Unverified Commit e42da374 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #19707 from bernt-matthias/set-linter 

[24.2] add missing linter name argument to linter report function calls
parents 5fcc4585 6f92f755

lib/galaxy/tool_util/linters/cwl.py

+11 −9
Original line number Diff line number Diff line
@@ -20,7 +20,7 @@ class CWLValid(Linter): 
            schema_loader.process_definition(raw_reference)

        except Exception:

            return

        lint_ctx.info("CWL appears to be valid.")

        lint_ctx.info("CWL appears to be valid.", linter=cls.name())





class CWLInValid(Linter):
@@ -30,7 +30,7 @@ class CWLInValid(Linter): 
        try:

            schema_loader.process_definition(raw_reference)

        except Exception as e:

            lint_ctx.error(f"Failed to valdiate CWL artifact: {e}")

            lint_ctx.error(f"Failed to valdiate CWL artifact: {e}", linter=cls.name())





class CWLVersionMissing(Linter):
@@ -39,7 +39,7 @@ class CWLVersionMissing(Linter): 
        raw_reference = schema_loader.raw_process_reference(tool_source.source_path)

        cwl_version = raw_reference.process_object.get("cwlVersion", None)

        if cwl_version is None:

            lint_ctx.error("CWL file does not contain a 'cwlVersion'")

            lint_ctx.error("CWL file does not contain a 'cwlVersion'", linter=cls.name())





class CWLVersionUnknown(Linter):
@@ -48,7 +48,9 @@ class CWLVersionUnknown(Linter): 
        raw_reference = schema_loader.raw_process_reference(tool_source.source_path)

        cwl_version = raw_reference.process_object.get("cwlVersion", None)

        if cwl_version not in ["v1.0"]:

            lint_ctx.warn(f"CWL version [{cwl_version}] is unknown, we recommend the v1.0 the stable release.")

            lint_ctx.warn(

                f"CWL version [{cwl_version}] is unknown, we recommend the v1.0 the stable release.", linter=cls.name()

            )





class CWLVersionGood(Linter):
@@ -57,7 +59,7 @@ class CWLVersionGood(Linter): 
        raw_reference = schema_loader.raw_process_reference(tool_source.source_path)

        cwl_version = raw_reference.process_object.get("cwlVersion", None)

        if cwl_version in ["v1.0"]:

            lint_ctx.info(f"Modern CWL version [{cwl_version}].")

            lint_ctx.info(f"Modern CWL version [{cwl_version}].", linter=cls.name())





class CWLDockerMissing(Linter):
@@ -65,7 +67,7 @@ class CWLDockerMissing(Linter): 
    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):

        _, containers, *_ = tool_source.parse_requirements_and_containers()

        if len(containers) == 0:

            lint_ctx.warn("Tool does not specify a DockerPull source.")

            lint_ctx.warn("Tool does not specify a DockerPull source.", linter=cls.name())





class CWLDockerGood(Linter):
@@ -74,7 +76,7 @@ class CWLDockerGood(Linter): 
        _, containers, *_ = tool_source.parse_requirements_and_containers()

        if len(containers) > 0:

            identifier = containers[0].identifier

            lint_ctx.info(f"Tool will run in Docker image [{identifier}].")

            lint_ctx.info(f"Tool will run in Docker image [{identifier}].", linter=cls.name())





class CWLDescriptionMissing(Linter):
@@ -82,7 +84,7 @@ class CWLDescriptionMissing(Linter): 
    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):

        help = tool_source.parse_help()

        if not help:

            lint_ctx.warn("Description of tool is empty or absent.")

            lint_ctx.warn("Description of tool is empty or absent.", linter=cls.name())





class CWLHelpTODO(Linter):
@@ -90,4 +92,4 @@ class CWLHelpTODO(Linter): 
    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):

        help = tool_source.parse_help()

        if help and "TODO" in help.content:

            lint_ctx.warn("Help contains TODO text.")
 
            lint_ctx.warn("Help contains TODO text.", linter=cls.name())

lib/galaxy/tool_util/linters/tests.py

+2 −1
Original line number Diff line number Diff line
@@ -158,7 +158,8 @@ class TestsAssertionValidation(Linter): 
                except Exception as e:

                    error_str = _cleanup_pydantic_error(e)

                    lint_ctx.warn(

                        f"Test {test_idx}: failed to validate assertions. Validation errors are [{error_str}]"

                        f"Test {test_idx}: failed to validate assertions. Validation errors are [{error_str}]",

                        linter=cls.name(),

                    )