Begg 2023

[DianaSpurite]

Adding Begg 2023 samples

Pull Request

This PR is for a

• [x] New Publication(s)
• [ ] Correction

For the following list(s):

• [ ] ancientmetagenome-environmental (README, ask @thedir-team-dirt for advice)
• [ ] ancientmetagenome-hostassociated (README, ask @thedir-team-bugparty for advice)
• [x] 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):

This is to close #1058

Checklist

• [x] Publication is published (preprints currently not accepted)?
• [x] Checked the publication is not already in the database?
• [x] Checked samples in this publication are not previously published data (newly re-sequenced metagenomes are OK!)?
• [x] Samples are shotgun metagenomes (hostassociated-singlegenome may also contain whole-genome enriched data)?
• [x] 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'?
• [x] 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)?
• [x] (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

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[bot]]

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json

Errors were found, please unfold below to see errors:

``` Validation Errors were found ┏━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ ┃ Offending value ┃ Line number ┃ Column ┃ Error ┃ ┡━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ │ hair │ 583 │ material │ 'hair' is not an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ └─────────────────┴─────────────┴──────────┴───────────────────────────────────┘ The following type of errors were found: • DatasetValidationError ```

[github-actions[bot]]

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json

Errors were found, please unfold below to see errors:

``` Validation Errors were found ┏━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ ┃ Offending value ┃ Line number ┃ Column ┃ Error ┃ ┡━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ │ hair │ 583 │ material │ 'hair' is not an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ └─────────────────┴─────────────┴──────────┴───────────────────────────────────┘ The following type of errors were found: • DatasetValidationError ```

[github-actions[bot]]

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json

Errors were found, please unfold below to see errors:

``` Validation Errors were found ┏━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ ┃ Offending value ┃ Line number ┃ Column ┃ Error ┃ ┡━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ │ hair │ 583 │ material │ 'hair' is not an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ None │ 583 │ archive │ 'None' is not an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/archive.json │ └─────────────────┴─────────────┴──────────┴───────────────────────────────────┘ The following type of errors were found: • DatasetValidationError ```

[github-actions[bot]]

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json

Errors were found, please unfold below to see errors:

``` Validation Errors were found ┏━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ ┃ Offending value ┃ Line number ┃ Column ┃ Error ┃ ┡━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ │ None │ 583 │ archive │ 'None' is not an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io/ │ │ │ │ │ AncientMetagenomeDir/assets/enums/ │ │ │ │ │ archive.json │ └─────────────────┴─────────────┴─────────┴────────────────────────────────────┘ The following type of errors were found: • DatasetValidationError ```

[jfy133]

Library metadta should be live tomorrow if 'First public' here is to be believed: https://www.ebi.ac.uk/ena/browser/view/PRJEB56343

[jfy133]

Still not live, contacted some of teh authors :(

[jfy133]

No response from authors so have to drop this :(