R/zzz.R

In natverse/flycircuit: Functions to support the analysis of the FlyCircuit single neuron dataset

# Set local directory for data storage and remote location for data download
.onLoad <- function(libname, pkgname) {
  # start by establishing location of data directory
  if(is.null(getOption('flycircuit.datadir'))) 
    options(flycircuit.datadir=file.path(rappdirs::user_data_dir(appname='rpkg-flycircuit'), 'data'))
  op<-options()
  dd=getOption('flycircuit.datadir')
  
  # Create directory if it does not already exist
  # NB this will never be acceptable behaviour for a CRAN package
  dir.create(file.path(dd), showWarnings=FALSE,
             recursive = TRUE)
  if(file.access(dd, mode=2)!=0)
    warning("flycircuit package .onLoad: Unable to write to options('flycircuit.datadir'):", dd,
            ". Please check directory exists and is writeable!", 
            immediate. = T, call. = FALSE)
  dd=normalizePath(dd, mustWork = FALSE)
  # set the normalised path back as option because this is easier to read
  options(flycircuit.datadir=dd)
  
  # then set the other options (if they have not already been set by the user)
  op.flycircuit=list(
    flycircuit.dbdir=file.path(dirname(dd),'db'),
    flycircuit.bigmatdir=file.path(dd,'bigmatrix'),
    flycircuit.ffdir=file.path(dd,'ff'),
    flycircuit.scoremat='kcs20scores',
    flycircuit.sidataurl=c('http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/flycircuit','http://virtualflybrain.org/data/VFB/nblast/flycircuit'),
    flycircuit.remote_overwrite=NULL
  )
  
  toset <- !(names(op.flycircuit) %in% names(op))
  if(any(toset)) options(op.flycircuit[toset])
  
  dir.create(file.path(getOption('flycircuit.dbdir')), showWarnings=FALSE)
  dir.create(file.path(getOption('flycircuit.bigmatdir')), showWarnings=FALSE)
  dir.create(file.path(getOption('flycircuit.ffdir')), showWarnings=FALSE)

  add_registrations()
  
  invisible()
}

.onAttach <- function(libname, pkgname) {
  invisible()
}

# environment to store downloaded data to avoid polluting global namespace
.extdata <- new.env()