ingest: fix csvtk quotes

[joverlee521]

The automated ingest workflow failed with a csvtk quoting error.¹ Following nextstrain/docker-base#209, we can now use csvtk fix-quotes and csvtk del-quotes to work around the quoting issue.

¹ https://github.com/nextstrain/zika/actions/runs/8926866948/job/24518932039#step:8:139

Checklist

• Checks pass
• Trial ingest run

[j23414]

Changes look good to me

[joverlee521]

The error was caused by a new zika record that had internal quotes in the submitter.affiliation:

{"accession": "OR701943.1", "completeness": "PARTIAL", "host": {"lineage": [{"name": "cellular organisms", "taxId": 131567}, {"name": "Eukaryota", "taxId": 2759}, {"name": "Opisthokonta", "taxId": 33154}, {"name": "Metazoa", "taxId": 33208}, {"name": "Eumetazoa", "taxId": 6072}, {"name": "Bilateria", "taxId": 33213}, {"name": "Protostomia", "taxId": 33317}, {"name": "Ecdysozoa", "taxId": 1206794}, {"name": "Panarthropoda", "taxId": 88770}, {"name": "Arthropoda", "taxId": 6656}, {"name": "Mandibulata", "taxId": 197563}, {"name": "Pancrustacea", "taxId": 197562}, {"name": "Hexapoda", "taxId": 6960}, {"name": "Insecta", "taxId": 50557}, {"name": "Dicondylia", "taxId": 85512}, {"name": "Pterygota", "taxId": 7496}, {"name": "Neoptera", "taxId": 33340}, {"name": "Endopterygota", "taxId": 33392}, {"name": "Diptera", "taxId": 7147}, {"name": "Nematocera", "taxId": 7148}, {"name": "Culicomorpha", "taxId": 43786}, {"name": "Culicoidea", "taxId": 41827}, {"name": "Culicidae", "taxId": 7157}, {"name": "Culicinae", "taxId": 43817}, {"name": "Aedini", "taxId": 1056966}, {"name": "Aedes", "taxId": 7158}, {"name": "Stegomyia", "taxId": 53541}, {"name": "Aedes aegypti", "taxId": 7159}], "organismName": "Aedes aegypti", "taxId": 7159}, "isAnnotated": true, "isolate": {"collectionDate": "2021-11-11", "name": "6PYUC2022"}, "length": 217, "location": {"geographicLocation": "Mexico: Yucatan, Merida", "geographicRegion": "North America"}, "nucleotide": {"sequenceHash": "6FD6033C"}, "proteinCount": 1, "releaseDate": "2024-05-01T00:00:00Z", "sourceDatabase": "GenBank", "submitter.affiliation": "Centro de Investigaciones Regionales \"Dr. Hideyo Noguchi\", Laboratorio de Arbovirologia", "submitter.country": "Mexico", "submitter.names": ["Argaez-Sierra,D.G.", "Baak-Baak,C.M.", "Cigarroa-Toledo,N.", "Garcia-Rejon,J.E.", "Tzuc-Dzul,J.C.", "Acosta-Viana,K.Y.", "Nunez-Corea,D.A."], "updateDate": "2024-05-01T00:00:00Z", "virus": {"lineage": [{"name": "Viruses", "taxId": 10239}, {"name": "Riboviria", "taxId": 2559587}, {"name": "Orthornavirae", "taxId": 2732396}, {"name": "Kitrinoviricota", "taxId": 2732406}, {"name": "Flasuviricetes", "taxId": 2732462}, {"name": "Amarillovirales", "taxId": 2732545}, {"name": "Flaviviridae", "taxId": 11050}, {"name": "Orthoflavivirus", "taxId": 3044782}, {"name": "Orthoflavivirus zikaense", "taxId": 3048459}, {"name": "Zika virus", "taxId": 64320}], "organismName": "Zika virus", "taxId": 64320}}

I confirmed locally that the output for format_ncbi_dataset_report has the correct quoting in submitter-affiliation.

accession	accession-rev	sourcedb	sra-accs	isolate-lineage	geo-region	geo-location	isolate-collection-date	release-date	update-date	length	host-name	isolate-lineage-source	biosample-acc	submitter-names	submitter-affiliation	submitter-country
OR701943	OR701943.1	GenBank		6PYUC2022	North America	Mexico: Yucatan, Merida	2021-11-11	2024-05-01T00:00:00Z	2024-05-01T00:00:00Z	217	Aedes aegypti			Argaez-Sierra,D.G.,Baak-Baak,C.M.,Cigarroa-Toledo,N.,Garcia-Rejon,J.E.,Tzuc-Dzul,J.C.,Acosta-Viana,K.Y.,Nunez-Corea,D.A.	Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Laboratorio de Arbovirologia	Mexico

The final produced metadata.tsv has double quoting in the institution column, but this is due to an augur curate passthru bug.

genbank_accession	genbank_accession_rev	strain	date	region	country	division	location	length	host	release_date	update_date	sra_accessions	authors	institution
OR701943	OR701943.1	6PYUC2022	2021-11-11	North America	Mexico	Yucatan	Merida	217	Aedes aegypti	2024-05-01	2024-05-01		Argaez-Sierra et al	"Centro de Investigaciones Regionales ""Dr. Hideyo Noguchi"", Laboratorio de Arbovirologia"

[joverlee521]

Merging to get our ingest going again, but I'll loop back to the augur curate issue`.

[joverlee521]

Manually triggered ingest-to-phylogenetic