Add Brealey 2021

[jfy133]

Pull Request

This PR is for a

• New Publication(s)
• Correction

For the following list(s):

• ancientmetagenome-anthropogenic (README)
• ancientmetagenome-environmental (README, ask @thedir-team-dirt for advice)
• ancientmetagenome-hostassociated (README, ask @thedir-team-bugparty for advice)
• ancientsinglegenome-hostassociated (README, ask @thedir-team-pathopeeps for advice)

New Publication

Publication Information

This pull request is to add samples from the following publication(s): 10.1016/j.cub.2021.08.010

This is to close #426

Checklist

• Publication is published (preprints currently not accepted)?
• Checked the publication is not already in the database?
• Checked samples in this publication are not previously published data (newly re-sequenced metagenomes are OK!)?
• Samples are shotgun metagenomes (hostassociated-singlegenome may also contain whole-genome enriched data)?
• Checked the list follows conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)?
• Changelog is updated to include the publication under 'Added'?
• [] Pull request has passed validation checks (see automated comment from github-bot)?
• Review requested from corresponding team (see list of lists above for each team)?
• (If applicable) Made a separate PR to add new categories to controlled lists (stored under /assets/enums, e.g. material or archive)? If so the corresponding PR is here:

If you do not know how to check errors in failed validation checks, expand here

Correction

This PR is for

• ancientmetagenome-hostassociated
• ancientsinglegenome-hostassociated
• ancientmetagenome-environmental
• ancientmetagenome-anthropogenic

Reference

This pull request is to correct samples from the following publication(s):

This is to close

Description

The issue is:

Checklist

• Checked the corrected entries follow conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)
• Changelog is updated to include the publication under 'Changed'?
• Pull request has passed validation checks (see automated comment from github-bot)?
• Review requested from corresponding team (see list of lists above for each team)?

[github-actions]

ancientMetagenomeDirCheck, version 1.2.1

Ancient Metagenome Host Associated

                        Validation Errors were found                        
┏━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Offending value ┃ Line number ┃    Column ┃ Error                        ┃
┡━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│            None │ 997         │ site_name │ None is not of type 'string' │
│            None │ 999         │ site_name │ None is not of type 'string' │
│            None │ 965         │ site_name │ None is not of type 'string' │
└─────────────────┴─────────────┴───────────┴──────────────────────────────┘
DatasetValidationError

[github-actions]

ancientMetagenomeDirCheck, version 1.2.1

Ancient Metagenome Host Associated

All is good, no errors were found !

Ancient Single Genome Host Associated

All is good, no errors were found !

Ancient Metagenome Environmental

All is good, no errors were found !

[ivelsko]

I think something is misaligned for this dataset. The lat/long coordinates and site_name don't align with the sample_name - for example UA021 has NA for lat/long but has entries in the publication table. I also can't match up the site_name with Spec.locality or Spec.parish in the published table. It looks like the published SampleID column got misaligned with the rest and now UaXXX samples are aligning with BEXXX sample information

[jfy133]

Uh oh... we had a much worse problem yesterday where something like that had indeed happened. I will check with Jaelle...

[github-actions]

ancientMetagenomeDirCheck, version 1.2.1

Ancient Metagenome Host Associated

All is good, no errors were found !

Ancient Single Genome Host Associated

All is good, no errors were found !

Ancient Metagenome Environmental

All is good, no errors were found !

[jfy133]

If you check the latest Zenodo upload the metadata should be fixed now

[github-actions]

ancientMetagenomeDirCheck, version 1.2.1

Ancient Metagenome Host Associated

All is good, no errors were found !

Ancient Single Genome Host Associated

All is good, no errors were found !

Ancient Metagenome Environmental

All is good, no errors were found !