Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fix: default metadata fields for ENA API v2.0 #148

Merged
merged 9 commits into from
May 3, 2023
Merged

fix: default metadata fields for ENA API v2.0 #148

merged 9 commits into from
May 3, 2023

Conversation

ejseqera
Copy link
Contributor

@ejseqera ejseqera commented May 3, 2023

ENA API was just updated as of 05/02/2023. Portal API spec for v2.0 has changed and is breaking the pipeline currently. This PR updates the default metadata fields fetched from ENA to match the new spec and updates the fields used to create id_mappings.csv.

PR checklist

  • 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 --outdir <OUTDIR>).
  • 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).

drpatelh and others added 9 commits November 9, 2021 15:26
@ejseqera ejseqera added the bug Something isn't working label May 3, 2023
@ejseqera ejseqera requested review from robsyme and maxulysse May 3, 2023 02:32
@github-actions
Copy link

github-actions bot commented May 3, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9e454f2

+| ✅ 153 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: lib/WorkflowFetchngs.groovy
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-05-03 02:34:07

robsyme
robsyme reviewed May 3, 2023
View reviewed changes
bin/sra_ids_to_runinfo.py
"run_accession",
"experiment_accession",
"sample_accession",
"secondary_sample_accession",
"study_accession",
"secondary_study_accession",
"parent_study",
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Rather than removing parent_study, might it be sensible to use the renamed version of this field, parent_study_accession?

Copy link
Contributor Author

@ejseqera ejseqera May 3, 2023 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

parent_study_accession is not a valid field in the run metadata available. This will throw an error so I've omitted it entirely. There does not seem to be a similar renamed field available.

bin/sra_ids_to_runinfo.py
@@ -84,7 +82,6 @@
"sample_title",
"experiment_title",
"study_title",
"description",
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The description field is not among the list of changed fields in the ENA Portal API changes document that you linked. Is this an unannounced change?

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Seems like it. I believe this was replaced with sample_description exclusively.

@robsyme
Copy link
Contributor

robsyme commented May 3, 2023

Great work Esha, thanks!

@ejseqera ejseqera merged commit f6a0d61 into nf-core:dev May 3, 2023
10 checks passed
@ejseqera ejseqera deleted the fixena branch May 3, 2023 19:43
@drpatelh drpatelh mentioned this pull request May 6, 2023
Closed
This was referenced May 10, 2023
Closed
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@robsyme robsyme robsyme left review comments

@maxulysse maxulysse maxulysse approved these changes

Assignees
No one assigned
Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
5 participants
@ejseqera @robsyme @maxulysse @drpatelh @Midnighter