R/zzz.R

In facileverse/FacileData: A fluent API for accessing multi-assay high-throughput genomics data

# .onLoad <- function(libname, pkgname) {
#   impl.prefix <- 'ftest'
#   ## This package serves as an "abstract implementation" to a FacileDb database.
#   ## The packages that implement access to a FacileWareHouse should define
#   ## the following options:
#   ##
#   ##   - *.datapath
#   ##   - *.dbpath
#   ##   - *.covdef
#   ##   - *.cachedir
#   ##
#   ## Since this FacileRepo package should not be tied to a specific FacileRepo
#   ## "implementation", we set the impl.prefex to be "ftest". This means that
#   ## this setup will create (or reuse) the following global options
#   ##
#   ##   - ftest.datapath
#   ##   - ftest.dbpath
#   ##   - ftest.covdef
#   ##   - ftest.cachedir
#
#   ## Default database this will point to is configured so everything works
#   ## when this package is loaded (deployed) on rescomp
#   ## TODO: Update this database path to a test db instead of Atezo
#
#   ## Until we create a test database and distribute within the package, I'm
#   ## affraid we can't avoid explicity defining the *.datapath. This is because
#   ## the unit tests are run in a "clean" (R --vanilla) environment which doesn't
#   ## load the stuff in your .Rprofile
#   ## dpath <- system.file('extdata', 'test', package='FacileData')
#   if (dir.exists('/gne')) {
#     dpath <- '/gne/home/lianogls/workspace/data/facile/test'
#   } else {
#     dpath <- '~/workspace/data/facile/test'
#   }
#   db.name <- 'TcgaDb-test.sqlite'
#   dpath <- getOption(sprintf('%s.datapath', impl.prefix), dpath)
#
#   pkg.opts <- list(
#     datapath=dpath,
#     dbpath=file.path(dpath, db.name),
#     cachedir=file.path(dpath, 'cache'),
#     covdef=file.path(dpath, 'sample-meta-definitions.yaml'))
#   names(pkg.opts) <- sprintf('%s.%s', impl.prefix, names(pkg.opts))
#
#   ## We only set these options if they aren't already set in the global options
#   ## The developers should set the appropriate options in the ~/.Rprofile
#   opts <- options()
#   toset <- !(names(pkg.opts) %in% names(opts))
#   if (any(toset)) {
#     options(pkg.opts[toset])
#   }
#
#   ## Check options
#   db.path <- getOption(paste0(impl.prefix, '.dbpath'))
#   if (!file.exists(db.path)) {
#     msg <- paste0(
#       "Default path to faciledb is not a valid file: ", db.path, "\n",
#       "Set options('facile.datapath') before loading the facilewarehouse ",
#       "package to a valid path to the SQLite database to skip this message.\n",
#       "A good place to do this for your local work is in your ~/.Rprofile")
#     ## warning(msg, immediate.=TRUE)
#   }
#
#   invisible()
# }