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Container warns if permission is denied #2270

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Merged
ewels merged 8 commits into from
May 3, 2023
Merged

Container warns if permission is denied #2270

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6795985
Container warns if permission is denied
adamrtalbot May 2, 2023
ec334da
Change to specific status codes
adamrtalbot May 2, 2023
8cb66f5
CHANGELOG
adamrtalbot May 2, 2023
0129cb3
Merge branch 'dev' into container_url_error
adamrtalbot May 2, 2023
7d87d6d
Raise warning for modules
adamrtalbot May 2, 2023
e4cd14a
More explicit errors regarding connecting to container URLs
adamrtalbot May 2, 2023
1087e8f
only check for url symbols for docker containers url
mirpedrol May 2, 2023
f067e87
Better error message when unable to connect to container
adamrtalbot May 2, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@

### Linting

- Warn if container access is denied ([#2270](https://github.com/nf-core/tools/pull/2270))

### Modules

### Subworkflows
Expand Down
16 changes: 9 additions & 7 deletions nf_core/modules/lint/main_nf.py
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Expand Up @@ -331,8 +331,14 @@ def check_process_section(self, lines, fix_version, progress_bar):
log.debug(f"Unable to connect to url '{urlunparse(url)}' due to error: {e}")
self.failed.append(("container_links", "Unable to connect to container URL", self.main_nf))
continue
if response.status_code != 200:
self.failed.append(("container_links", "Unable to connect to container URL", self.main_nf))
if not response.ok:
self.failed.append(
(
"container_links",
f"Unable to connect to {response.url}, status code: {response.status_code}",
self.main_nf,
)
)

# Check that all bioconda packages have build numbers
# Also check for newer versions
Expand Down Expand Up @@ -581,9 +587,5 @@ def _container_type(line):
if url_match:
return "singularity"
return None
if (
line.startswith("biocontainers/")
or line.startswith("quay.io/")
or (line.count("/") == 1 and line.count(":") == 1)
):
if line.count("/") >= 1 and line.count(":") == 1:
return "docker"