How to download .sqlite file for all OrgDB in one go ?

[cparsania]

Hi,

I got the list of species and OrgDB objects using code below. How can I download all .sqlite files in one go ?

library(magrittr)
#> Warning: package 'magrittr' was built under R version 4.1.2
metadata <- EuPathDB::download_eupath_metadata(webservice = "fungidb")
#> Unable to find species names for 1 species.
#> Pneumocystis sp. 'macacae' P2C
#> Warning in xref_species(valid = taxa_xref[["matched_metadata"]], invalid =
#> taxa_xref[["unmatched_metadata"]], : How in the flying hell are these still
#> here: Melampsora larici-populina 98AG31.

metadata_tbl <- tibble::enframe(metadata) %>% 
        dplyr::filter(name != "invalid") %>% tidyr::unnest()
#> Warning: `cols` is now required when using unnest().
#> Please use `cols = c(value)`

metadata_tbl_sub <- metadata_tbl %>% 
        dplyr::select(GenusSpecies, TaxonUnmodified, TaxonXref,DataProvider, Genome,OrgdbPkg, OrgdbFile)

metadata_tbl_sub$OrgdbFile %>% head()
#> [1] "EuPathDB/OrgDb/3.14/org.Aluchuensis.IFO.4308.v59.eg.sqlite"               
#> [2] "EuPathDB/OrgDb/3.14/org.Eglyceriae.E277.v59.eg.sqlite"                    
#> [3] "EuPathDB/OrgDb/3.14/org.Aversicolor.CBS.583.65.v59.eg.sqlite"             
#> [4] "EuPathDB/OrgDb/3.14/org.Asydowii.CBS.593.65.v59.eg.sqlite"                
#> [5] "EuPathDB/OrgDb/3.14/org.Pcinnamomi.var.cinnamomi.CBS.144.22.v59.eg.sqlite"
#> [6] "EuPathDB/OrgDb/3.14/org.Awentii.DTO.134E9.v59.eg.sqlite"

^{Created on 2022-10-18 with reprex v2.0.2}