fix datatypes linter

better consideration of auto and inputs

Author: bernt-matthias

lib/galaxy/tool_util/linters/datatypes.py

@@ -6,6 +6,8 @@
     Union,
 )
 
+from packaging.version import Version
+
 # from galaxy import config
 from galaxy.tool_util.lint import Linter
 from galaxy.util import (
@@ -68,6 +70,7 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
         tool_xml = getattr(tool_source, "xml_tree", None)
         if not tool_xml:
             return
+        profile = tool_source.parse_profile()
         # get Galaxy built-in dataypes
         datatypes = _parse_datatypes(DATATYPES_CONF)
         # add custom tool data types
@@ -84,15 +87,19 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
                 formats = elem.get(attrib, "").split(",")
                 # Certain elements (e.g. `data`) can only have one format. This
                 # is checked separately by linting against the XSD.
-                if "auto" in formats:
-                    if elem.tag == "param":
+                if elem.tag == "param":
+                    if any(format in ["auto", "input"] for format in formats):
                         lint_ctx.error(
-                            "Format [auto] can not be used for tool or tool test inputs",
+                            "Invalid format (auto or input) in tool or tool test inputs",
                             linter=cls.name(),
                             node=elem,
                         )
-                    continue
+                        continue
                 for format in formats:
+                    if Version(str(profile)) <= Version("16.04") and format == "input":
+                        continue
+                    if format == "auto":
+                        continue
                     if format not in datatypes:
                         lint_ctx.error(
                             f"Unknown datatype [{format}] used in {elem.tag} element",

lib/galaxy/tool_util/linters/tests.py

@@ -250,7 +250,7 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
                 name = name.split("|")[-1]
                 xpaths = [f"@name='{name}'", f"@argument='{name}'", f"@argument='-{name}'", f"@argument='--{name}'"]
                 if "_" in name:
-                    xpaths += [f"@argument='-{name.replace('_', '-')}'", f"@argument='--{name.replace('_', '-')}'"]
+                    xpaths += [f"@argument='{name.replace('_', '-')}'", f"@argument='-{name.replace('_', '-')}'", f"@argument='--{name.replace('_', '-')}'"]
                 found = False
                 for xp in xpaths:
                     inxpath = f".//inputs//param[{xp}]"

test/unit/tool_util/test_tool_linters.py

@@ -2205,7 +2205,7 @@ def test_valid_datatypes(lint_ctx):
     assert "Unknown datatype [collection_format] used in collection" in lint_ctx.error_messages
     assert "Unknown datatype [invalid] used in param" in lint_ctx.error_messages
     assert "Unknown datatype [invalid] used in discover_datasets" in lint_ctx.error_messages
-    assert "Format [auto] can not be used for tool or tool test inputs" in lint_ctx.error_messages  # 2x
+    assert "Invalid format (auto or input) in tool or tool test inputs" in lint_ctx.error_messages  # 2x
     assert len(lint_ctx.error_messages) == 8