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handle errors when updating module version #1671

Merged
merged 13 commits into from
Aug 1, 2022
Merged

handle errors when updating module version #1671

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1cc6bad
handle errors when updating module version
mirpedrol Jul 13, 2022
ee53829
fix printing exception error
mirpedrol Jul 13, 2022
6ff568b
Update nf_core/modules/lint/main_nf.py
mirpedrol Jul 14, 2022
550ca5b
allow single and double quotes when matching container links
mirpedrol Jul 14, 2022
09f53c1
Merge branch 'update-module' of https://github.com/mirpedrol/tools in…
mirpedrol Jul 14, 2022
79e0e22
add InterfaceError to error handling
mirpedrol Jul 14, 2022
9d04df4
remove wrong InterfaceError
mirpedrol Jul 20, 2022
0490556
Merge branch 'dev' into update-module
mirpedrol Jul 21, 2022
f280975
Merge branch 'dev' into update-module
mirpedrol Jul 25, 2022
c1dff36
capture requests error
mirpedrol Jul 25, 2022
2a62796
capture sqlite errors
mirpedrol Jul 29, 2022
775afe4
update CHANGELOG
mirpedrol Aug 1, 2022
dee98e6
Merge branch 'dev' into update-module
mirpedrol Aug 1, 2022
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41 changes: 24 additions & 17 deletions nf_core/modules/lint/main_nf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -281,24 +281,31 @@ def check_process_section(self, lines, fix_version, progress_bar):
package, ver = bp.split("=", 1)
# If a new version is available and fix is True, update the version
if fix_version:
if _fix_module_version(self, bioconda_version, last_ver, singularity_tag, response):
progress_bar.print(f"[blue]INFO[/blue]\t Updating package '{package}' {ver} -> {last_ver}")
log.debug(f"Updating package {package} {ver} -> {last_ver}")
self.passed.append(
(
"bioconda_latest",
f"Conda package has been updated to the latest available: `{bp}`",
self.main_nf,
)
)
try:
fixed = _fix_module_version(self, bioconda_version, last_ver, singularity_tag, response)
except Exception as e:
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fixed = False
log.debug(f"Unable to update package {package} due to error: {e}")
else:
progress_bar.print(
f"[blue]INFO[/blue]\t Tried to update package. Unable to update package '{package}' {ver} -> {last_ver}"
)
log.debug(f"Unable to update package {package} {ver} -> {last_ver}")
self.warned.append(
("bioconda_latest", f"Conda update: {package} `{ver}` -> `{last_ver}`", self.main_nf)
)
if fixed:
progress_bar.print(f"[blue]INFO[/blue]\t Updating package '{package}' {ver} -> {last_ver}")
log.debug(f"Updating package {package} {ver} -> {last_ver}")
self.passed.append(
(
"bioconda_latest",
f"Conda package has been updated to the latest available: `{bp}`",
self.main_nf,
)
)
else:
progress_bar.print(
f"[blue]INFO[/blue]\t Tried to update package. Unable to update package '{package}' {ver} -> {last_ver}"
)
log.debug(f"Unable to update package {package} {ver} -> {last_ver}")
self.warned.append(
("bioconda_latest", f"Conda update: {package} `{ver}` -> `{last_ver}`", self.main_nf)
)
# Add available update as a warning
else:
self.warned.append(
("bioconda_latest", f"Conda update: {package} `{ver}` -> `{last_ver}`", self.main_nf)
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