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update ebi api url in fetch_sra_runinfo #26

Merged
merged 1 commit into from
Jul 22, 2021
Merged

update ebi api url in fetch_sra_runinfo #26

merged 1 commit into from
Jul 22, 2021

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alaindomissy
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PR checklist

  • [ x] This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
    • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
    • If necessary, also make a PR on the nf-core/fetchngs branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

The following test fails:

echo SRX681985 > id.txt
sra_ids_to_runinfo.py id.txt SRX681985&.runinfo.tsv

with this error:
ERROR: Connection failed
Error code '500'`, size: 2325 (max: 255)

replacing the ebi url path
from http://www.ebi.ac.uk/ena/data/warehouse/filereport
to https://www.ebi.ac.uk/ena/portal/api/filereport
prevents this error

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github-actions bot commented Jul 22, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cc3d5fe

+| ✅ 129 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: bin/scrape_software_versions.py
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File does not exist: assets/multiqc_config.yaml

✅ Tests passed:

Run details

  • nf-core/tools version 2.0.1
  • Run at 2021-07-22 16:23:25

drpatelh
drpatelh approved these changes Jul 22, 2021
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Awesome! Thanks @alaindomissy :) I knew something like this was causing the tests to fail on the other PRs and you have saved me digging into it!! Getting used to these breaking changes from the EBI API...

@drpatelh drpatelh merged commit d904bb5 into nf-core:dev Jul 22, 2021
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@drpatelh drpatelh drpatelh approved these changes

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@alaindomissy @drpatelh