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Merged
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Nov 2, 2025
Merged

implement some suggestions by refurb #381

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17 changes: 7 additions & 10 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 @@ -6,6 +6,7 @@
import hashlib
import uuid
from collections.abc import Mapping, MutableSequence, Sequence
from contextlib import suppress
from typing import Any, Optional, cast

from ruamel import yaml
Expand All @@ -30,11 +31,9 @@ def expand_stream_shortcuts(process: cwl.CommandLineTool) -> cwl.CommandLineTool
result = copy.deepcopy(process)
stdout_path = process.stdout
if not stdout_path:
stdout_path = str(
hashlib.sha1( # nosec
json_dumps(cwl.save(process)).encode("utf-8")
).hexdigest()
)
stdout_path = hashlib.sha1( # nosec
json_dumps(cwl.save(process)).encode("utf-8")
).hexdigest()
result.stdout = stdout_path
result.outputs[index].type_ = "File"
output.outputBinding = cwl.CommandOutputBinding(stdout_path, None, None)
Expand Down Expand Up @@ -534,12 +533,10 @@ def empty_inputs(
elif param.source is None and param.default:
result[param_id] = param.default
else:
try:
with suppress(WorkflowException):
result[param_id] = example_input(
utils.type_for_source(process_or_step.run, param.source, parent)
)
except WorkflowException:
pass
return result


Expand Down Expand Up @@ -797,8 +794,8 @@ def process_workflow_reqs_and_hints(
isinstance(expr_result, Mapping)
and "class" in expr_result
and (
expr_result["class"] == "File"
or expr_result["class"] == "Directory"
expr_result["class"]
in ("File", "Directory")
)
):
target = cwl.InputParameter(
Expand Down
17 changes: 7 additions & 10 deletions cwl_utils/cwl_v1_1_expression_refactor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
import hashlib
import uuid
from collections.abc import Mapping, MutableSequence, Sequence
from contextlib import suppress
from typing import Any, Optional, cast

from ruamel import yaml
Expand All @@ -30,11 +31,9 @@ def expand_stream_shortcuts(process: cwl.CommandLineTool) -> cwl.CommandLineTool
result = copy.deepcopy(process)
stdout_path = process.stdout
if not stdout_path:
stdout_path = str(
hashlib.sha1( # nosec
json_dumps(cwl.save(process)).encode("utf-8")
).hexdigest()
)
stdout_path = hashlib.sha1( # nosec
json_dumps(cwl.save(process)).encode("utf-8")
).hexdigest()
result.stdout = stdout_path
result.outputs[index].type_ = "File"
output.outputBinding = cwl.CommandOutputBinding(stdout_path, None, None)
Expand Down Expand Up @@ -532,12 +531,10 @@ def empty_inputs(
elif param.source is None and param.default:
result[param_id] = param.default
else:
try:
with suppress(WorkflowException):
result[param_id] = example_input(
utils.type_for_source(process_or_step.run, param.source, parent)
)
except WorkflowException:
pass
return result


Expand Down Expand Up @@ -799,8 +796,8 @@ def process_workflow_reqs_and_hints(
isinstance(expr_result, Mapping)
and "class" in expr_result
and (
expr_result["class"] == "File"
or expr_result["class"] == "Directory"
expr_result["class"]
in ("File", "Directory")
)
):
target = cwl.WorkflowInputParameter(
Expand Down
17 changes: 7 additions & 10 deletions cwl_utils/cwl_v1_2_expression_refactor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
import hashlib
import uuid
from collections.abc import Mapping, MutableSequence, Sequence
from contextlib import suppress
from typing import Any, Optional, cast

from ruamel import yaml
Expand All @@ -30,11 +31,9 @@ def expand_stream_shortcuts(process: cwl.CommandLineTool) -> cwl.CommandLineTool
result = copy.deepcopy(process)
stdout_path = process.stdout
if not stdout_path:
stdout_path = str(
hashlib.sha1( # nosec
json_dumps(cwl.save(process)).encode("utf-8")
).hexdigest()
)
stdout_path = hashlib.sha1( # nosec
json_dumps(cwl.save(process)).encode("utf-8")
).hexdigest()
result.stdout = stdout_path
result.outputs[index].type_ = "File"
output.outputBinding = cwl.CommandOutputBinding(stdout_path, None, None)
Expand Down Expand Up @@ -532,12 +531,10 @@ def empty_inputs(
elif param.source is None and param.default:
result[param_id] = param.default
else:
try:
with suppress(WorkflowException):
result[param_id] = example_input(
utils.type_for_source(process_or_step.run, param.source, parent)
)
except WorkflowException:
pass
return result


Expand Down Expand Up @@ -894,8 +891,8 @@ def process_workflow_reqs_and_hints(
isinstance(expr_result, Mapping)
and "class" in expr_result
and (
expr_result["class"] == "File"
or expr_result["class"] == "Directory"
expr_result["class"]
in ("File", "Directory")
)
):
target = cwl.WorkflowInputParameter(
Expand Down
4 changes: 2 additions & 2 deletions cwl_utils/docker_extract.py
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
#!/usr/bin/env python3
# SPDX-License-Identifier: Apache-2.0
import argparse
import os
import sys
from collections.abc import Iterator
from pathlib import Path
from typing import cast

import ruamel.yaml
Expand Down Expand Up @@ -51,7 +51,7 @@ def run(args: argparse.Namespace) -> list[cwl.DockerRequirement]:
sys.exit(1)

if args.dir:
os.makedirs(args.dir, exist_ok=True)
Path(args.dir).mkdir(parents=True, exist_ok=True)

top = cwl.load_document_by_uri(args.input)
reqs: list[cwl.DockerRequirement] = []
Expand Down
7 changes: 3 additions & 4 deletions cwl_utils/expression.py
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Original file line number Diff line number Diff line change
Expand Up @@ -252,8 +252,7 @@ def dump(string: str) -> str:
scan = scan[w[1] :]
w = scanner(scan)
if convert_to_expression:
parts.append(f'"{scan}"') # noqa: B907
parts.append(";}")
parts.extend((f'"{scan}"', ";}")) # noqa: B907
else:
parts.append(scan)
return "".join(parts)
Expand Down Expand Up @@ -290,8 +289,8 @@ def do_eval(
:param timeout: The maximum number of seconds to wait while executing.
"""
runtime = cast(MutableMapping[str, Union[int, str, None]], copy.deepcopy(resources))
runtime["tmpdir"] = tmpdir if tmpdir else None
runtime["outdir"] = outdir if outdir else None
runtime["tmpdir"] = tmpdir or None
runtime["outdir"] = outdir or None

rootvars = cast(
CWLObjectType,
Expand Down
8 changes: 2 additions & 6 deletions cwl_utils/expression_refactor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -139,11 +139,7 @@ def refactor(args: argparse.Namespace) -> int:
if not isinstance(result, MutableSequence):
result_json = save(
result,
base_url=(
result.loadingOptions.fileuri
if result.loadingOptions.fileuri
else ""
),
base_url=(result.loadingOptions.fileuri or ""),
)
# ^^ Setting the base_url and keeping the default value
# for relative_uris=True means that the IDs in the generated
Expand All @@ -155,7 +151,7 @@ def refactor(args: argparse.Namespace) -> int:
]
walk_tree(result_json)
# ^ converts multiline strings to nice multiline YAML
with open(output, "w", encoding="utf-8") as output_filehandle:
with output.open("w", encoding="utf-8") as output_filehandle:
output_filehandle.write(
"#!/usr/bin/env cwl-runner\n"
) # TODO: teach the codegen to do this?
Expand Down
4 changes: 2 additions & 2 deletions cwl_utils/graph_split.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ def arg_parser() -> argparse.ArgumentParser:
"-C",
"--outdir",
type=str,
default=os.getcwd(),
default=Path.cwd(),
help="Output folder for the unpacked CWL files.",
)
return parser
Expand Down Expand Up @@ -194,7 +194,7 @@ def rewrite(
else:
document[key] = f"{referrant_file}#{sub}"
elif isinstance(value, list):
new_sources = list()
new_sources = []
for entry in value:
if entry.startswith("#" + doc_id):
new_sources.append(entry[len(doc_id) + 2 :])
Expand Down
19 changes: 7 additions & 12 deletions cwl_utils/image_puller.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
# SPDX-License-Identifier: Apache-2.0
"""Classes for docker-extract."""
import logging
import os
import subprocess # nosec
from abc import ABC, abstractmethod
from pathlib import Path
Expand Down Expand Up @@ -53,11 +52,9 @@ class DockerImagePuller(ImagePuller):

def get_image_name(self) -> str:
"""Get the name of the tarball."""
name = "".join(self.req.split("/")) + ".tar"
# Replace colons with underscores in the name.
# See https://github.com/containers/podman/issues/489
name = name.replace(":", "_")
return name
return ("".join(self.req.split("/")) + ".tar").replace(":", "_")

def generate_udocker_loading_command(self) -> str:
"""Generate the udocker loading command."""
Expand All @@ -70,14 +67,14 @@ def save_docker_image(self) -> None:
ImagePuller._run_command_pull(cmd_pull)
_LOGGER.info(f"Image successfully pulled: {self.req}")
if self.save_directory:
dest = os.path.join(self.save_directory, self.get_image_name())
dest = Path(self.save_directory, self.get_image_name())
if self.save_directory and self.force_pull:
os.remove(dest)
dest.unlink()
cmd_save = [
self.cmd,
"save",
"-o",
dest,
str(dest),
self.req,
]
subprocess.run(cmd_save, check=True) # nosec
Expand Down Expand Up @@ -111,10 +108,8 @@ def save_docker_image(self) -> None:
save_directory: str | Path
if self.save_directory:
save_directory = self.save_directory
if (
os.path.exists(os.path.join(save_directory, self.get_image_name()))
and not self.force_pull
):
target = Path(save_directory, self.get_image_name())
if target.exists() and not self.force_pull:
_LOGGER.info(f"Already cached {self.req} with Singularity.")
return
_LOGGER.info(f"Pulling {self.req} with Singularity...")
Expand All @@ -127,7 +122,7 @@ def save_docker_image(self) -> None:
cmd_pull.extend(
[
"--name",
os.path.join(save_directory, self.get_image_name()),
str(target),
f"docker://{self.req}",
]
)
Expand Down
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