Commit 7e4c9da6 authored by Matthias Bernt's avatar Matthias Bernt
Browse files

add missing lintername argument to linter report function calls 

wo this we can not filter in planemo
parent 3586026f

lib/galaxy/tool_util/linters/cwl.py

+9 −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 +48,7 @@ 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 +57,7 @@ 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 +65,7 @@ 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 +74,7 @@ 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 +82,7 @@ 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 +90,4 @@ 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()

                    )