More than one stdio tag found, behavior undefined.")
+        return
+
+    stdio = stdios[0]
+    for child in list(stdio):
+        if child.tag == "regex":
+            _lint_regex(child, lint_ctx)
+        elif child.tag == "exit_code":
+            _lint_exit_code(child, lint_ctx)
+        else:
+            message = "Unknown stdio child tag discovered [%s]. "
+            message += "Valid options are exit_code and regex."
+            lint_ctx.warn(message % child.tag)
+
+
+def _lint_exit_code(child, lint_ctx):
+    for key in child.attrib.keys():
+        if key not in ["description", "level", "range"]:
+            lint_ctx.warn("Unknown attribute [%s] encountered on exit_code tag." % key)
+
+
+def _lint_regex(child, lint_ctx):
+    for key in child.attrib.keys():
+        if key not in ["description", "level", "match", "source"]:
+            lint_ctx.warn("Unknown attribute [%s] encountered on regex tag." % key)