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Lint container URLs in double quotes #2085

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Merged
mirpedrol merged 3 commits into from
Dec 1, 2022
Merged

Lint container URLs in double quotes #2085

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51fe1dd
don't allow double quotes in container strings regex
mirpedrol Dec 1, 2022
607cd57
avoid too many double quotes when specifying container links
mirpedrol Dec 1, 2022
0de2066
Merge branch 'dev' into lint-container-quotes
mirpedrol Dec 1, 2022
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12 changes: 9 additions & 3 deletions nf_core/modules/lint/main_nf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -254,14 +254,14 @@ def check_process_section(self, lines, fix_version, progress_bar):
self.passed.append(("process_standard_label", "Correct process label", self.main_nf))
else:
self.warned.append(("process_standard_label", "Process label unspecified", self.main_nf))
for l in lines:
for i, l in enumerate(lines):
if _container_type(l) == "bioconda":
bioconda_packages = [b for b in l.split() if "bioconda::" in b]
l = l.strip(" '\"")
if _container_type(l) == "singularity":
# e.g. "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :" -> v1.2.0_cv1
# e.g. "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :" -> 0.11.9--0
match = re.search(r"(?:/)?(?:biocontainers_)?(?::)?([A-Za-z\d\-_.]+?)(?:\.img)?['\"]", l)
match = re.search(r"(?:/)?(?:biocontainers_)?(?::)?([A-Za-z\d\-_.]+?)(?:\.img)?'", l)
if match is not None:
singularity_tag = match.group(1)
self.passed.append(("singularity_tag", f"Found singularity tag: {singularity_tag}", self.main_nf))
Expand All @@ -271,13 +271,19 @@ def check_process_section(self, lines, fix_version, progress_bar):
if _container_type(l) == "docker":
# e.g. "quay.io/biocontainers/krona:2.7.1--pl526_5' }" -> 2.7.1--pl526_5
# e.g. "biocontainers/biocontainers:v1.2.0_cv1' }" -> v1.2.0_cv1
match = re.search(r"(?:[/])?(?::)?([A-Za-z\d\-_.]+)['\"]", l)
match = re.search(r"(?:[/])?(?::)?([A-Za-z\d\-_.]+)'", l)
if match is not None:
docker_tag = match.group(1)
self.passed.append(("docker_tag", f"Found docker tag: {docker_tag}", self.main_nf))
else:
self.failed.append(("docker_tag", "Unable to parse docker tag", self.main_nf))
docker_tag = None
if l.startswith("container"):
container_section = l + lines[i + 1] + lines[i + 2]
if container_section.count('"') > 2:
self.failed.append(
("container_links", "Too many double quotes found when specifying containers", self.main_nf)
)

# Check that all bioconda packages have build numbers
# Also check for newer versions
Expand Down