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Fix breaking changes introduced in the NCBI API #102

Merged
merged 6 commits into from
Jul 1, 2022
Merged

Fix breaking changes introduced in the NCBI API #102

merged 6 commits into from
Jul 1, 2022

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drpatelh
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@drpatelh drpatelh commented Jul 1, 2022 •
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See #99

NCBI recently updated their base API URLs which broke the functionality in this pipeline to fetch metadata for SRA and GEO ids.

I can't find a way to obtain GEO metadata using the current APIs so I will strip this functionality out of the pipeline and add it back in when a robust solution exists.

✅ Fixed for SRA ids

I have fixed the base URL for fetching SRA metadata based on the docs here

Old URL

https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=runinfo&term=SRR14593545

New URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?id=SRR14593545&db=sra&rettype=runinfo&retmode=text

❌ Broken for GEO ids

I tried to update the base URL for fetching GEO metadata based on the docs here but it is still broken....

Old URL

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4907283&targ=gsm&view=data&form=text

New URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?id=GSM4907283&db=gds&rettype=runinfo&retmode=text

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github-actions bot commented Jul 1, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3696f40

+| ✅ 143 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: lib/WorkflowFetchngs.groovy
  • nextflow_config - Config manifest.version should end in dev: '1.7'
  • readme - README did not have a Nextflow minimum version badge.

❔ 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 2.4.1
  • Run at 2022-07-01 15:36:40

maxulysse
maxulysse reviewed Jul 1, 2022
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@drpatelh drpatelh merged commit 80bdaa8 into nf-core:dev Jul 1, 2022
@drpatelh drpatelh mentioned this pull request Jul 1, 2022
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@hukai916
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To fetch metadata given GEO id, will ffq help: https://github.com/pachterlab/ffq ? Seems that ffq calls esearch utilities first and parse the results to obtain a full meta table.

@drpatelh
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Hi @hukai916 ! Yep, I have already created a draft PR to add in a ffq implementation #100 and just created an issue to officially track this feature #110

@adf-ncgr adf-ncgr mentioned this pull request Oct 13, 2022
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@drpatelh drpatelh modified the milestones: 1.8, 1.9 Nov 4, 2022
@Midnighter
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Using esearch first also works here:

  1. https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&term=GSM4907283
  2. https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sra&id=12420761&rettype=runinfo&retmode=text

@ejseqera
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ejseqera commented May 9, 2023

An eutils workflow for working with GEO IDs is somewhat described here: https://www.ncbi.nlm.nih.gov/geo/info/geo_paccess.html (updated March 27 2023)

@ejseqera ejseqera assigned ejseqera and unassigned ejseqera May 9, 2023
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@drpatelh @hukai916 @Midnighter @ejseqera @maxulysse