diff planemo/lib/python3.7/site-packages/galaxy/tool_util/linters/command.py @ 1:56ad4e20f292 draft

"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/planemo/lib/python3.7/site-packages/galaxy/tool_util/linters/command.py	Fri Jul 31 00:32:28 2020 -0400
@@ -0,0 +1,49 @@
+"""This module contains a linting function for a tool's command description.
+
+A command description describes how to build the command-line to execute
+from supplied inputs.
+"""
+
+
+def lint_command(tool_xml, lint_ctx):
+    """Ensure tool contains exactly one command and check attributes."""
+    root = tool_xml.getroot()
+    commands = root.findall("command")
+    if len(commands) > 1:
+        lint_ctx.error("More than one command tag found, behavior undefined.")
+        return
+
+    if len(commands) == 0:
+        lint_ctx.error("No command tag found, must specify a command template to execute.")
+        return
+
+    command = get_command(tool_xml)
+    if "TODO" in command:
+        lint_ctx.warn("Command template contains TODO text.")
+
+    command_attrib = command.attrib
+    interpreter_type = None
+    for key, value in command_attrib.items():
+        if key == "interpreter":
+            interpreter_type = value
+        elif key == "detect_errors":
+            detect_errors = value
+            if detect_errors not in ["default", "exit_code", "aggressive"]:
+                lint_ctx.warn("Unknown detect_errors attribute [%s]" % detect_errors)
+
+    interpreter_info = ""
+    if interpreter_type:
+        interpreter_info = " with interpreter of type [%s]" % interpreter_type
+    if interpreter_type:
+        lint_ctx.info("Command uses deprecated 'interpreter' attribute.")
+    lint_ctx.info("Tool contains a command%s." % interpreter_info)
+
+
+def get_command(tool_xml):
+    """Get command XML element from supplied XML root."""
+    root = tool_xml.getroot()
+    commands = root.findall("command")
+    command = None
+    if len(commands) == 1:
+        command = commands[0]
+    return command