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Regenerate prsers with fixed CWL versions
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8 files changed

+313
-656
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8 files changed

+313
-656
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‎cwl_utils/parser/__init__.py‎

Lines changed: 6 additions & 44 deletions
Original file line numberDiff line numberDiff line change
@@ -2,9 +2,9 @@
22

33
import os
44
from abc import ABC
5-
from collections.abc import MutableMapping, MutableSequence, Sequence
5+
from collections.abc import MutableMapping, MutableSequence
66
from pathlib import Path
7-
from typing import Any, Literal, Optional, TypeAlias, cast
7+
from typing import Any, Optional, TypeAlias, cast
88
from urllib.parse import unquote_plus, urlparse
99

1010
from schema_salad.exceptions import ValidationException
@@ -76,26 +76,6 @@ class NoType(ABC):
7676
OutputSchema: TypeAlias = (
7777
cwl_v1_0.OutputSchema | cwl_v1_1.OutputSchema | cwl_v1_2.OutputSchema
7878
)
79-
BasicOutputTypeSchemas: TypeAlias = (
80-
OutputArraySchema
81-
| OutputEnumSchema
82-
| OutputRecordSchema
83-
| str
84-
| Literal[
85-
"null",
86-
"boolean",
87-
"int",
88-
"long",
89-
"float",
90-
"double",
91-
"string",
92-
"File",
93-
"Directory",
94-
"stderr",
95-
"stdout",
96-
]
97-
)
98-
OutputTypeSchemas: TypeAlias = BasicOutputTypeSchemas | Sequence[BasicOutputTypeSchemas]
9979
"""Type union for a CWL v1.x OutputSchema object."""
10080
Workflow: TypeAlias = cwl_v1_0.Workflow | cwl_v1_1.Workflow | cwl_v1_2.Workflow
10181
WorkflowTypes = (cwl_v1_0.Workflow, cwl_v1_1.Workflow, cwl_v1_2.Workflow)
@@ -132,10 +112,12 @@ class NoType(ABC):
132112
| cwl_v1_2.WorkflowStepOutput
133113
)
134114
"""Type union for a CWL v1.x WorkflowStepOutput object."""
115+
Operation: TypeAlias = cwl_v1_2.Operation
116+
"""Type union for a CWL v1.x Operation object."""
135117
OperationInputParameter: TypeAlias = cwl_v1_2.OperationInputParameter
136-
"""Type union for a CWL v1.x WorkflowInputParameter object."""
118+
"""Type union for a CWL v1.x OperationInputParameter object."""
137119
OperationOutputParameter: TypeAlias = cwl_v1_2.OperationOutputParameter
138-
"""Type union for a CWL v1.x WorkflowOutputParameter object."""
120+
"""Type union for a CWL v1.x OperationOutputParameter object."""
139121
CommandLineTool: TypeAlias = (
140122
cwl_v1_0.CommandLineTool | cwl_v1_1.CommandLineTool | cwl_v1_2.CommandLineTool
141123
)
@@ -255,26 +237,6 @@ class NoType(ABC):
255237
)
256238
"""Type Union for a CWL v1.x RecordSchema object."""
257239

258-
BasicInputTypeSchemas: TypeAlias = (
259-
InputArraySchema
260-
| InputEnumSchema
261-
| InputRecordSchema
262-
| str
263-
| Literal[
264-
"null",
265-
"boolean",
266-
"int",
267-
"long",
268-
"float",
269-
"double",
270-
"string",
271-
"File",
272-
"Directory",
273-
"stdin",
274-
]
275-
)
276-
InputTypeSchemas: TypeAlias = BasicInputTypeSchemas | Sequence[BasicInputTypeSchemas]
277-
278240
File: TypeAlias = cwl_v1_0.File | cwl_v1_1.File | cwl_v1_2.File
279241
"""Type Union for a CWL v1.x File object."""
280242
SecondaryFileSchema: TypeAlias = (

‎cwl_utils/parser/cwl_v1_0.py‎

Lines changed: 11 additions & 49 deletions
Original file line numberDiff line numberDiff line change
@@ -8315,7 +8315,7 @@ class Process(Saveable, metaclass=ABCMeta):
83158315
hints: None | Sequence[Any | CUDARequirement | DockerRequirement | EnvVarRequirement | InitialWorkDirRequirement | InlineJavascriptRequirement | InplaceUpdateRequirement | LoadListingRequirement | MPIRequirement | MultipleInputFeatureRequirement | NetworkAccess | ResourceRequirement | ScatterFeatureRequirement | SchemaDefRequirement | Secrets | ShellCommandRequirement | ShmSize | SoftwareRequirement | StepInputExpressionRequirement | SubworkflowFeatureRequirement | TimeLimit | WorkReuse]
83168316
label: None | str
83178317
doc: None | str
8318-
cwlVersion: Literal["draft-2", "draft-3.dev1", "draft-3.dev2", "draft-3.dev3", "draft-3.dev4", "draft-3.dev5", "draft-3", "draft-4.dev1", "draft-4.dev2", "draft-4.dev3", "v1.0.dev4", "v1.0"] | None
8318+
cwlVersion: Literal["v1.0"] | None
83198319

83208320

83218321
class InlineJavascriptRequirement(ProcessRequirement):
@@ -14691,7 +14691,7 @@ def __init__(
1469114691
hints: None | Sequence[Any | CUDARequirement | DockerRequirement | EnvVarRequirement | InitialWorkDirRequirement | InlineJavascriptRequirement | InplaceUpdateRequirement | LoadListingRequirement | MPIRequirement | MultipleInputFeatureRequirement | NetworkAccess | ResourceRequirement | ScatterFeatureRequirement | SchemaDefRequirement | Secrets | ShellCommandRequirement | ShmSize | SoftwareRequirement | StepInputExpressionRequirement | SubworkflowFeatureRequirement | TimeLimit | WorkReuse] = None,
1469214692
label: None | str = None,
1469314693
doc: None | str = None,
14694-
cwlVersion: Literal["draft-2", "draft-3.dev1", "draft-3.dev2", "draft-3.dev3", "draft-3.dev4", "draft-3.dev5", "draft-3", "draft-4.dev1", "draft-4.dev2", "draft-4.dev3", "v1.0.dev4", "v1.0"] | None = None,
14694+
cwlVersion: Literal["v1.0"] | None = None,
1469514695
baseCommand: None | Sequence[str] | str = None,
1469614696
arguments: None | Sequence[CommandLineBinding | str] = None,
1469714697
stdin: None | str = None,
@@ -14718,7 +14718,7 @@ def __init__(
1471814718
self.hints: None | Sequence[Any | CUDARequirement | DockerRequirement | EnvVarRequirement | InitialWorkDirRequirement | InlineJavascriptRequirement | InplaceUpdateRequirement | LoadListingRequirement | MPIRequirement | MultipleInputFeatureRequirement | NetworkAccess | ResourceRequirement | ScatterFeatureRequirement | SchemaDefRequirement | Secrets | ShellCommandRequirement | ShmSize | SoftwareRequirement | StepInputExpressionRequirement | SubworkflowFeatureRequirement | TimeLimit | WorkReuse] = hints
1471914719
self.label: None | str = label
1472014720
self.doc: None | str = doc
14721-
self.cwlVersion: Literal["draft-2", "draft-3.dev1", "draft-3.dev2", "draft-3.dev3", "draft-3.dev4", "draft-3.dev5", "draft-3", "draft-4.dev1", "draft-4.dev2", "draft-4.dev3", "v1.0.dev4", "v1.0"] | None = cwlVersion
14721+
self.cwlVersion: Literal["v1.0"] | None = cwlVersion
1472214722
self.class_: Final[str] = "CommandLineTool"
1472314723
self.baseCommand: None | Sequence[str] | str = baseCommand
1472414724
self.arguments: None | Sequence[CommandLineBinding | str] = arguments
@@ -18260,7 +18260,7 @@ def __init__(
1826018260
hints: None | Sequence[Any | CUDARequirement | DockerRequirement | EnvVarRequirement | InitialWorkDirRequirement | InlineJavascriptRequirement | InplaceUpdateRequirement | LoadListingRequirement | MPIRequirement | MultipleInputFeatureRequirement | NetworkAccess | ResourceRequirement | ScatterFeatureRequirement | SchemaDefRequirement | Secrets | ShellCommandRequirement | ShmSize | SoftwareRequirement | StepInputExpressionRequirement | SubworkflowFeatureRequirement | TimeLimit | WorkReuse] = None,
1826118261
label: None | str = None,
1826218262
doc: None | str = None,
18263-
cwlVersion: Literal["draft-2", "draft-3.dev1", "draft-3.dev2", "draft-3.dev3", "draft-3.dev4", "draft-3.dev5", "draft-3", "draft-4.dev1", "draft-4.dev2", "draft-4.dev3", "v1.0.dev4", "v1.0"] | None = None,
18263+
cwlVersion: Literal["v1.0"] | None = None,
1826418264
extension_fields: MutableMapping[str, Any] | None = None,
1826518265
loadingOptions: LoadingOptions | None = None,
1826618266
) -> None:
@@ -18279,7 +18279,7 @@ def __init__(
1827918279
self.hints: None | Sequence[Any | CUDARequirement | DockerRequirement | EnvVarRequirement | InitialWorkDirRequirement | InlineJavascriptRequirement | InplaceUpdateRequirement | LoadListingRequirement | MPIRequirement | MultipleInputFeatureRequirement | NetworkAccess | ResourceRequirement | ScatterFeatureRequirement | SchemaDefRequirement | Secrets | ShellCommandRequirement | ShmSize | SoftwareRequirement | StepInputExpressionRequirement | SubworkflowFeatureRequirement | TimeLimit | WorkReuse] = hints
1828018280
self.label: None | str = label
1828118281
self.doc: None | str = doc
18282-
self.cwlVersion: Literal["draft-2", "draft-3.dev1", "draft-3.dev2", "draft-3.dev3", "draft-3.dev4", "draft-3.dev5", "draft-3", "draft-4.dev1", "draft-4.dev2", "draft-4.dev3", "v1.0.dev4", "v1.0"] | None = cwlVersion
18282+
self.cwlVersion: Literal["v1.0"] | None = cwlVersion
1828318283
self.class_: Final[str] = "ExpressionTool"
1828418284
self.expression: str = expression
1828518285

@@ -20986,7 +20986,7 @@ def __init__(
2098620986
hints: None | Sequence[Any | CUDARequirement | DockerRequirement | EnvVarRequirement | InitialWorkDirRequirement | InlineJavascriptRequirement | InplaceUpdateRequirement | LoadListingRequirement | MPIRequirement | MultipleInputFeatureRequirement | NetworkAccess | ResourceRequirement | ScatterFeatureRequirement | SchemaDefRequirement | Secrets | ShellCommandRequirement | ShmSize | SoftwareRequirement | StepInputExpressionRequirement | SubworkflowFeatureRequirement | TimeLimit | WorkReuse] = None,
2098720987
label: None | str = None,
2098820988
doc: None | str = None,
20989-
cwlVersion: Literal["draft-2", "draft-3.dev1", "draft-3.dev2", "draft-3.dev3", "draft-3.dev4", "draft-3.dev5", "draft-3", "draft-4.dev1", "draft-4.dev2", "draft-4.dev3", "v1.0.dev4", "v1.0"] | None = None,
20989+
cwlVersion: Literal["v1.0"] | None = None,
2099020990
extension_fields: MutableMapping[str, Any] | None = None,
2099120991
loadingOptions: LoadingOptions | None = None,
2099220992
) -> None:
@@ -21005,7 +21005,7 @@ def __init__(
2100521005
self.hints: None | Sequence[Any | CUDARequirement | DockerRequirement | EnvVarRequirement | InitialWorkDirRequirement | InlineJavascriptRequirement | InplaceUpdateRequirement | LoadListingRequirement | MPIRequirement | MultipleInputFeatureRequirement | NetworkAccess | ResourceRequirement | ScatterFeatureRequirement | SchemaDefRequirement | Secrets | ShellCommandRequirement | ShmSize | SoftwareRequirement | StepInputExpressionRequirement | SubworkflowFeatureRequirement | TimeLimit | WorkReuse] = hints
2100621006
self.label: None | str = label
2100721007
self.doc: None | str = doc
21008-
self.cwlVersion: Literal["draft-2", "draft-3.dev1", "draft-3.dev2", "draft-3.dev3", "draft-3.dev4", "draft-3.dev5", "draft-3", "draft-4.dev1", "draft-4.dev2", "draft-4.dev3", "v1.0.dev4", "v1.0"] | None = cwlVersion
21008+
self.cwlVersion: Literal["v1.0"] | None = cwlVersion
2100921009
self.class_: Final[str] = "Workflow"
2101021010
self.steps: Sequence[WorkflowStep] = steps
2101121011

@@ -23201,7 +23201,7 @@ def __init__(
2320123201
hints: None | Sequence[Any | CUDARequirement | DockerRequirement | EnvVarRequirement | InitialWorkDirRequirement | InlineJavascriptRequirement | InplaceUpdateRequirement | LoadListingRequirement | MPIRequirement | MultipleInputFeatureRequirement | NetworkAccess | ResourceRequirement | ScatterFeatureRequirement | SchemaDefRequirement | Secrets | ShellCommandRequirement | ShmSize | SoftwareRequirement | StepInputExpressionRequirement | SubworkflowFeatureRequirement | TimeLimit | WorkReuse] = None,
2320223202
label: None | str = None,
2320323203
doc: None | str = None,
23204-
cwlVersion: Literal["draft-2", "draft-3.dev1", "draft-3.dev2", "draft-3.dev3", "draft-3.dev4", "draft-3.dev5", "draft-3", "draft-4.dev1", "draft-4.dev2", "draft-4.dev3", "v1.0.dev4", "v1.0"] | None = None,
23204+
cwlVersion: Literal["v1.0"] | None = None,
2320523205
extension_fields: MutableMapping[str, Any] | None = None,
2320623206
loadingOptions: LoadingOptions | None = None,
2320723207
) -> None:
@@ -23220,7 +23220,7 @@ def __init__(
2322023220
self.hints: None | Sequence[Any | CUDARequirement | DockerRequirement | EnvVarRequirement | InitialWorkDirRequirement | InlineJavascriptRequirement | InplaceUpdateRequirement | LoadListingRequirement | MPIRequirement | MultipleInputFeatureRequirement | NetworkAccess | ResourceRequirement | ScatterFeatureRequirement | SchemaDefRequirement | Secrets | ShellCommandRequirement | ShmSize | SoftwareRequirement | StepInputExpressionRequirement | SubworkflowFeatureRequirement | TimeLimit | WorkReuse] = hints
2322123221
self.label: None | str = label
2322223222
self.doc: None | str = doc
23223-
self.cwlVersion: Literal["draft-2", "draft-3.dev1", "draft-3.dev2", "draft-3.dev3", "draft-3.dev4", "draft-3.dev5", "draft-3", "draft-4.dev1", "draft-4.dev2", "draft-4.dev3", "v1.0.dev4", "v1.0"] | None = cwlVersion
23223+
self.cwlVersion: Literal["v1.0"] | None = cwlVersion
2322423224
self.class_: Final[str] = "ProcessGenerator"
2322523225
self.run: CommandLineTool | ExpressionTool | ProcessGenerator | Workflow | str = run
2322623226

@@ -24054,16 +24054,6 @@ def __init__(
2405424054
"deep_listing": "http://commonwl.org/cwltool#LoadListingRequirement/loadListing/LoadListingEnum/deep_listing",
2405524055
"dotproduct": "https://w3id.org/cwl/cwl#ScatterMethod/dotproduct",
2405624056
"double": "http://www.w3.org/2001/XMLSchema#double",
24057-
"draft-2": "https://w3id.org/cwl/cwl#draft-2",
24058-
"draft-3": "https://w3id.org/cwl/cwl#draft-3",
24059-
"draft-3.dev1": "https://w3id.org/cwl/cwl#draft-3.dev1",
24060-
"draft-3.dev2": "https://w3id.org/cwl/cwl#draft-3.dev2",
24061-
"draft-3.dev3": "https://w3id.org/cwl/cwl#draft-3.dev3",
24062-
"draft-3.dev4": "https://w3id.org/cwl/cwl#draft-3.dev4",
24063-
"draft-3.dev5": "https://w3id.org/cwl/cwl#draft-3.dev5",
24064-
"draft-4.dev1": "https://w3id.org/cwl/cwl#draft-4.dev1",
24065-
"draft-4.dev2": "https://w3id.org/cwl/cwl#draft-4.dev2",
24066-
"draft-4.dev3": "https://w3id.org/cwl/cwl#draft-4.dev3",
2406724057
"enum": "https://w3id.org/cwl/salad#enum",
2406824058
"flat_crossproduct": "https://w3id.org/cwl/cwl#ScatterMethod/flat_crossproduct",
2406924059
"float": "http://www.w3.org/2001/XMLSchema#float",
@@ -24082,7 +24072,6 @@ def __init__(
2408224072
"string": "http://www.w3.org/2001/XMLSchema#string",
2408324073
"union": "https://w3id.org/cwl/salad#union",
2408424074
"v1.0": "https://w3id.org/cwl/cwl#v1.0",
24085-
"v1.0.dev4": "https://w3id.org/cwl/cwl#v1.0.dev4",
2408624075
})
2408724076
_rvocab.update({
2408824077
"https://w3id.org/cwl/salad#Any": "Any",
@@ -24176,16 +24165,6 @@ def __init__(
2417624165
"http://commonwl.org/cwltool#LoadListingRequirement/loadListing/LoadListingEnum/deep_listing": "deep_listing",
2417724166
"https://w3id.org/cwl/cwl#ScatterMethod/dotproduct": "dotproduct",
2417824167
"http://www.w3.org/2001/XMLSchema#double": "double",
24179-
"https://w3id.org/cwl/cwl#draft-2": "draft-2",
24180-
"https://w3id.org/cwl/cwl#draft-3": "draft-3",
24181-
"https://w3id.org/cwl/cwl#draft-3.dev1": "draft-3.dev1",
24182-
"https://w3id.org/cwl/cwl#draft-3.dev2": "draft-3.dev2",
24183-
"https://w3id.org/cwl/cwl#draft-3.dev3": "draft-3.dev3",
24184-
"https://w3id.org/cwl/cwl#draft-3.dev4": "draft-3.dev4",
24185-
"https://w3id.org/cwl/cwl#draft-3.dev5": "draft-3.dev5",
24186-
"https://w3id.org/cwl/cwl#draft-4.dev1": "draft-4.dev1",
24187-
"https://w3id.org/cwl/cwl#draft-4.dev2": "draft-4.dev2",
24188-
"https://w3id.org/cwl/cwl#draft-4.dev3": "draft-4.dev3",
2418924168
"https://w3id.org/cwl/salad#enum": "enum",
2419024169
"https://w3id.org/cwl/cwl#ScatterMethod/flat_crossproduct": "flat_crossproduct",
2419124170
"http://www.w3.org/2001/XMLSchema#float": "float",
@@ -24204,7 +24183,6 @@ def __init__(
2420424183
"http://www.w3.org/2001/XMLSchema#string": "string",
2420524184
"https://w3id.org/cwl/salad#union": "union",
2420624185
"https://w3id.org/cwl/cwl#v1.0": "v1.0",
24207-
"https://w3id.org/cwl/cwl#v1.0.dev4": "v1.0.dev4",
2420824186
})
2420924187

2421024188
strtype: Final = _PrimitiveLoader(str)
@@ -24288,25 +24266,9 @@ def __init__(
2428824266
union_of_None_type_or_CWLObjectTypeLoader, "CWLInputFile", "@list", True
2428924267
)
2429024268
CWLInputFileLoader: Final = map_of_union_of_None_type_or_CWLObjectTypeLoader
24291-
CWLVersionLoader: Final = _EnumLoader(
24292-
(
24293-
"draft-2",
24294-
"draft-3.dev1",
24295-
"draft-3.dev2",
24296-
"draft-3.dev3",
24297-
"draft-3.dev4",
24298-
"draft-3.dev5",
24299-
"draft-3",
24300-
"draft-4.dev1",
24301-
"draft-4.dev2",
24302-
"draft-4.dev3",
24303-
"v1.0.dev4",
24304-
"v1.0",
24305-
),
24306-
"CWLVersion",
24307-
)
24269+
CWLVersionLoader: Final = _EnumLoader(("v1.0",), "CWLVersion")
2430824270
"""
24309-
Version symbols for published CWL document versions.
24271+
Current version symbol for CWL documents.
2431024272
"""
2431124273
ExpressionLoader: Final = _ExpressionLoader(str)
2431224274
InputRecordFieldLoader: Final = _RecordLoader(InputRecordField, None, None)

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