C14 Vagene2018

[KaHea-21]

Pull Request

• Adding C14 Vagene2018

This PR is for a

• New Publication(s)
• Correction

For the following list(s):

• ancientmetagenome-environmental (README)
• ancientmetagenome-hostassociated (README)
• ancientsinglegenome-hostassociated (README)

This is to close

PR Workflow

1. Open this PR with sample metadata on the samples metadata sheet (:tada: you're already here!)
2. Wait for checks for sample metdata to pass
3. (If checks fail) make corrections, and push changes to this branch (no need to open a new PR!)
4. (Once passed) comment on this PR @spaam-bot please autofill <table_name> <project_id> to get a half-filled template! (may take a minute or so to get the comment with the file)
5. Fill in the template, and verify autofilled data correct!
6. Once filled in, append(!) the new rows from the TEMPLATE file to the end of the corresponding library metadata file, and update this PR
7. Wait for checks for library metadata to pass
8. Request review!

Pre-review checklist (new publications)

• 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 and not amplicon data
  • Note: 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)?
• Once sample table validation completed Library metadata has been added
  • Use @spaam-bot please autofill <table_name> <project_id> to get a half-filled template! May take a minute or so to get the comment with the file
  • Fill in template, and verify autofill data correct!
  • Once filled in, append(!) the new rows to the end of the corresponding library metadata file
• Changelog is updated to include the publication under 'Added'?

[github-actions]

amdirt, version 1.6.5

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 904, in resolve_from_url
document = self.store[url]
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/jsonschema/_utils.py", line 28, in getitem
return self.store[self.normalize(uri)]
KeyError: 'https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/requests/models.py", line 974, in json
return complexjson.loads(self.text, **kwargs)
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/json/init.py", line 346, in loads
return _default_decoder.decode(s)
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/json/decoder.py", line 353, in raw_decode
obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 60 column 9 (char 1917)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 907, in resolve_from_url
document = self.resolve_remote(url)
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 1010, in resolve_remote
result = requests.get(uri).json()
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/requests/models.py", line 978, in json
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
requests.exceptions.JSONDecodeError: Expecting ',' delimiter: line 60 column 9 (char 1917)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.9.21/x64/bin/amdirt", line 8, in
sys.exit(cli())
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/click/core.py", line 1161, in call
return self.main(*args, **kwargs)
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/click/core.py", line 1082, in main
rv = self.invoke(ctx)
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/click/core.py", line 1697, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/click/core.py", line 1443, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/click/core.py", line 788, in invoke
return __callback(*args, **kwargs)
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/click/decorators.py", line 33, in new_func
return f(get_current_context(), *args, **kwargs)
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/amdirt/cli.py", line 104, in validate
run_validation(**kwargs, **ctx.obj)
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/amdirt/validate/init.py", line 21, in run_validation
v.validate_schema()
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/amdirt/validate/domain/init.py", line 234, in validate_schema
for err in validator.iter_errors(self.dataset_json):
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 284, in iter_errors
for error in errors:
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/jsonschema/_legacy_validators.py", line 126, in items_draft6_draft7_draft201909
yield from validator.descend(item, items, path=index)
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 301, in descend
for error in self.evolve(schema=schema).iter_errors(instance):
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 284, in iter_errors
for error in errors:
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 332, in properties
yield from validator.descend(
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 301, in descend
for error in self.evolve(schema=schema).iter_errors(instance):
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 284, in iter_errors
for error in errors:
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 294, in ref
scope, resolved = validator.resolver.resolve(ref)
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 893, in resolve
return url, self._remote_cache(url)
File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 909, in resolve_from_url
raise exceptions.RefResolutionError(exc)
jsonschema.exceptions.RefResolutionError: Expecting ',' delimiter: line 60 column 9 (char 1917)

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

Dates

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_dates.tsv

Error	Source	Column	Row	Message
Dataset Parsing Error	ancientsinglegenome-hostassociated_dates.tsv	-	-	Unable to parse string "." at position 19