update onsite#40
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📝 WalkthroughWalkthroughUpdate ONSITE to pyonsite 0.0.3 and migrate module IO from idXML to idparquet: environment and container refs updated, Nextflow process outputs and per-algorithm -out targets changed, meta.yml I/O patterns adjusted, tests/test-data and CI download step switched to idparquet. ChangesONSITE Module v0.0.3 Update
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Actionable comments posted: 1
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@modules/bigbio/onsite/meta.yml`:
- Around line 38-39: Update the meta.yml entry so the description matches the
pattern value: change the description field (currently "Protein/peptide
identifications file in idXML format") to refer to idparquet (e.g.,
"Protein/peptide identifications file in idparquet format") so the 'description'
and 'pattern' keys are consistent.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
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Configuration used: defaults
Review profile: CHILL
Plan: Pro
Run ID: 3a1bc770-27dc-43e8-b09a-dfec8cae2506
📒 Files selected for processing (5)
modules/bigbio/onsite/environment.ymlmodules/bigbio/onsite/main.nfmodules/bigbio/onsite/meta.ymlmodules/bigbio/onsite/tests/main.nf.testtests/config/test_data.config
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Actionable comments posted: 1
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In @.github/workflows/ci.yml:
- Around line 176-179: The download loop using curl in the for loop (iterating
over psms.parquet proteins.parquet protein_groups.parquet search_params.parquet
and using $DIR/$f and $BASE_URL/$f) can silently succeed on HTTP errors and hang
without timeouts; update the curl invocation to fail-fast and bounded by adding
-f (to treat HTTP errors as failures), -S for error output, explicit timeouts
(e.g. --connect-timeout and --max-time), and retry limits (e.g. --retry and
--retry-delay or --retry-connrefused), and ensure the loop exits on any curl
failure (e.g. by checking curl's exit code or enabling set -euo pipefail in the
script) so a bad download fails the CI immediately.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
ℹ️ Review info
⚙️ Run configuration
Configuration used: defaults
Review profile: CHILL
Plan: Pro
Run ID: 91af71ba-05ff-4468-95c0-c355c185d90b
📒 Files selected for processing (2)
.github/workflows/ci.ymltests/config/test_data.config
🚧 Files skipped from review as they are similar to previous changes (1)
- tests/config/test_data.config
| for f in psms.parquet proteins.parquet protein_groups.parquet search_params.parquet; do | ||
| echo "Downloading $f ..." | ||
| curl -sL -o "$DIR/$f" "$BASE_URL/$f" | ||
| done |
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Make the onsite fixture download fail-fast and bounded.
At Line 178, curl -sL can silently succeed on HTTP errors and has no timeout/retry controls. That can produce opaque nf-test failures later or flaky CI hangs.
Suggested hardening
- name: Download onsite test data directory
if: matrix.module == 'bigbio/onsite'
run: |
+ set -euo pipefail
DIR="tests/data/onsite/Phospho_redissolve_final_01_clean_perc.idparquet"
mkdir -p "$DIR"
BASE_URL="https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-ci-github/onsite/Phospho_redissolve_final_01_clean_perc.idparquet"
for f in psms.parquet proteins.parquet protein_groups.parquet search_params.parquet; do
echo "Downloading $f ..."
- curl -sL -o "$DIR/$f" "$BASE_URL/$f"
+ curl --fail --show-error --location \
+ --retry 3 --retry-all-errors --retry-delay 2 \
+ --connect-timeout 15 --max-time 120 \
+ -o "$DIR/$f" "$BASE_URL/$f"
+ test -s "$DIR/$f"
done
ls -lh "$DIR"🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In @.github/workflows/ci.yml around lines 176 - 179, The download loop using
curl in the for loop (iterating over psms.parquet proteins.parquet
protein_groups.parquet search_params.parquet and using $DIR/$f and $BASE_URL/$f)
can silently succeed on HTTP errors and hang without timeouts; update the curl
invocation to fail-fast and bounded by adding -f (to treat HTTP errors as
failures), -S for error output, explicit timeouts (e.g. --connect-timeout and
--max-time), and retry limits (e.g. --retry and --retry-delay or
--retry-connrefused), and ensure the loop exits on any curl failure (e.g. by
checking curl's exit code or enabling set -euo pipefail in the script) so a bad
download fails the CI immediately.
1 participant
Pull Request
Description
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main.nfincludes process definitionmeta.ymlincludes complete documentationenvironment.ymlspecifies dependenciesModule Type
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