split command linter

lib/galaxy/tool_util/linters/command.py

@@ -1,54 +1,88 @@
-"""This module contains a linting function for a tool's command description.
+"""This module contains linters for a tool's command description.
 
 A command description describes how to build the command-line to execute
 from supplied inputs.
 """
+from typing import TYPE_CHECKING
 
+from galaxy.tool_util.lint import Linter
 
-def lint_command(tool_xml, lint_ctx):
-    """Ensure tool contains exactly one command and check attributes."""
-    root = tool_xml.find("./command")
-    if root is None:
-        root = tool_xml.getroot()
-
-    commands = tool_xml.findall("./command")
-    if len(commands) > 1:
-        lint_ctx.error("More than one command tag found, behavior undefined.", node=commands[1])
-        return
-
-    if len(commands) == 0:
-        lint_ctx.error("No command tag found, must specify a command template to execute.", node=root)
-        return
-
-    command = get_command(tool_xml)
-    if command.text is None:
-        lint_ctx.error("Command is empty.", node=root)
-    elif "TODO" in command.text:
-        lint_ctx.warn("Command template contains TODO text.", node=command)
-
-    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(f"Unknown detect_errors attribute [{detect_errors}]", node=command)
-
-    interpreter_info = ""
-    if interpreter_type:
-        interpreter_info = f" with interpreter of type [{interpreter_type}]"
-    if interpreter_type:
-        lint_ctx.warn("Command uses deprecated 'interpreter' attribute.", node=command)
-    lint_ctx.info(f"Tool contains a command{interpreter_info}.", node=command)
-
-
-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
+if TYPE_CHECKING:
+    from galaxy.tool_util.lint import LintContext
+    from galaxy.tool_util.parser.interface import ToolSource
+
+
+class CommandMultiple(Linter):
+    @classmethod
+    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
+        tool_xml = getattr(tool_source, "xml_tree", None)
+        if not tool_xml:
+            return
+        commands = tool_xml.findall("./command")
+        if len(commands) > 1:
+            lint_ctx.error("More than one command tag found, behavior undefined.", node=commands[1])
+
+
+class CommandMissing(Linter):
+    @classmethod
+    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
+        tool_xml = getattr(tool_source, "xml_tree", None)
+        if not tool_xml:
+            return
+        root = tool_xml.find("./command") or tool_xml.getroot()
+        command = tool_xml.find("./command")
+        if command is None:
+            lint_ctx.error("No command tag found, must specify a command template to execute.", node=root)
+
+
+class CommandEmpty(Linter):
+    @classmethod
+    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
+        tool_xml = getattr(tool_source, "xml_tree", None)
+        if not tool_xml:
+            return
+        root = tool_xml.find("./command") or tool_xml.getroot()
+        command = tool_xml.find("./command")
+        if command is not None and command.text is None:
+            lint_ctx.error("Command is empty.", node=root)
+
+
+class CommandTODO(Linter):
+    @classmethod
+    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
+        tool_xml = getattr(tool_source, "xml_tree", None)
+        if not tool_xml:
+            return
+        command = tool_xml.find("./command")
+        if command is not None and command.text is not None and "TODO" in command.text:
+            lint_ctx.warn("Command template contains TODO text.", node=command)
+
+
+class CommandInterpreterDeprecated(Linter):
+    @classmethod
+    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
+        tool_xml = getattr(tool_source, "xml_tree", None)
+        if not tool_xml:
+            return
+        command = tool_xml.find("./command")
+        if command is None:
+            return
+        interpreter_type = command.attrib.get("interpreter", None)
+        if interpreter_type is not None:
+            lint_ctx.warn("Command uses deprecated 'interpreter' attribute.", node=command)
+
+
+class CommandInfo(Linter):
+    @classmethod
+    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
+        tool_xml = getattr(tool_source, "xml_tree", None)
+        if not tool_xml:
+            return
+        command = tool_xml.find("./command")
+        if command is None:
+            return
+        interpreter_type = command.attrib.get("interpreter", None)
+        interpreter_info = ""
+        if interpreter_type:
+            interpreter_info = f" with interpreter of type [{interpreter_type}]"
+        lint_ctx.info(f"Tool contains a command{interpreter_info}.", node=command)

test/unit/tool_util/test_tool_linters.py

@@ -62,8 +62,8 @@
 # tests tool xml for command linter
 COMMAND_MULTIPLE = """
 <tool>
-    <command/>
-    <command/>
+    <command>ls</command>
+    <command>df</command>
 </tool>
 """
 COMMAND_MISSING = """
@@ -957,35 +957,39 @@ def test_citations_valid(lint_ctx):
 
 
 def test_command_multiple(lint_ctx):
-    tool_xml_tree = get_xml_tree(COMMAND_MULTIPLE)
-    run_lint_module(lint_ctx, command, tool_xml_tree)
-    assert "More than one command tag found, behavior undefined." in lint_ctx.error_messages
-    assert len(lint_ctx.error_messages) == 1
-    assert not lint_ctx.info_messages
+    tool_source = get_xml_tool_source(COMMAND_MULTIPLE)
+    run_lint_module(lint_ctx, command, tool_source)
+    assert lint_ctx.error_messages == ["More than one command tag found, behavior undefined."]
+    assert lint_ctx.info_messages == ["Tool contains a command."]
     assert not lint_ctx.valid_messages
     assert not lint_ctx.warn_messages
 
 
 def test_command_missing(lint_ctx):
-    tool_xml_tree = get_xml_tree(COMMAND_MISSING)
-    run_lint_module(lint_ctx, command, tool_xml_tree)
-    assert "No command tag found, must specify a command template to execute." in lint_ctx.error_messages
+    tool_source = get_xml_tool_source(COMMAND_MISSING)
+    run_lint_module(lint_ctx, command, tool_source)
+    assert lint_ctx.error_messages == ["No command tag found, must specify a command template to execute."]
+    assert not lint_ctx.info_messages
+    assert not lint_ctx.valid_messages
+    assert not lint_ctx.warn_messages
 
 
 def test_command_todo(lint_ctx):
-    tool_xml_tree = get_xml_tree(COMMAND_TODO)
-    run_lint_module(lint_ctx, command, tool_xml_tree)
-    assert "Tool contains a command." in lint_ctx.info_messages
-    assert "Command template contains TODO text." in lint_ctx.warn_messages
+    tool_source = get_xml_tool_source(COMMAND_TODO)
+    run_lint_module(lint_ctx, command, tool_source)
+    assert not lint_ctx.error_messages
+    assert lint_ctx.info_messages == ["Tool contains a command."]
+    assert lint_ctx.warn_messages == ["Command template contains TODO text."]
+    assert not lint_ctx.valid_messages
 
 
 def test_command_detect_errors_interpreter(lint_ctx):
-    tool_xml_tree = get_xml_tree(COMMAND_DETECT_ERRORS_INTERPRETER)
-    run_lint_module(lint_ctx, command, tool_xml_tree)
-    assert "Command uses deprecated 'interpreter' attribute." in lint_ctx.warn_messages
-    assert "Tool contains a command with interpreter of type [python]." in lint_ctx.info_messages
-    assert "Unknown detect_errors attribute [nonsense]" in lint_ctx.warn_messages
-    assert "Command is empty." in lint_ctx.error_messages
+    tool_source = get_xml_tool_source(COMMAND_DETECT_ERRORS_INTERPRETER)
+    run_lint_module(lint_ctx, command, tool_source)
+    assert lint_ctx.error_messages == ["Command is empty."]
+    assert lint_ctx.warn_messages == ["Command uses deprecated 'interpreter' attribute."]
+    assert lint_ctx.info_messages == ["Tool contains a command with interpreter of type [python]."]
+    assert not lint_ctx.valid_messages
 
 
 def test_general_missing_tool_id_name_version(lint_ctx):