full test coverage for command linter

- info->warn for deprecated interpreter attribute
- add error for empty command text
- fix check for TODO in command

lib/galaxy/tool_util/linters/command.py

@@ -24,7 +24,9 @@ def lint_command(tool_xml, lint_ctx):
         return
 
     command = get_command(tool_xml)
-    if "TODO" in command:
+    if command.text is None:
+        lint_ctx.error("Command is empty.", line=root_line, xpath=root_path)
+    elif "TODO" in command.text:
         lint_ctx.warn("Command template contains TODO text.", line=command.sourceline, xpath=tool_xml.getpath(command))
 
     command_attrib = command.attrib
@@ -41,7 +43,7 @@ def lint_command(tool_xml, lint_ctx):
     if interpreter_type:
         interpreter_info = f" with interpreter of type [{interpreter_type}]"
     if interpreter_type:
-        lint_ctx.info("Command uses deprecated 'interpreter' attribute.", line=command.sourceline, xpath=tool_xml.getpath(command))
+        lint_ctx.warn("Command uses deprecated 'interpreter' attribute.", line=command.sourceline, xpath=tool_xml.getpath(command))
     lint_ctx.info(f"Tool contains a command{interpreter_info}.", line=command.sourceline, xpath=tool_xml.getpath(command))
 
 

test/unit/tool_util/test_tool_linters.py

@@ -5,6 +5,7 @@ import pytest
 from galaxy.tool_util.lint import LintContext
 from galaxy.tool_util.linters import (
     citations,
+    command,
     general,
     help,
     inputs,
@@ -45,6 +46,31 @@ CITATIONS_VALID = """
     </citations>
 </tool>
 """
+
+# tests tool xml for command linter
+COMMAND_MULTIPLE = """
+<tool>
+    <command/>
+    <command/>
+</tool>
+"""
+COMMAND_MISSING = """
+<tool/>
+"""
+COMMAND_TODO = """
+<tool>
+    <command>
+        ## TODO
+    </command>
+</tool>
+"""
+COMMAND_DETECT_ERRORS_INTERPRETER = """
+<tool>
+    <command detect_errors="nonsense" interpreter="python"/>
+</tool>
+"""
+
+
 # tests tool xml for general linter
 GENERAL_MISSING_TOOL_ID_NAME_VERSION = """
 <tool profile="2109">
@@ -513,6 +539,34 @@ TESTS = [
             'Found 1 likely valid citations.' in x.valid_messages
             and len(x.info_messages) == 0 and len(x.valid_messages) == 1 and len(x.warn_messages) == 0 and len(x.error_messages) == 0
     ),
+    (
+        COMMAND_MULTIPLE, command.lint_command,
+        lambda x:
+            'More than one command tag found, behavior undefined.' in x.error_messages
+            and len(x.info_messages) == 0 and len(x.valid_messages) == 0 and len(x.warn_messages) == 0 and len(x.error_messages) == 1
+    ),
+    (
+        COMMAND_MISSING, command.lint_command,
+        lambda x:
+            'No command tag found, must specify a command template to execute.' in x.error_messages
+            and len(x.info_messages) == 0 and len(x.valid_messages) == 0 and len(x.warn_messages) == 0 and len(x.error_messages) == 1
+    ),
+    (
+        COMMAND_TODO, command.lint_command,
+        lambda x:
+            'Tool contains a command.' in x.info_messages
+            and 'Command template contains TODO text.' in x.warn_messages
+            and len(x.info_messages) == 1 and len(x.valid_messages) == 0 and len(x.warn_messages) == 1 and len(x.error_messages) == 0
+    ),
+    (
+        COMMAND_DETECT_ERRORS_INTERPRETER, command.lint_command,
+        lambda x:
+            "Command uses deprecated 'interpreter' attribute." in x.warn_messages
+            and 'Tool contains a command with interpreter of type [python].' in x.info_messages
+            and 'Unknown detect_errors attribute [nonsense]' in x.warn_messages
+            and 'Command is empty.' in x.error_messages
+            and len(x.info_messages) == 1 and len(x.valid_messages) == 0 and len(x.warn_messages) == 2 and len(x.error_messages) == 1
+    ),
     (
         GENERAL_MISSING_TOOL_ID_NAME_VERSION, general.lint_general,
         lambda x:
@@ -794,6 +848,10 @@ TEST_IDS = [
     'citations: absent',
     'citations: errors',
     'citations: valid',
+    'command: multiple',
+    'command: missing',
+    'command: todo',
+    'command: detect_errors and interpreter',
     'general: missing tool id, name, version; invalid profile',
     'general: whitespace in version, id, name',
     'general: requirement without version',