fetch-from-ncbi-virus: Pass options directly to ncbi-virus-url

Simplify the bash script by directly passing these options to the script
that uses them.

This requires changing the order so that required arguments are
specified before options.

fetch-from-ncbi-virus

@@ -1,16 +1,10 @@
 #!/usr/bin/env bash
-# usage: fetch-from-ncbi-virus [options] <ncbi_taxon_id> <github_repo>
+# usage: fetch-from-ncbi-virus <ncbi_taxon_id> <github_repo> [options]
 #
 # Fetch metadata and nucleotide sequences from [NCBI Virus](https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/)
 # and output NDJSON records to stdout.
 #
-# options:
-#
-#   --filter=<filter_query>                                 Filter criteria to add as `fq` param values for the NCBI Virus URL
-#                                                           May be specified multiple times.
-#
-#   --field=<output_column_name>:<ncbi_virus_field_name>    Metadata fields to add as `fl` param values for the NCBI Virus URL
-#                                                           May be specified multiple times.
+# [options] are passed directly to ncbi-virus-url. See that script for usage details.
 #
 # Originally copied from "bin/fetch-from-genbank" in nextstrain/ncov-ingest:
 #   https://github.com/nextstrain/ncov-ingest/blob/2a5f255329ee5bdf0cabc8b8827a700c92becbe4/bin/fetch-from-genbank
@@ -21,27 +15,13 @@ bin="$(dirname "$0")"
 
 
 main() {
-    declare -a filters
-    declare -a fields
-
-    for arg; do
-        case "$arg" in
-            --filter=*)
-                filters+=("${arg#*=}")
-                shift;;
-            --field=*)
-                fields+=("${arg#*=}")
-                shift;;
-            *)
-                break;;
-        esac
-    done
-
     local ncbi_taxon_id="${1:?NCBI taxon id is required.}"
     local github_repo="${2:?A GitHub repository with owner and repository name is required as the second argument}"
+    declare -a ncbi_virus_url_options
+    ncbi_virus_url_options=("${@:3}")
 
     local ncbi_virus_url
-    ncbi_virus_url="$("$bin"/ncbi-virus-url --ncbi-taxon-id "$ncbi_taxon_id" --filters "${filters[@]}" --fields "${fields[@]}")"
+    ncbi_virus_url="$("$bin"/ncbi-virus-url --ncbi-taxon-id "$ncbi_taxon_id" "${ncbi_virus_url_options[@]}")"
 
     fetch "$ncbi_virus_url" "$github_repo" | "$bin"/csv-to-ndjson
 }

tests/fetch-from-ncbi-virus/filter-and-fields.t

@@ -1,19 +1,17 @@
 Get the virus lineage IDs for 4 early Dengue sequences, testing the options --filter and --field.
 
-  $ $TESTDIR/../../fetch-from-ncbi-virus \
-  > --filter='CreateDate_dt:([1987-11-29T00:00:00Z TO 1987-11-29T00:00:01Z])' \
-  > --field='viruslineage_ids:VirusLineageId_ss' \
-  > 12637 nextstrain/ingest
+  $ $TESTDIR/../../fetch-from-ncbi-virus 12637 nextstrain/ingest \
+  > --filters 'CreateDate_dt:([1987-11-29T00:00:00Z TO 1987-11-29T00:00:01Z])' \
+  > --fields 'viruslineage_ids:VirusLineageId_ss'
   {"genbank_accession":"X05375","genbank_accession_rev":"X05375.1","database":"GenBank","strain":"","region":"","location":"","collected":"","submitted":"1987-11-29T00:00:00Z","updated":"2016-07-26T00:00:00Z","length":"360","host":"","isolation_source":"","bioproject_accession":"","biosample_accession":"","sra_accession":"","title":"Dengue virus type 2 genomic RNA for envelope protein E N-term","authors":"Biedrzycka,A., Cauchi,M.R., Bartholomeusz,A., Gorman,J.J., Wright,P.J.","submitting_organization":"","publications":"2952760","sequence":"GTAACTTATGGGACGTGTACCACCACAGGAGAACACAGAAGAGAAAAAAGATCAGTGGCACTCGTTCCACATGTGGGAATGGGACTGGAGACACGAACTGAAACATGGATGTCATCAGAAGGGGCCTGGAAACATGCCCAGAGAATTGAAACTTGGATCTTGAGACATCCAGGCTTTACCATAATGGCAGCAATCCTGGCATACACCATAGGAACGACACATTTCCAAAGAGCCCTGATTTTCATCTTACTGACAGCTGTCGCTCCTTCAATGACAATGCGTTGCATAGGAATATCAAATAGAGACTTTGTAGAAGGGGTTTCAGGAGGAAGCTGGGTTGACATAGTCTTAGAACATGGA","viruslineage_ids":"10239,2559587,2732396,2732406,2732462,2732545,11050,11051,12637,11060"}
   {"genbank_accession":"X05376","genbank_accession_rev":"X05376.1","database":"GenBank","strain":"","region":"","location":"","collected":"","submitted":"1987-11-29T00:00:00Z","updated":"2016-07-26T00:00:00Z","length":"360","host":"","isolation_source":"","bioproject_accession":"","biosample_accession":"","sra_accession":"","title":"Dengue virus type 2 genomic RNA for NS1 protein N-term","authors":"Biedrzycka,A., Cauchi,M.R., Bartholomeusz,A., Gorman,J.J., Wright,P.J.","submitting_organization":"","publications":"2952760","sequence":"ACAACAATGAGGGGAGCGAAGAGAATGGCCATTTTAGGTGACACAGCTTGGGATTTTGGATCCCTGGGAGGAGTGTTTACATCTATAGGAAAGGCTCTCCACCAAGTTTTCGGAGCAATCTATGGGGCTGCCTTCAGTGGGGTCTCATGGACTATGAAAATCCTCATAGGAGTCATTATCACATGGATAGGAATGAATTCACGCAGCACCTCACTTTCTGTGTCACTAGTATTGGTGGGAGTCGTGACGCTGTATTTGGGAGTTATGGTGCAGGCCGATAGTGGTTGCGTTGTGAGCTGGAAAAACAAAGAACTGAAGTGTGGCAGTGGGATTTTCATCACAGACAACGTGCACACATGG","viruslineage_ids":"10239,2559587,2732396,2732406,2732462,2732545,11050,11051,12637,11060"}
   {"genbank_accession":"X05377","genbank_accession_rev":"X05377.1","database":"GenBank","strain":"","region":"","location":"","collected":"","submitted":"1987-11-29T00:00:00Z","updated":"2016-07-26T00:00:00Z","length":"360","host":"","isolation_source":"","bioproject_accession":"","biosample_accession":"","sra_accession":"","title":"Dengue virus type 2 genomic RNA for NS3 protein N-term","authors":"Biedrzycka,A., Cauchi,M.R., Bartholomeusz,A., Gorman,J.J., Wright,P.J.","submitting_organization":"","publications":"2952760","sequence":"CTCACTGTGTGCTACGTGCTCACTGGACGATCGGCCGATTTGGAACTGGAGAGAGCCGCCGATGTCAAATGGGAAGATCAGGCAGAGATATCAGGAAGCAGTCCAATCCTGTCAATAACAATATCAGAAGATGGTAGCATGTCGATAAAAAACGAAGAGGAAGAACAAACACTGACCATACTCATTAGAACAGGATTGCTGGTGATCTCAGGACTTTTTCCTGTATCAATACCAATCACGGCAGCAGCATGGTACCTGTGGGAAGTGAAGAAACAACGGGCTGGAGTATTGTGGGATGTCCCTTCACCCCCACCCGTGGGAAAGGCTGAACTGGAAGATGGAGCCTATAGAATCAAGCAA","viruslineage_ids":"10239,2559587,2732396,2732406,2732462,2732545,11050,11051,12637,11060"}
   {"genbank_accession":"X05378","genbank_accession_rev":"X05378.1","database":"GenBank","strain":"","region":"","location":"","collected":"","submitted":"1987-11-29T00:00:00Z","updated":"2016-07-26T00:00:00Z","length":"360","host":"","isolation_source":"","bioproject_accession":"","biosample_accession":"","sra_accession":"","title":"Dengue virus type 2 genomic RNA for NS5 protein N-term","authors":"Biedrzycka,A., Cauchi,M.R., Bartholomeusz,A., Gorman,J.J., Wright,P.J.","submitting_organization":"","publications":"2952760","sequence":"GATCCAATACCCTATGATCCAAAGTTTGAAAAGCAGTTGGGACAAGTAATGCTCCTAGTCCTCTGCGGGACTCAAGTGTTGATGATGAGGACTACATGGGCTCTGTGTGAGGCTTTAACCTTAGCGACCGGGCCTATCTCCACATTGTGGGAAGGAAATCCAGGGAGGTTTTGGAACACTACCATTGCAGTGTCAATGGCTAACATTTTTAGAGGGAGTTACTTGGCCGGAGCTGGACTTCTCTTTTCCATCATGAAGAACACAACCAACACGAGAAGGGGAACTGGCAACATAGGAGAGACGCTTGGAGAGAAATGGAAAAGCCGATTGAACGCATTGGGGAAAAGTGAATTCCAGATC","viruslineage_ids":"10239,2559587,2732396,2732406,2732462,2732545,11050,11051,12637,11060"}
 
 Do the same but without --field.
 
-  $ $TESTDIR/../../fetch-from-ncbi-virus \
-  > --filter='CreateDate_dt:([1987-11-29T00:00:00Z TO 1987-11-29T00:00:01Z])' \
-  > 12637 nextstrain/ingest
+  $ $TESTDIR/../../fetch-from-ncbi-virus 12637 nextstrain/ingest \
+  > --filters 'CreateDate_dt:([1987-11-29T00:00:00Z TO 1987-11-29T00:00:01Z])'
   {"genbank_accession":"X05375","genbank_accession_rev":"X05375.1","database":"GenBank","strain":"","region":"","location":"","collected":"","submitted":"1987-11-29T00:00:00Z","updated":"2016-07-26T00:00:00Z","length":"360","host":"","isolation_source":"","bioproject_accession":"","biosample_accession":"","sra_accession":"","title":"Dengue virus type 2 genomic RNA for envelope protein E N-term","authors":"Biedrzycka,A., Cauchi,M.R., Bartholomeusz,A., Gorman,J.J., Wright,P.J.","submitting_organization":"","publications":"2952760","sequence":"GTAACTTATGGGACGTGTACCACCACAGGAGAACACAGAAGAGAAAAAAGATCAGTGGCACTCGTTCCACATGTGGGAATGGGACTGGAGACACGAACTGAAACATGGATGTCATCAGAAGGGGCCTGGAAACATGCCCAGAGAATTGAAACTTGGATCTTGAGACATCCAGGCTTTACCATAATGGCAGCAATCCTGGCATACACCATAGGAACGACACATTTCCAAAGAGCCCTGATTTTCATCTTACTGACAGCTGTCGCTCCTTCAATGACAATGCGTTGCATAGGAATATCAAATAGAGACTTTGTAGAAGGGGTTTCAGGAGGAAGCTGGGTTGACATAGTCTTAGAACATGGA"}
   {"genbank_accession":"X05376","genbank_accession_rev":"X05376.1","database":"GenBank","strain":"","region":"","location":"","collected":"","submitted":"1987-11-29T00:00:00Z","updated":"2016-07-26T00:00:00Z","length":"360","host":"","isolation_source":"","bioproject_accession":"","biosample_accession":"","sra_accession":"","title":"Dengue virus type 2 genomic RNA for NS1 protein N-term","authors":"Biedrzycka,A., Cauchi,M.R., Bartholomeusz,A., Gorman,J.J., Wright,P.J.","submitting_organization":"","publications":"2952760","sequence":"ACAACAATGAGGGGAGCGAAGAGAATGGCCATTTTAGGTGACACAGCTTGGGATTTTGGATCCCTGGGAGGAGTGTTTACATCTATAGGAAAGGCTCTCCACCAAGTTTTCGGAGCAATCTATGGGGCTGCCTTCAGTGGGGTCTCATGGACTATGAAAATCCTCATAGGAGTCATTATCACATGGATAGGAATGAATTCACGCAGCACCTCACTTTCTGTGTCACTAGTATTGGTGGGAGTCGTGACGCTGTATTTGGGAGTTATGGTGCAGGCCGATAGTGGTTGCGTTGTGAGCTGGAAAAACAAAGAACTGAAGTGTGGCAGTGGGATTTTCATCACAGACAACGTGCACACATGG"}
   {"genbank_accession":"X05377","genbank_accession_rev":"X05377.1","database":"GenBank","strain":"","region":"","location":"","collected":"","submitted":"1987-11-29T00:00:00Z","updated":"2016-07-26T00:00:00Z","length":"360","host":"","isolation_source":"","bioproject_accession":"","biosample_accession":"","sra_accession":"","title":"Dengue virus type 2 genomic RNA for NS3 protein N-term","authors":"Biedrzycka,A., Cauchi,M.R., Bartholomeusz,A., Gorman,J.J., Wright,P.J.","submitting_organization":"","publications":"2952760","sequence":"CTCACTGTGTGCTACGTGCTCACTGGACGATCGGCCGATTTGGAACTGGAGAGAGCCGCCGATGTCAAATGGGAAGATCAGGCAGAGATATCAGGAAGCAGTCCAATCCTGTCAATAACAATATCAGAAGATGGTAGCATGTCGATAAAAAACGAAGAGGAAGAACAAACACTGACCATACTCATTAGAACAGGATTGCTGGTGATCTCAGGACTTTTTCCTGTATCAATACCAATCACGGCAGCAGCATGGTACCTGTGGGAAGTGAAGAAACAACGGGCTGGAGTATTGTGGGATGTCCCTTCACCCCCACCCGTGGGAAAGGCTGAACTGGAAGATGGAGCCTATAGAATCAAGCAA"}