fauna

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## Description of proposed changes Updates to the assay date parsing in tdb/elife_upload: - make parsing of assay date from fstem a little more robust - use the fstem's assay...

joverlee521

script/delete_records: Add option to match fields with regex pattern

2

Uses rethinkdb's `match` command to filter for records with field value that matches the provided regex pattern. See rethinkdb docs for more details: https://rethinkdb.com/api/python/match/ This was prompted by our need...

joverlee521

Revisit tdb/upload's `index_fields`

1

### Context Currently all titer data uploaded to fauna use the [tdb/upload's `index_fields`](https://github.com/nextstrain/fauna/blob/898179533778535fdaad41479d3b689c6ef0ee7c/tdb/upload.py#L51) to [create the record index](https://github.com/nextstrain/fauna/blob/898179533778535fdaad41479d3b689c6ef0ee7c/tdb/upload.py#L386-L399). If there are any changes in these field values, then the generated...

joverlee521

### Context In addition to ferret serological data, we also now receive individual-level human serological data. These new data do not have the same columns and values as the ferret...

huddlej

# Description From personal correspondence, use `aws s3` to upload the metadata and sequence files. > `nextstrain remote` is not intended for general S3 operations (e.g. operations not on dataset...

j23414

feat: BV-BRC support

1

### Context ViPR is being replaced with BV-BRC with final transfer possibly occurring by the end of the year (2022-12-31) which might disrupt pathogen builds. ### Description For any pathogen...

j23414

Geolocation assignments fail for duplicate location names

2

### Current Behavior 1. Locations defined in the `source-data/geo_synonyms.tsv` are ingested with the [label column as the key in 3 dicts](https://github.com/nextstrain/fauna/blob/master/vdb/upload.py#L257-L260) for location, division, and country. This means if there...

joverlee521

Bumps [express](https://github.com/expressjs/express) from 4.16.4 to 4.17.3. Release notes Sourced from express's releases. 4.17.3 deps: accepts@~1.3.8 deps: mime-types@~2.1.34 deps: [email protected] deps: [email protected] deps: [email protected] deps: [email protected] deps: [email protected] deps: [email protected] deps:...

dependabot[bot]

Bumps [certifi](https://github.com/certifi/python-certifi) from 2020.6.20 to 2022.12.7. Commits 9e9e840 2022.12.07 b81bdb2 2022.09.24 939a28f 2022.09.14 aca828a 2022.06.15.2 de0eae1 Only use importlib.resources's new files() / Traversable API on Python ≥3.11 ... b8eb5e9 2022.06.15.1...

dependabot[bot]

Bumps [qs](https://github.com/ljharb/qs) to 6.11.0 and updates ancestor dependency [express](https://github.com/expressjs/express). These dependencies need to be updated together. Updates `qs` from 6.5.2 to 6.11.0 Changelog Sourced from qs's changelog. 6.11.0 [New] [Fix]...

dependabot[bot]