Ingest currently blocked by NCBI Virus changes

[joverlee521]

Current Behavior

Although this repo is not using the centralized ingest script fetch-from-ncbi-virus, the ingest pipeline is pulling from NCBI Virus URLs defined in the ingest config:

rsv/ingest/config/config.yaml

Lines 6 to 8 in 4098eb6

	a: "https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/vvsearch2/?fq=%7B%21tag%3DSeqType_s%7DSeqType_s%3A%28%22Nucleotide%22%29&fq=VirusLineageId_ss%3A%28208893%29&q=%2A%3A%2A&cmd=download&dlfmt=csv&fl=genbank_accession%3Aid%2Cgenbank_accession_rev%3AAccVer_s%2Cdatabase%3ASourceDB_s%2Cstrain%3AIsolate_s%2Cregion%3ARegion_s%2Clocation%3ACountryFull_s%2Ccollected%3ACollectionDate_s%2Csubmitted%3ACreateDate_dt%2Clength%3ASLen_i%2Chost%3AHost_s%2Cisolation_source%3AIsolation_csv%2Cbioproject_accession%3ABioProject_s%2Cbiosample_accession%3ABioSample_s%2Csra_accession%3ASRALink_csv%2Ctitle%3ADefinition_s%2Cauthors%3AAuthors_csv%2Cpublications%3APubMed_csv%2Csequence%3ANucleotide_seq&sort=SourceDB_s+desc%2C+CollectionDate_s+asc%2C+id+asc&email=hello%40nextstrain.org"
	b: "https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/vvsearch2/?fq=%7B%21tag%3DSeqType_s%7DSeqType_s%3A%28%22Nucleotide%22%29&fq=VirusLineageId_ss%3A%28208895%29&q=%2A%3A%2A&cmd=download&dlfmt=csv&fl=genbank_accession%3Aid%2Cgenbank_accession_rev%3AAccVer_s%2Cdatabase%3ASourceDB_s%2Cstrain%3AIsolate_s%2Cregion%3ARegion_s%2Clocation%3ACountryFull_s%2Ccollected%3ACollectionDate_s%2Csubmitted%3ACreateDate_dt%2Clength%3ASLen_i%2Chost%3AHost_s%2Cisolation_source%3AIsolation_csv%2Cbioproject_accession%3ABioProject_s%2Cbiosample_accession%3ABioSample_s%2Csra_accession%3ASRALink_csv%2Ctitle%3ADefinition_s%2Cauthors%3AAuthors_csv%2Cpublications%3APubMed_csv%2Csequence%3ANucleotide_seq&sort=SourceDB_s+desc%2C+CollectionDate_s+asc%2C+id+asc&email=hello%40nextstrain.org"
	general: "https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/vvsearch2/?fq=%7B%21tag%3DSeqType_s%7DSeqType_s%3A%28%22Nucleotide%22%29&fq=VirusLineageId_ss%3A%2811250%29&q=%2A%3A%2A&cmd=download&dlfmt=csv&fl=genbank_accession%3Aid%2Cgenbank_accession_rev%3AAccVer_s%2Cdatabase%3ASourceDB_s%2Cstrain%3AIsolate_s%2Cregion%3ARegion_s%2Clocation%3ACountryFull_s%2Ccollected%3ACollectionDate_s%2Csubmitted%3ACreateDate_dt%2Clength%3ASLen_i%2Chost%3AHost_s%2Cisolation_source%3AIsolation_csv%2Cbioproject_accession%3ABioProject_s%2Cbiosample_accession%3ABioSample_s%2Csra_accession%3ASRALink_csv%2Ctitle%3ADefinition_s%2Cauthors%3AAuthors_csv%2Cpublications%3APubMed_csv%2Csequence%3ANucleotide_seq&sort=SourceDB_s+desc%2C+CollectionDate_s+asc%2C+id+asc&email=hello%40nextstrain.org"

This results in the same issues in the ingest pipeline described in nextstrain/ingest#18 and nextstrain/mpox#178

The metadata.tsv and sequences.fasta on S3 at s3://nextstrain-data/files/workflows/rsv/a/ and s3://nextstrain-data/files/workflows/rsv/b/ are empty.