Merge pull request #16684 from davelopez/tool_linter_validate_regex

Include `regex` when linting validators

lib/galaxy/tool_util/lint.py

@@ -83,10 +83,13 @@ def __init__(self, level: str, message: str, **kwargs):
     def __eq__(self, other) -> bool:
         """
         add equal operator to easy lookup of a message in a
-        List[LintMessage] which is usefull in tests
+        List[LintMessage] which is useful in tests.
+
+        If the other object is a string, it is loosely checked if the
+        string is contained in the message.
         """
         if isinstance(other, str):
-            return self.message == other
+            return other in self.message
         if isinstance(other, LintMessage):
             return self.message == other.message
         return False

lib/galaxy/tool_util/linters/inputs.py

@@ -1,4 +1,5 @@
 """This module contains a linting functions for tool inputs."""
+import ast
 import re
 from typing import TYPE_CHECKING
 
@@ -395,14 +396,17 @@ def lint_inputs(tool_source: "ToolSource", lint_ctx: "LintContext"):
                         f"Parameter [{param_name}]: attribute '{attrib}' is incompatible with validator of type '{vtype}'",
                         node=validator,
                     )
-            if vtype == "expression":
+            if vtype in ["expression", "regex"]:
                 if validator.text is None:
                     lint_ctx.error(
-                        f"Parameter [{param_name}]: expression validators are expected to contain text", node=validator
+                        f"Parameter [{param_name}]: {vtype} validators are expected to contain text", node=validator
                     )
                 else:
                     try:
-                        re.compile(validator.text)
+                        if vtype == "regex":
+                            re.compile(validator.text)
+                        else:
+                            ast.parse(validator.text, mode="eval")
                     except Exception as e:
                         lint_ctx.error(
                             f"Parameter [{param_name}]: '{validator.text}' is no valid regular expression: {str(e)}",

test/unit/tool_util/test_tool_linters.py

@@ -410,7 +410,9 @@
             <validator type="in_range">TEXT</validator>
             <validator type="regex" filename="blah"/>
             <validator type="expression"/>
-            <validator type="expression">[</validator>
+            <validator type="regex">[</validator>
+            <validator type="expression">(</validator>
+            <validator type="expression">value and "," not in value</validator>
             <validator type="value_in_data_table"/>
         </param>
         <param name="another_param_name" type="data" format="bed">
@@ -1384,10 +1386,12 @@ def test_inputs_validator_incompatibilities(lint_ctx):
         in lint_ctx.error_messages
     )
     assert "Parameter [param_name]: expression validators are expected to contain text" in lint_ctx.error_messages
+    assert "Parameter [param_name]: regex validators are expected to contain text" in lint_ctx.error_messages
     assert (
         "Parameter [param_name]: '[' is no valid regular expression: unterminated character set at position 0"
         in lint_ctx.error_messages
     )
+    assert "Parameter [param_name]: '(' is no valid regular expression" in lint_ctx.error_messages
     assert (
         "Parameter [another_param_name]: 'metadata' validators need to define the 'check' or 'skip' attribute(s)"
         in lint_ctx.error_messages
@@ -1407,7 +1411,7 @@ def test_inputs_validator_incompatibilities(lint_ctx):
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert len(lint_ctx.warn_messages) == 1
-    assert len(lint_ctx.error_messages) == 9
+    assert len(lint_ctx.error_messages) == 11
 
 
 def test_inputs_validator_correct(lint_ctx):