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"id" is a required field in for Parameters and WorkflowSteps #380

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"id" is a required field in for Parameters and WorkflowSteps #380

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4 changes: 3 additions & 1 deletion cwl_utils/cwl_v1_2_expression_refactor.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
60 changes: 30 additions & 30 deletions cwl_utils/parser/cwl_v1_2.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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] = {}
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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
Expand Down
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