## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----bioconductor, eval = FALSE----------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("HubPub") ## ----load, message = FALSE---------------------------------------------------- library(HubPub) ## ----create------------------------------------------------------------------- fl <- tempdir() create_pkg(file.path(fl, "examplePkg"), "ExperimentHub") ## ----resource----------------------------------------------------------------- metadata <- hub_metadata( Title = "ENCODE", Description = "a test entry", BiocVersion = "4.1", Genome = NA_character_, SourceType = "JSON", SourceUrl = "http://www.encodeproject.org", SourceVersion = "x.y.z", Species = NA_character_, TaxonomyId = as.integer(9606), Coordinate_1_based = NA, DataProvider = "ENCODE Project", Maintainer = "tst person ", RDataClass = "Rda", DispatchClass = "Rda", Location_Prefix = "s3://experimenthub/", RDataPath = "ENCODExplorerData/encode_df_lite.rda", Tags = "ENCODE:Homo sapiens" ) add_resource(file.path(fl, "examplePkg"), metadata) ## ----read_metadata------------------------------------------------------------ resource <- file.path(fl, "examplePkg", "inst", "extdata", "metadata.csv") tst <- read.csv(resource) tst ## ----publish------------------------------------------------------------------ ## For publishing directories with multiple files fl <- tempdir() utils::write.csv(mtcars, file = file.path(fl, "mtcars1.csv")) utils::write.csv(mtcars, file = file.path(fl, "mtcars2.csv")) publish_resource(fl, "test_dir") ## For publishing a single file utils::write.csv(mtcars, file = file.path(fl, "mtcars3.csv")) publish_resource(file.path(fl, "mtcars3.csv"), "test_dir") ## ----session_info------------------------------------------------------------- sessionInfo()