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galaxy.tool_util.linters package¶
This package contains linting functions for Galaxy tools.
Submodules¶
galaxy.tool_util.linters.citations module¶
This module contains citation linters.
Citations describe references that should be used when consumers of the tool publish results.
- class galaxy.tool_util.linters.citations.CitationsMissing[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.citations.CitationsNoText[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.citations.CitationsFound[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.citations.CitationsNoValid[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
galaxy.tool_util.linters.command module¶
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.
- class galaxy.tool_util.linters.command.CommandMissing[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.command.CommandEmpty[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.command.CommandTODO[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.command.CommandInterpreterDeprecated[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.command.CommandInfo[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
galaxy.tool_util.linters.cwl module¶
Linter for CWL tools.
- class galaxy.tool_util.linters.cwl.CWLValid[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.cwl.CWLInValid[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.cwl.CWLVersionMissing[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.cwl.CWLVersionUnknown[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.cwl.CWLVersionGood[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.cwl.CWLDockerMissing[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.cwl.CWLDockerGood[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.cwl.CWLDescriptionMissing[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.cwl.CWLHelpTODO[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
galaxy.tool_util.linters.general module¶
This module contains linting functions for general aspects of the tool.
- class galaxy.tool_util.linters.general.ToolVersionMissing[source]¶
Bases:
Linter
Tools must have a version
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.ToolVersionPEP404[source]¶
Bases:
Linter
Tools should have a PEP404 compliant version.
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.ToolVersionWhitespace[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.ToolVersionValid[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.ToolNameMissing[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.ToolNameWhitespace[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.ToolNameValid[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.ToolIDMissing[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.ToolIDWhitespace[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.ToolIDValid[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.ToolProfileInvalid[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.ToolProfileLegacy[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.ToolProfileValid[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.RequirementNameMissing[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.RequirementVersionMissing[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.RequirementVersionWhitespace[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.ResourceRequirementExpression[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.BioToolsValid[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.general.EDAMTermsValid[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
galaxy.tool_util.linters.help module¶
This module contains a linting function for a tool’s help.
- class galaxy.tool_util.linters.help.HelpMissing[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.help.HelpEmpty[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.help.HelpPresent[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.help.HelpTODO[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.help.HelpInvalidRST[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.help.HelpValidRST[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
galaxy.tool_util.linters.inputs module¶
This module contains a linting functions for tool inputs.
- class galaxy.tool_util.linters.inputs.InputsNum[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsMissing[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsMissingDataSource[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsDatasourceTags[source]¶
Bases:
Linter
Lint that datasource tools have display and uihints tags
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsName[source]¶
Bases:
Linter
Lint params define a name
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsNameRedundantArgument[source]¶
Bases:
Linter
Lint params define a name
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsNameEmpty[source]¶
Bases:
Linter
Lint params define a non-empty name
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsNameValid[source]¶
Bases:
Linter
Lint params define valid cheetah placeholder
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsNameDuplicate[source]¶
Bases:
Linter
Lint params with duplicate names
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsNameDuplicateOutput[source]¶
Bases:
Linter
Lint params names that are also used in outputs
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsTypeChildCombination[source]¶
Bases:
Linter
Lint for invalid parameter type child combinations
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsDataFormat[source]¶
Bases:
Linter
Lint for data params wo format
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsDataOptionsMultiple[source]¶
Bases:
Linter
Lint for data params with multiple options tags
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsDataOptionsAttrib[source]¶
Bases:
Linter
Lint for data params with options that have invalid attributes
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsDataOptionsFilterAttribFiltersType[source]¶
Bases:
Linter
Lint for valid filter types for data parameters if options set options_filter_attribute
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsDataOptionsFiltersType[source]¶
Bases:
Linter
Lint for valid filter types for data parameters if options do not set options_filter_attribute
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsDataOptionsFiltersRef[source]¶
Bases:
Linter
Lint for set ref for filters of data parameters
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsSelectDynamicOptions[source]¶
Bases:
Linter
Lint for select with deprecated dynamic_options attribute
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsSelectOptionsDef[source]¶
Bases:
Linter
Lint for valid ways to define select options
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsSelectOptionsDefConditional[source]¶
Bases:
Linter
Lint for valid ways to define select options (for a select in a conditional)
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsSelectOptionValueMissing[source]¶
Bases:
Linter
Lint for select option tags without value
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsSelectOptionDuplicateValue[source]¶
Bases:
Linter
Lint for select option with same value
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsSelectOptionDuplicateText[source]¶
Bases:
Linter
Lint for select option with same text
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsSelectOptionsMultiple[source]¶
Bases:
Linter
Lint dynamic options select for multiple options tags
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsSelectOptionsDefinesOptions[source]¶
Bases:
Linter
Lint dynamic options select for the potential to define options
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsSelectOptionsDeprecatedAttr[source]¶
Bases:
Linter
Lint dynamic options select deprecated attributes
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsSelectOptionsFromDatasetAndDatatable[source]¶
Bases:
Linter
Lint dynamic options select for from_dataset and from_data_table
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsSelectOptionsMetaFileKey[source]¶
Bases:
Linter
Lint dynamic options select: meta_file_key attribute can only be used with from_dataset
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsBoolDistinctValues[source]¶
Bases:
Linter
Lint booleans for distinct true/false value
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsBoolProblematic[source]¶
Bases:
Linter
Lint booleans for problematic values, i.e. truevalue being false and vice versa
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsSelectSingleCheckboxes[source]¶
Bases:
Linter
Lint selects that allow only a single selection but display as checkboxes
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsSelectMandatoryCheckboxes[source]¶
Bases:
Linter
Lint selects that are mandatory but display as checkboxes
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsSelectMultipleRadio[source]¶
Bases:
Linter
Lint selects that allow only multiple selections but display as radio
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.InputsSelectOptionalRadio[source]¶
Bases:
Linter
Lint selects that are optional but display as radio
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ValidatorParamIncompatible[source]¶
Bases:
Linter
Lint for validator type - parameter type incompatibilities
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ValidatorAttribIncompatible[source]¶
Bases:
Linter
Lint for incompatibilities between validator type and given attributes
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ValidatorHasText[source]¶
Bases:
Linter
Lint that parameters that need text have text
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ValidatorHasNoText[source]¶
Bases:
Linter
Lint that parameters that need no text have no text
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ValidatorExpression[source]¶
Bases:
Linter
Lint that checks expressions / regexp (ignoring FutureWarning)
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ValidatorExpressionFuture[source]¶
Bases:
Linter
Lint that checks expressions / regexp FutureWarnings
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ValidatorMinMax[source]¶
Bases:
Linter
Lint for min/max for validator that need it
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ValidatorDatasetMetadataEqualValue[source]¶
Bases:
Linter
Lint dataset_metadata_equal needs value or value_json
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ValidatorDatasetMetadataEqualValueOrJson[source]¶
Bases:
Linter
Lint dataset_metadata_equal needs either value or value_json
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ValidatorMetadataCheckSkip[source]¶
Bases:
Linter
Lint metadata needs check or skip
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ValidatorTableName[source]¶
Bases:
Linter
Lint table_name is present if needed
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ValidatorMetadataName[source]¶
Bases:
Linter
Lint metadata_name is present if needed
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ConditionalParamTypeBool[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ConditionalParamType[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ConditionalParamIncompatibleAttributes[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ConditionalWhenMissing[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ConditionalOptionMissing[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.inputs.ConditionalOptionMissingBoolean[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
galaxy.tool_util.linters.outputs module¶
This module contains a linting functions for tool outputs.
- class galaxy.tool_util.linters.outputs.OutputsMissing[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.outputs.OutputsOutput[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.outputs.OutputsNameInvalidCheetah[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.outputs.OutputsNameDuplicated[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.outputs.OutputsLabelDuplicatedFilter[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.outputs.OutputsLabelDuplicatedNoFilter[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.outputs.OutputsCollectionType[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.outputs.OutputsNumber[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.outputs.OutputsFormatInput[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.outputs.OutputsFormat[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.outputs.OutputsFormatSourceIncomp[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
galaxy.tool_util.linters.stdio module¶
This module contains a linting functions for tool error detection.
- class galaxy.tool_util.linters.stdio.StdIOAbsenceLegacy[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.stdio.StdIOAbsence[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.stdio.StdIORegex[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
galaxy.tool_util.linters.tests module¶
This module contains a linting functions for tool tests.
- class galaxy.tool_util.linters.tests.TestsMissing[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsMissingDatasource[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsAssertsMultiple[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsAssertsHasNQuant[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsAssertsHasSizeQuant[source]¶
Bases:
Linter
has_size needs at least one of size (or value), min, max
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsAssertsHasSizeOrValueQuant[source]¶
Bases:
Linter
has_size should not have size and value
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsExpectNumOutputs[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsParamInInputs[source]¶
Bases:
Linter
really simple linter that test parameters are also present in the inputs
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsOutputName[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsOutputDefined[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsOutputCorresponding[source]¶
Bases:
Linter
Linter checking if test/output corresponds to outputs/data
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsOutputCollectionCorresponding[source]¶
Bases:
Linter
Linter checking if test/collection corresponds to outputs/output_collection
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsOutputCompareAttrib[source]¶
Bases:
Linter
Linter checking compatibility of output attributes with the value of the compare attribute
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsOutputCheckDiscovered[source]¶
Bases:
Linter
Linter checking that discovered elements of outputs are tested with a count attribute or listing some discovered_dataset
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsOutputCollectionCheckDiscovered[source]¶
Bases:
Linter
Linter checking that discovered elements of output collections are tested with a count attribute or listing some elements
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsOutputCollectionCheckDiscoveredNested[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsOutputFailing[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsExpectNumOutputsFailing[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsHasExpectations[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsNoValid[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
- class galaxy.tool_util.linters.tests.TestsValid[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context
galaxy.tool_util.linters.xml_order module¶
This module contains a linter for tool XML block order.
For more information on the IUC standard for XML block order see - https://github.com/galaxy-iuc/standards.
- class galaxy.tool_util.linters.xml_order.XMLOrder[source]¶
Bases:
Linter
- classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]¶
should add at most one message to the lint context