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Add partially auto-generated test file schema
To generate dataclasses in generated/galaxy from xsd: ``` pip install 'xsdata[cli]' cd lib/galaxy/tool_util/schemas xsdata ../xsd/galaxy.xsd --unnest-classes --kw-only --docstring-style Accessible --ignore-patterns --max-line-length 10000 ``` Fix up tool test schema for workflow particularities (and xsdata odditites) ``` python postprocess_schema.py ``` To generate json schema (requires pydantic 2.0 to deal with recursive data classes): ``` python test_file_from_xsd.py > test_file_schema.json ``` To validate a workflow test file with check-jsonschema ``` check-jsonschema --traceback-mode full --schemafile test_file_schema.json sra-manifest-to-concatenated-fastqs-tests.yml ``` TODO: - jobs is not modeled - element / element_tests needs work - special handling for primitive workflow parameter output values - de-RST-ify description fields
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <Config xmlns="http://pypi.org/project/xsdata" version="23.6"> | ||
| <Extensions> | ||
| <Extension type="class" class=".*" import=".config.BaseSetting" prepend="false" applyIfDerived="true"/> | ||
| </Extensions> | ||
| </Config> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,305 @@ | ||
| from generated.galaxy import ( | ||
| Action, | ||
| Actions, | ||
| ActionsConditional, | ||
| ActionsConditionalFilter, | ||
| ActionsConditionalFilterType, | ||
| ActionsConditionalWhen, | ||
| ActionsOption, | ||
| ActionsOptionType, | ||
| ActionType, | ||
| AssertAttributeIs, | ||
| AssertAttributeMatches, | ||
| AssertElementText, | ||
| AssertElementTextIs, | ||
| AssertElementTextMatches, | ||
| AssertHasArchiveMember, | ||
| AssertHasElementWithPath, | ||
| AssertHasH5Attribute, | ||
| AssertHasH5Keys, | ||
| AssertHasJsonPropertyWithText, | ||
| AssertHasJsonPropertyWithValue, | ||
| AssertHasLine, | ||
| AssertHasLineMatching, | ||
| AssertHasNcolumns, | ||
| AssertHasNelementsWithPath, | ||
| AssertHasNlines, | ||
| AssertHasSize, | ||
| AssertHasText, | ||
| AssertHasTextMatching, | ||
| AssertIsValidXml, | ||
| AssertNotHasText, | ||
| AssertXmlelement, | ||
| ChangeFormat, | ||
| ChangeFormatWhen, | ||
| Citation, | ||
| Citations, | ||
| CitationType, | ||
| Code, | ||
| CodeHook, | ||
| Column, | ||
| Command, | ||
| CompareType, | ||
| Conditional, | ||
| ConditionalWhen, | ||
| ConfigFile, | ||
| ConfigFiles, | ||
| ConfigFileSources, | ||
| ConfigInputs, | ||
| Container, | ||
| ContainerType, | ||
| Creator, | ||
| DetectErrorType, | ||
| DisplayType, | ||
| EdamOperations, | ||
| EdamTopics, | ||
| EntryPoint, | ||
| EntryPointPort, | ||
| EntryPoints, | ||
| EntryPointUrl, | ||
| EnvironmentVariable, | ||
| EnvironmentVariableInject, | ||
| EnvironmentVariables, | ||
| ExitCode, | ||
| Expression, | ||
| ExpressionType, | ||
| Filter, | ||
| FilterType, | ||
| HierarchyType, | ||
| Inputs, | ||
| InputType, | ||
| LevelType, | ||
| Macros, | ||
| MethodType, | ||
| Options, | ||
| Organization, | ||
| Output, | ||
| OutputCollection, | ||
| OutputCollectionDiscoverDatasets, | ||
| OutputData, | ||
| OutputDiscoverDatasets, | ||
| Outputs, | ||
| Parallelism, | ||
| Param, | ||
| ParamConversion, | ||
| ParamDefault, | ||
| ParamDefaultCollection, | ||
| ParamDefaultElement, | ||
| ParamDrillDownOption, | ||
| ParamOptions, | ||
| ParamSelectOption, | ||
| ParamType, | ||
| PermissiveBooleanValue, | ||
| Person, | ||
| Regex, | ||
| Repeat, | ||
| RequestParameter, | ||
| RequestParameterAppend, | ||
| RequestParameterAppendValue, | ||
| RequestParameterGalaxyNameType, | ||
| RequestParameterTranslation, | ||
| RequestParameterValueTranslation, | ||
| RequestParameterValueTranslationValue, | ||
| RequiredFileExclude, | ||
| RequiredFileInclude, | ||
| RequiredFileReferenceType, | ||
| RequiredFiles, | ||
| Requirement, | ||
| Requirements, | ||
| RequirementType, | ||
| Resource, | ||
| ResourceType, | ||
| Sanitizer, | ||
| SanitizerMapping, | ||
| SanitizerMappingAdd, | ||
| SanitizerMappingRemove, | ||
| SanitizerValid, | ||
| SanitizerValidAdd, | ||
| SanitizerValidRemove, | ||
| Section, | ||
| SourceType, | ||
| Stdio, | ||
| TargetType, | ||
| Test, | ||
| TestAssertions, | ||
| TestCollection, | ||
| TestCompositeData, | ||
| TestConditional, | ||
| TestDiscoveredDataset, | ||
| TestExtraFile, | ||
| TestOutput, | ||
| TestOutputCollection, | ||
| TestOutputCompareType, | ||
| TestOutputMetadata, | ||
| TestParam, | ||
| TestParamMetadata, | ||
| TestRepeat, | ||
| Tests, | ||
| TestSection, | ||
| Tool, | ||
| ToolAction, | ||
| ToolTypeType, | ||
| TracksterAction, | ||
| TracksterConf, | ||
| Uihints, | ||
| UrlmethodType, | ||
| Validator, | ||
| ValidatorType, | ||
| VersionCommand, | ||
| Xref, | ||
| Xrefs, | ||
| XrefType, | ||
| ) | ||
|
|
||
| __all__ = [ | ||
| "Action", | ||
| "ActionType", | ||
| "Actions", | ||
| "ActionsConditional", | ||
| "ActionsConditionalFilter", | ||
| "ActionsConditionalFilterType", | ||
| "ActionsConditionalWhen", | ||
| "ActionsOption", | ||
| "ActionsOptionType", | ||
| "AssertAttributeIs", | ||
| "AssertAttributeMatches", | ||
| "AssertElementText", | ||
| "AssertElementTextIs", | ||
| "AssertElementTextMatches", | ||
| "AssertHasArchiveMember", | ||
| "AssertHasElementWithPath", | ||
| "AssertHasH5Attribute", | ||
| "AssertHasH5Keys", | ||
| "AssertHasJsonPropertyWithText", | ||
| "AssertHasJsonPropertyWithValue", | ||
| "AssertHasLine", | ||
| "AssertHasLineMatching", | ||
| "AssertHasNcolumns", | ||
| "AssertHasNelementsWithPath", | ||
| "AssertHasNlines", | ||
| "AssertHasSize", | ||
| "AssertHasText", | ||
| "AssertHasTextMatching", | ||
| "AssertIsValidXml", | ||
| "AssertNotHasText", | ||
| "AssertXmlelement", | ||
| "ChangeFormat", | ||
| "ChangeFormatWhen", | ||
| "Citation", | ||
| "CitationType", | ||
| "Citations", | ||
| "Code", | ||
| "CodeHook", | ||
| "Column", | ||
| "Command", | ||
| "CompareType", | ||
| "Conditional", | ||
| "ConditionalWhen", | ||
| "ConfigFile", | ||
| "ConfigFileSources", | ||
| "ConfigFiles", | ||
| "ConfigInputs", | ||
| "Container", | ||
| "ContainerType", | ||
| "Creator", | ||
| "DetectErrorType", | ||
| "DisplayType", | ||
| "EdamOperations", | ||
| "EdamTopics", | ||
| "EntryPoint", | ||
| "EntryPointPort", | ||
| "EntryPointUrl", | ||
| "EntryPoints", | ||
| "EnvironmentVariable", | ||
| "EnvironmentVariableInject", | ||
| "EnvironmentVariables", | ||
| "ExitCode", | ||
| "Expression", | ||
| "ExpressionType", | ||
| "Filter", | ||
| "FilterType", | ||
| "HierarchyType", | ||
| "InputType", | ||
| "Inputs", | ||
| "LevelType", | ||
| "Macros", | ||
| "MethodType", | ||
| "Options", | ||
| "Organization", | ||
| "Output", | ||
| "OutputCollection", | ||
| "OutputCollectionDiscoverDatasets", | ||
| "OutputData", | ||
| "OutputDiscoverDatasets", | ||
| "Outputs", | ||
| "Parallelism", | ||
| "Param", | ||
| "ParamConversion", | ||
| "ParamDefault", | ||
| "ParamDefaultCollection", | ||
| "ParamDefaultElement", | ||
| "ParamDrillDownOption", | ||
| "ParamOptions", | ||
| "ParamSelectOption", | ||
| "ParamType", | ||
| "PermissiveBooleanValue", | ||
| "Person", | ||
| "Regex", | ||
| "Repeat", | ||
| "RequestParameter", | ||
| "RequestParameterAppend", | ||
| "RequestParameterAppendValue", | ||
| "RequestParameterGalaxyNameType", | ||
| "RequestParameterTranslation", | ||
| "RequestParameterValueTranslation", | ||
| "RequestParameterValueTranslationValue", | ||
| "RequiredFileExclude", | ||
| "RequiredFileInclude", | ||
| "RequiredFileReferenceType", | ||
| "RequiredFiles", | ||
| "Requirement", | ||
| "RequirementType", | ||
| "Requirements", | ||
| "Resource", | ||
| "ResourceType", | ||
| "Sanitizer", | ||
| "SanitizerMapping", | ||
| "SanitizerMappingAdd", | ||
| "SanitizerMappingRemove", | ||
| "SanitizerValid", | ||
| "SanitizerValidAdd", | ||
| "SanitizerValidRemove", | ||
| "Section", | ||
| "SourceType", | ||
| "Stdio", | ||
| "TargetType", | ||
| "Test", | ||
| "TestAssertions", | ||
| "TestCollection", | ||
| "TestCompositeData", | ||
| "TestConditional", | ||
| "TestDiscoveredDataset", | ||
| "TestExtraFile", | ||
| "TestOutput", | ||
| "TestOutputCollection", | ||
| "TestOutputCompareType", | ||
| "TestOutputMetadata", | ||
| "TestParam", | ||
| "TestParamMetadata", | ||
| "TestRepeat", | ||
| "TestSection", | ||
| "Tests", | ||
| "ToolAction", | ||
| "ToolTypeType", | ||
| "TracksterAction", | ||
| "TracksterConf", | ||
| "Uihints", | ||
| "UrlmethodType", | ||
| "Validator", | ||
| "ValidatorType", | ||
| "VersionCommand", | ||
| "Tool", | ||
| "Xref", | ||
| "XrefType", | ||
| "Xrefs", | ||
| ] |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,12 @@ | ||
| from pydantic import ConfigDict | ||
|
|
||
| alias_lookup = { | ||
| "assert_contents": "asserts", | ||
| "element": "element_tests", | ||
| } | ||
|
|
||
|
|
||
| class BaseSetting: | ||
| __pydantic_config__ = ConfigDict( | ||
| extra="forbid", alias_generator=lambda field_name: alias_lookup.get(field_name, field_name) | ||
| ) |
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