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rename singularity image #1956

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Merged
merged 4 commits into from
Jan 8, 2024
Merged

rename singularity image #1956

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93554c2
rename singularity image
Dec 11, 2023
76425e1
tox modifications
Dec 11, 2023
559ef39
use shutil.move instead of os.rename on network filesystem
Dec 12, 2023
5d3b0bd
add image argument to pass name
Dec 17, 2023
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69 changes: 45 additions & 24 deletions cwltool/singularity.py
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Original file line number Diff line number Diff line change
Expand Up @@ -171,29 +171,44 @@ def get_image(
cache_folder = create_tmp_dir(tmp_outdir_prefix)

absolute_path = os.path.abspath(cache_folder)
dockerfile_path = os.path.join(absolute_path, "Dockerfile")
singularityfile_path = dockerfile_path + ".def"
# if you do not set APPTAINER_TMPDIR will crash
# WARNING: 'nodev' mount option set on /tmp, it could be a
# source of failure during build process
# FATAL: Unable to create build: 'noexec' mount option set on
# /tmp, temporary root filesystem won't be usable at this location
with open(dockerfile_path, "w") as dfile:
dfile.write(dockerRequirement["dockerFile"])

singularityfile = SingularityWriter(DockerParser(dockerfile_path).parse()).convert()
with open(singularityfile_path, "w") as file:
file.write(singularityfile)

os.environ["APPTAINER_TMPDIR"] = absolute_path
singularity_options = ["--fakeroot"] if not shutil.which("proot") else []
Client.build(
recipe=singularityfile_path,
build_folder=absolute_path,
sudo=False,
options=singularity_options,
)
found = True
if "dockerImageId" in dockerRequirement:
image_name = dockerRequirement["dockerImageId"]
image_path = os.path.join(absolute_path, image_name)
if os.path.exists(image_path):
found = True
if found is False:
dockerfile_path = os.path.join(absolute_path, "Dockerfile")
singularityfile_path = dockerfile_path + ".def"
# if you do not set APPTAINER_TMPDIR will crash
# WARNING: 'nodev' mount option set on /tmp, it could be a
# source of failure during build process
# FATAL: Unable to create build: 'noexec' mount option set on
# /tmp, temporary root filesystem won't be usable at this location
with open(dockerfile_path, "w") as dfile:
dfile.write(dockerRequirement["dockerFile"])

singularityfile = SingularityWriter(DockerParser(dockerfile_path).parse()).convert()
with open(singularityfile_path, "w") as file:
file.write(singularityfile)

os.environ["APPTAINER_TMPDIR"] = absolute_path
singularity_options = ["--fakeroot"] if not shutil.which("proot") else []
if "dockerImageId" in dockerRequirement:
Client.build(
recipe=singularityfile_path,
build_folder=absolute_path,
image=dockerRequirement["dockerImageId"],
sudo=False,
options=singularity_options,
)
else:
Client.build(
recipe=singularityfile_path,
build_folder=absolute_path,
sudo=False,
options=singularity_options,
)
found = True
elif "dockerImageId" not in dockerRequirement and "dockerPull" in dockerRequirement:
match = re.search(pattern=r"([a-z]*://)", string=dockerRequirement["dockerPull"])
img_name = _normalize_image_id(dockerRequirement["dockerPull"])
Expand Down Expand Up @@ -326,7 +341,13 @@ def get_from_requirements(
if not self.get_image(cast(Dict[str, str], r), pull_image, tmp_outdir_prefix, force_pull):
raise WorkflowException("Container image {} not found".format(r["dockerImageId"]))

return os.path.abspath(cast(str, r["dockerImageId"]))
if "CWL_SINGULARITY_CACHE" in os.environ:
cache_folder = os.environ["CWL_SINGULARITY_CACHE"]
img_path = os.path.join(cache_folder, cast(str, r["dockerImageId"]))
else:
img_path = cast(str, r["dockerImageId"])

return os.path.abspath(img_path)

@staticmethod
def append_volume(runtime: List[str], source: str, target: str, writable: bool = False) -> None:
Expand Down