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Add more TypedDict definitions #393

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82 changes: 43 additions & 39 deletions cwl_utils/cwl_v1_0_expression_refactor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
import copy
import hashlib
import uuid
from collections.abc import Mapping, MutableSequence, Sequence
from collections.abc import MutableSequence, Sequence
from contextlib import suppress
from typing import Any, Optional, cast

Expand All @@ -18,10 +18,13 @@
from cwl_utils.errors import JavascriptException, WorkflowException
from cwl_utils.expression import do_eval, interpolate
from cwl_utils.types import (
CWLDirectoryType,
CWLFileType,
CWLObjectType,
CWLOutputType,
CWLParameterContext,
CWLRuntimeParameterContext,
is_file_or_directory,
)


Expand Down Expand Up @@ -547,31 +550,37 @@ def example_input(some_type: Any) -> Any:
"""Produce a fake input for the given type."""
# TODO: accept some sort of context object with local custom type definitions
if some_type == "Directory":
return {
"class": "Directory",
"location": "https://www.example.com/example",
"basename": "example",
"listing": [
{
"class": "File",
"basename": "example.txt",
"size": 23,
"contents": "hoopla",
"nameroot": "example",
"nameext": "txt",
}
],
}
return CWLDirectoryType(
**{
"class": "Directory",
"location": "https://www.example.com/example",
"basename": "example",
"listing": [
CWLFileType(
**{
"class": "File",
"basename": "example.txt",
"size": 23,
"contents": "hoopla",
"nameroot": "example",
"nameext": "txt",
}
)
],
}
)
if some_type == "File":
return {
"class": "File",
"location": "https://www.example.com/example.txt",
"basename": "example.txt",
"size": 23,
"contents": "hoopla",
"nameroot": "example",
"nameext": "txt",
}
return CWLFileType(
**{
"class": "File",
"location": "https://www.example.com/example.txt",
"basename": "example.txt",
"size": 23,
"contents": "hoopla",
"nameroot": "example",
"nameext": "txt",
}
)
if some_type == "int":
return 23
if some_type == "string":
Expand All @@ -581,12 +590,14 @@ def example_input(some_type: Any) -> Any:
return None


EMPTY_FILE: CWLOutputType = {
"class": "File",
"basename": "em.pty",
"nameroot": "em",
"nameext": "pty",
}
EMPTY_FILE = CWLFileType(
**{
"class": "File",
"basename": "em.pty",
"nameroot": "em",
"nameext": "pty",
}
)

TOPLEVEL_SF_EXPR_ERROR = (
"Input '{}'. Sorry, CWL Expressions as part of a secondaryFiles "
Expand Down Expand Up @@ -793,14 +804,7 @@ def process_workflow_reqs_and_hints(
resources={},
)
modified = True
if (
isinstance(expr_result, Mapping)
and "class" in expr_result
and (
expr_result["class"]
in ("File", "Directory")
)
):
if is_file_or_directory(expr_result):
target = cwl.InputParameter(
id=None,
type_=expr_result["class"],
Expand Down
82 changes: 43 additions & 39 deletions cwl_utils/cwl_v1_1_expression_refactor.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
import copy
import hashlib
import uuid
from collections.abc import Mapping, MutableSequence, Sequence
from collections.abc import MutableSequence, Sequence
from contextlib import suppress
from typing import Any, Optional, cast

Expand All @@ -18,10 +18,13 @@
from cwl_utils.errors import JavascriptException, WorkflowException
from cwl_utils.expression import do_eval, interpolate
from cwl_utils.types import (
CWLDirectoryType,
CWLFileType,
CWLObjectType,
CWLOutputType,
CWLParameterContext,
CWLRuntimeParameterContext,
is_file_or_directory,
)


Expand Down Expand Up @@ -545,31 +548,37 @@ def example_input(some_type: Any) -> Any:
"""Produce a fake input for the given type."""
# TODO: accept some sort of context object with local custom type definitions
if some_type == "Directory":
return {
"class": "Directory",
"location": "https://www.example.com/example",
"basename": "example",
"listing": [
{
"class": "File",
"basename": "example.txt",
"size": 23,
"contents": "hoopla",
"nameroot": "example",
"nameext": "txt",
}
],
}
return CWLDirectoryType(
**{
"class": "Directory",
"location": "https://www.example.com/example",
"basename": "example",
"listing": [
CWLFileType(
**{
"class": "File",
"basename": "example.txt",
"size": 23,
"contents": "hoopla",
"nameroot": "example",
"nameext": "txt",
}
)
],
}
)
if some_type == "File":
return {
"class": "File",
"location": "https://www.example.com/example.txt",
"basename": "example.txt",
"size": 23,
"contents": "hoopla",
"nameroot": "example",
"nameext": "txt",
}
return CWLFileType(
**{
"class": "File",
"location": "https://www.example.com/example.txt",
"basename": "example.txt",
"size": 23,
"contents": "hoopla",
"nameroot": "example",
"nameext": "txt",
}
)
if some_type == "int":
return 23
if some_type == "string":
Expand All @@ -579,12 +588,14 @@ def example_input(some_type: Any) -> Any:
return None


EMPTY_FILE: CWLOutputType = {
"class": "File",
"basename": "em.pty",
"nameroot": "em",
"nameext": "pty",
}
EMPTY_FILE = CWLFileType(
**{
"class": "File",
"basename": "em.pty",
"nameroot": "em",
"nameext": "pty",
}
)

TOPLEVEL_SF_EXPR_ERROR = (
"Input '{}'. Sorry, CWL Expressions as part of a secondaryFiles "
Expand Down Expand Up @@ -795,14 +806,7 @@ def process_workflow_reqs_and_hints(
resources={},
)
modified = True
if (
isinstance(expr_result, Mapping)
and "class" in expr_result
and (
expr_result["class"]
in ("File", "Directory")
)
):
if is_file_or_directory(expr_result):
target = cwl.WorkflowInputParameter(
id=None,
type_=expr_result["class"],
Expand Down
70 changes: 40 additions & 30 deletions 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 @@ -18,6 +18,8 @@
from cwl_utils.errors import JavascriptException, WorkflowException
from cwl_utils.expression import do_eval, interpolate
from cwl_utils.types import (
CWLDirectoryType,
CWLFileType,
CWLObjectType,
CWLOutputType,
CWLParameterContext,
Expand Down Expand Up @@ -545,31 +547,37 @@ def example_input(some_type: Any) -> Any:
"""Produce a fake input for the given type."""
# TODO: accept some sort of context object with local custom type definitions
if some_type == "Directory":
return {
"class": "Directory",
"location": "https://www.example.com/example",
"basename": "example",
"listing": [
{
"class": "File",
"basename": "example.txt",
"size": 23,
"contents": "hoopla",
"nameroot": "example",
"nameext": "txt",
}
],
}
return CWLDirectoryType(
**{
"class": "Directory",
"location": "https://www.example.com/example",
"basename": "example",
"listing": [
CWLFileType(
**{
"class": "File",
"basename": "example.txt",
"size": 23,
"contents": "hoopla",
"nameroot": "example",
"nameext": "txt",
}
)
],
}
)
if some_type == "File":
return {
"class": "File",
"location": "https://www.example.com/example.txt",
"basename": "example.txt",
"size": 23,
"contents": "hoopla",
"nameroot": "example",
"nameext": "txt",
}
return CWLFileType(
**{
"class": "File",
"location": "https://www.example.com/example.txt",
"basename": "example.txt",
"size": 23,
"contents": "hoopla",
"nameroot": "example",
"nameext": "txt",
}
)
if some_type == "int":
return 23
if some_type == "string":
Expand All @@ -579,12 +587,14 @@ def example_input(some_type: Any) -> Any:
return None


EMPTY_FILE: CWLOutputType = {
"class": "File",
"basename": "em.pty",
"nameroot": "em",
"nameext": "pty",
}
EMPTY_FILE = CWLFileType(
**{
"class": "File",
"basename": "em.pty",
"nameroot": "em",
"nameext": "pty",
}
)

TOPLEVEL_SF_EXPR_ERROR = (
"Input '{}'. Sorry, CWL Expressions as part of a secondaryFiles "
Expand Down
19 changes: 10 additions & 9 deletions cwl_utils/expression.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,19 @@
import json
from collections.abc import Awaitable, MutableMapping
from enum import Enum
from typing import Any, Literal, Union, cast
from typing import Any, Union, cast

from schema_salad.utils import json_dumps

from cwl_utils.errors import JavascriptException, SubstitutionError, WorkflowException
from cwl_utils.loghandler import _logger
from cwl_utils.sandboxjs import JSEngine, default_timeout, get_js_engine, param_re
from cwl_utils.types import CWLObjectType, CWLOutputType, CWLParameterContext
from cwl_utils.types import (
CWLObjectType,
CWLOutputType,
CWLParameterContext,
is_cwl_parameter_context_key,
)
from cwl_utils.utils import bytes2str_in_dicts


Expand Down Expand Up @@ -123,19 +128,15 @@ def evaluator(
if first_symbol_end + 1 == len(ex) and first_symbol == "null":
return None
try:
if first_symbol in ("inputs", "self", "runtime"):
symbol = cast(
Literal["inputs"] | Literal["self"] | Literal["runtime"],
first_symbol,
)
if is_cwl_parameter_context_key(first_symbol):
if inspect.iscoroutinefunction(js_engine.regex_eval):
return asyncio.get_event_loop().run_until_complete(
cast(
Awaitable[CWLOutputType],
js_engine.regex_eval(
first_symbol,
ex[first_symbol_end:-1],
cast(CWLOutputType, obj[symbol]),
cast(CWLOutputType, obj[first_symbol]),
**kwargs,
),
)
Expand All @@ -146,7 +147,7 @@ def evaluator(
js_engine.regex_eval(
first_symbol,
ex[first_symbol_end:-1],
cast(CWLOutputType, obj[symbol]),
cast(CWLOutputType, obj[first_symbol]),
**kwargs,
),
)
Expand Down
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