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

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2782966
"id" is a required field in for Parameters and WorkflowSteps
mr-c Oct 30, 2025
6f4a2d3
now with IdentifierRequired
mr-c Dec 8, 2025
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4 changes: 3 additions & 1 deletion cwl_utils/cwl_v1_2_expression_refactor.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -712,7 +712,9 @@ 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
74 changes: 40 additions & 34 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 @@ -4378,6 +4378,10 @@ class Identified(Saveable):
pass


class IdentifierRequired(Identified):
pass


class LoadContents(Saveable):
pass

Expand All @@ -4394,7 +4398,7 @@ class OutputFormat(Saveable):
pass


class Parameter(FieldBase, Documented, Identified):
class Parameter(FieldBase, Documented, IdentifierRequired):
"""
Define an input or output parameter to a process.

Expand Down Expand Up @@ -13750,12 +13754,12 @@ 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 +13841,7 @@ 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 +13889,7 @@ 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 +14508,12 @@ 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 +14583,7 @@ 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 +14631,7 @@ 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 +19326,12 @@ 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 +19397,7 @@ 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 +19445,7 @@ 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 +19831,12 @@ 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 +19918,7 @@ 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 +19966,7 @@ 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 +21316,12 @@ 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 +21399,7 @@ 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 +21447,7 @@ 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 @@ -21994,7 +21998,7 @@ class Sink(Saveable):
pass


class WorkflowStepInput(Identified, Sink, LoadContents, Labeled):
class WorkflowStepInput(IdentifierRequired, Sink, LoadContents, Labeled):
"""
The input of a workflow step connects an upstream parameter (from the
workflow inputs, or the outputs of other workflows steps) with the input
Expand Down Expand Up @@ -22111,7 +22115,7 @@ 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 +22194,7 @@ 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 +22242,7 @@ 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 @@ -22732,7 +22736,7 @@ def save(
)


class WorkflowStepOutput(Identified):
class WorkflowStepOutput(IdentifierRequired):
"""
Associate an output parameter of the underlying process with a workflow
parameter. The workflow parameter (given in the `id` field) be may be used
Expand All @@ -22749,7 +22753,7 @@ 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 +22794,7 @@ 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 +22842,7 @@ 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 @@ -22897,7 +22901,7 @@ def save(
attrs = frozenset(["id"])


class WorkflowStep(Identified, Labeled, Documented):
class WorkflowStep(IdentifierRequired, Labeled, Documented):
"""
A workflow step is an executable element of a workflow. It specifies the
underlying process implementation (such as `CommandLineTool` or another
Expand Down Expand Up @@ -22985,10 +22989,10 @@ 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 +23076,7 @@ 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 +23124,7 @@ 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 +24976,12 @@ 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 +25059,7 @@ 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 +25107,7 @@ 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 +25671,12 @@ 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 +25742,7 @@ 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 +25790,7 @@ 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 @@ -29219,6 +29223,7 @@ def save(
"File": "https://w3id.org/cwl/cwl#File",
"IOSchema": "https://w3id.org/cwl/cwl#IOSchema",
"Identified": "https://w3id.org/cwl/cwl#Identified",
"IdentifierRequired": "https://w3id.org/cwl/cwl#IdentifierRequired",
"InitialWorkDirRequirement": "https://w3id.org/cwl/cwl#InitialWorkDirRequirement",
"InlineJavascriptRequirement": "https://w3id.org/cwl/cwl#InlineJavascriptRequirement",
"InplaceUpdateRequirement": "https://w3id.org/cwl/cwl#InplaceUpdateRequirement",
Expand Down Expand Up @@ -29371,6 +29376,7 @@ def save(
"https://w3id.org/cwl/cwl#File": "File",
"https://w3id.org/cwl/cwl#IOSchema": "IOSchema",
"https://w3id.org/cwl/cwl#Identified": "Identified",
"https://w3id.org/cwl/cwl#IdentifierRequired": "IdentifierRequired",
"https://w3id.org/cwl/cwl#InitialWorkDirRequirement": "InitialWorkDirRequirement",
"https://w3id.org/cwl/cwl#InlineJavascriptRequirement": "InlineJavascriptRequirement",
"https://w3id.org/cwl/cwl#InplaceUpdateRequirement": "InplaceUpdateRequirement",
Expand Down
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