diff --git a/cwl_utils/cwl_v1_2_expression_refactor.py b/cwl_utils/cwl_v1_2_expression_refactor.py index 48c8c706..2f0c029e 100755 --- a/cwl_utils/cwl_v1_2_expression_refactor.py +++ b/cwl_utils/cwl_v1_2_expression_refactor.py @@ -715,7 +715,9 @@ def process_workflow_inputs_and_outputs( source_type_items.append("null") elif source_type_items != "null": source_type_items = ["null", source_type_items] - source_type = cwl.CommandInputParameter(type_=source_type_items) + source_type = cwl.CommandInputParameter( + id=None, type_=source_type_items + ) replace_expr_with_etool( expression, etool_id, diff --git a/cwl_utils/parser/cwl_v1_2.py b/cwl_utils/parser/cwl_v1_2.py index b24ac23c..6bfc4de4 100644 --- a/cwl_utils/parser/cwl_v1_2.py +++ b/cwl_utils/parser/cwl_v1_2.py @@ -13750,12 +13750,12 @@ class CommandInputParameter(InputParameter): def __init__( self, + id: Any, type_: Any, label: Optional[Any] = None, secondaryFiles: Optional[Any] = None, streamable: Optional[Any] = None, doc: Optional[Any] = None, - id: Optional[Any] = None, format: Optional[Any] = None, loadContents: Optional[Any] = None, loadListing: Optional[Any] = None, @@ -13837,7 +13837,7 @@ def fromDoc( try: id = load_field( _doc.get("id"), - uri_union_of_None_type_or_strtype_True_False_None_None, + uri_strtype_True_False_None_None, baseuri, loadingOptions, lc=_doc.get("id") @@ -13885,7 +13885,7 @@ def fromDoc( if docRoot is not None: id = docRoot else: - id = "_:" + str(_uuid__.uuid4()) + _errors__.append(ValidationException("missing id")) if not __original_id_is_none: baseuri = cast(str, id) label = None @@ -14504,12 +14504,12 @@ class CommandOutputParameter(OutputParameter): def __init__( self, + id: Any, type_: Any, label: Optional[Any] = None, secondaryFiles: Optional[Any] = None, streamable: Optional[Any] = None, doc: Optional[Any] = None, - id: Optional[Any] = None, format: Optional[Any] = None, outputBinding: Optional[Any] = None, extension_fields: Optional[dict[str, Any]] = None, @@ -14579,7 +14579,7 @@ def fromDoc( try: id = load_field( _doc.get("id"), - uri_union_of_None_type_or_strtype_True_False_None_None, + uri_strtype_True_False_None_None, baseuri, loadingOptions, lc=_doc.get("id") @@ -14627,7 +14627,7 @@ def fromDoc( if docRoot is not None: id = docRoot else: - id = "_:" + str(_uuid__.uuid4()) + _errors__.append(ValidationException("missing id")) if not __original_id_is_none: baseuri = cast(str, id) label = None @@ -19322,12 +19322,12 @@ class ExpressionToolOutputParameter(OutputParameter): def __init__( self, + id: Any, type_: Any, label: Optional[Any] = None, secondaryFiles: Optional[Any] = None, streamable: Optional[Any] = None, doc: Optional[Any] = None, - id: Optional[Any] = None, format: Optional[Any] = None, extension_fields: Optional[dict[str, Any]] = None, loadingOptions: Optional[LoadingOptions] = None, @@ -19393,7 +19393,7 @@ def fromDoc( try: id = load_field( _doc.get("id"), - uri_union_of_None_type_or_strtype_True_False_None_None, + uri_strtype_True_False_None_None, baseuri, loadingOptions, lc=_doc.get("id") @@ -19441,7 +19441,7 @@ def fromDoc( if docRoot is not None: id = docRoot else: - id = "_:" + str(_uuid__.uuid4()) + _errors__.append(ValidationException("missing id")) if not __original_id_is_none: baseuri = cast(str, id) label = None @@ -19827,12 +19827,12 @@ class WorkflowInputParameter(InputParameter): def __init__( self, + id: Any, type_: Any, label: Optional[Any] = None, secondaryFiles: Optional[Any] = None, streamable: Optional[Any] = None, doc: Optional[Any] = None, - id: Optional[Any] = None, format: Optional[Any] = None, loadContents: Optional[Any] = None, loadListing: Optional[Any] = None, @@ -19914,7 +19914,7 @@ def fromDoc( try: id = load_field( _doc.get("id"), - uri_union_of_None_type_or_strtype_True_False_None_None, + uri_strtype_True_False_None_None, baseuri, loadingOptions, lc=_doc.get("id") @@ -19962,7 +19962,7 @@ def fromDoc( if docRoot is not None: id = docRoot else: - id = "_:" + str(_uuid__.uuid4()) + _errors__.append(ValidationException("missing id")) if not __original_id_is_none: baseuri = cast(str, id) label = None @@ -21312,12 +21312,12 @@ class WorkflowOutputParameter(OutputParameter): def __init__( self, + id: Any, type_: Any, label: Optional[Any] = None, secondaryFiles: Optional[Any] = None, streamable: Optional[Any] = None, doc: Optional[Any] = None, - id: Optional[Any] = None, format: Optional[Any] = None, outputSource: Optional[Any] = None, linkMerge: Optional[Any] = None, @@ -21395,7 +21395,7 @@ def fromDoc( try: id = load_field( _doc.get("id"), - uri_union_of_None_type_or_strtype_True_False_None_None, + uri_strtype_True_False_None_None, baseuri, loadingOptions, lc=_doc.get("id") @@ -21443,7 +21443,7 @@ def fromDoc( if docRoot is not None: id = docRoot else: - id = "_:" + str(_uuid__.uuid4()) + _errors__.append(ValidationException("missing id")) if not __original_id_is_none: baseuri = cast(str, id) label = None @@ -22111,7 +22111,7 @@ class WorkflowStepInput(Identified, Sink, LoadContents, Labeled): def __init__( self, - id: Optional[Any] = None, + id: Any, source: Optional[Any] = None, linkMerge: Optional[Any] = None, pickValue: Optional[Any] = None, @@ -22190,7 +22190,7 @@ def fromDoc( try: id = load_field( _doc.get("id"), - uri_union_of_None_type_or_strtype_True_False_None_None, + uri_strtype_True_False_None_None, baseuri, loadingOptions, lc=_doc.get("id") @@ -22238,7 +22238,7 @@ def fromDoc( if docRoot is not None: id = docRoot else: - id = "_:" + str(_uuid__.uuid4()) + _errors__.append(ValidationException("missing id")) if not __original_id_is_none: baseuri = cast(str, id) source = None @@ -22749,7 +22749,7 @@ class WorkflowStepOutput(Identified): def __init__( self, - id: Optional[Any] = None, + id: Any, extension_fields: Optional[dict[str, Any]] = None, loadingOptions: Optional[LoadingOptions] = None, ) -> None: @@ -22790,7 +22790,7 @@ def fromDoc( try: id = load_field( _doc.get("id"), - uri_union_of_None_type_or_strtype_True_False_None_None, + uri_strtype_True_False_None_None, baseuri, loadingOptions, lc=_doc.get("id") @@ -22838,7 +22838,7 @@ def fromDoc( if docRoot is not None: id = docRoot else: - id = "_:" + str(_uuid__.uuid4()) + _errors__.append(ValidationException("missing id")) if not __original_id_is_none: baseuri = cast(str, id) extension_fields: dict[str, Any] = {} @@ -22985,10 +22985,10 @@ class WorkflowStep(Identified, Labeled, Documented): def __init__( self, + id: Any, in_: Any, out: Any, run: Any, - id: Optional[Any] = None, label: Optional[Any] = None, doc: Optional[Any] = None, requirements: Optional[Any] = None, @@ -23072,7 +23072,7 @@ def fromDoc( try: id = load_field( _doc.get("id"), - uri_union_of_None_type_or_strtype_True_False_None_None, + uri_strtype_True_False_None_None, baseuri, loadingOptions, lc=_doc.get("id") @@ -23120,7 +23120,7 @@ def fromDoc( if docRoot is not None: id = docRoot else: - id = "_:" + str(_uuid__.uuid4()) + _errors__.append(ValidationException("missing id")) if not __original_id_is_none: baseuri = cast(str, id) label = None @@ -24972,12 +24972,12 @@ class OperationInputParameter(InputParameter): def __init__( self, + id: Any, type_: Any, label: Optional[Any] = None, secondaryFiles: Optional[Any] = None, streamable: Optional[Any] = None, doc: Optional[Any] = None, - id: Optional[Any] = None, format: Optional[Any] = None, loadContents: Optional[Any] = None, loadListing: Optional[Any] = None, @@ -25055,7 +25055,7 @@ def fromDoc( try: id = load_field( _doc.get("id"), - uri_union_of_None_type_or_strtype_True_False_None_None, + uri_strtype_True_False_None_None, baseuri, loadingOptions, lc=_doc.get("id") @@ -25103,7 +25103,7 @@ def fromDoc( if docRoot is not None: id = docRoot else: - id = "_:" + str(_uuid__.uuid4()) + _errors__.append(ValidationException("missing id")) if not __original_id_is_none: baseuri = cast(str, id) label = None @@ -25667,12 +25667,12 @@ class OperationOutputParameter(OutputParameter): def __init__( self, + id: Any, type_: Any, label: Optional[Any] = None, secondaryFiles: Optional[Any] = None, streamable: Optional[Any] = None, doc: Optional[Any] = None, - id: Optional[Any] = None, format: Optional[Any] = None, extension_fields: Optional[dict[str, Any]] = None, loadingOptions: Optional[LoadingOptions] = None, @@ -25738,7 +25738,7 @@ def fromDoc( try: id = load_field( _doc.get("id"), - uri_union_of_None_type_or_strtype_True_False_None_None, + uri_strtype_True_False_None_None, baseuri, loadingOptions, lc=_doc.get("id") @@ -25786,7 +25786,7 @@ def fromDoc( if docRoot is not None: id = docRoot else: - id = "_:" + str(_uuid__.uuid4()) + _errors__.append(ValidationException("missing id")) if not __original_id_is_none: baseuri = cast(str, id) label = None