R/zzz.R

In saezlab/OmnipathR: OmniPath web service client and more

#!/usr/bin/env Rscript

#
#  This file is part of the `OmnipathR` R package
#
#  Copyright
#  2018-2024
#  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
#
#  File author(s): Alberto Valdeolivas
#                  Dénes Türei (turei.denes@gmail.com)
#                  Attila Gábor
#
#  Distributed under the MIT (Expat) License.
#  See accompanying file `LICENSE` or find a copy at
#      https://directory.fsf.org/wiki/License:Expat
#
#  Website: https://r.omnipathdb.org/
#  Git repo: https://github.com/saezlab/OmnipathR
#


#' @importFrom rmarkdown pandoc_version
#' @importFrom logger log_trace
#' @noRd
.onLoad <- function(libname, pkgname){

    omnipath_init_config()
    patch_logger_metavar()
    patch_logger_appender()
    omnipath_init_log(pkgname = pkgname)
    logger::log_info('Welcome to OmnipathR!')

    buildserver <- .on_buildserver()

    if(buildserver){

        omnipath_set_console_loglevel('trace')

    }

    omnipath_init_cache()

    if(buildserver) {

        logger::log_trace('Running on a build server, wiping cache.')
        cachedir <- omnipath_get_cachedir()
        logger::log_trace('Cache is at `%s`.', cachedir)
        logger::log_trace('Contains %i files.', length(list.files(cachedir)))
        logger::log_trace(
            'Cache is locked: %s.',
            'cache.lock' %in% list.files(cachedir)
        )
        tryCatch(
            omnipath_cache_wipe(),
            error = function(e){
                logger::log_error('Failed to wipe cache: %s.', e)
                logger::log_trace('On a build server, unlocking cache db.')
            }
        )
        omnipath_unlock_cache_db()

        # report pandoc version for Bioc build server debugging
        logger::log_trace('Pandoc version: `%s`.', pandoc_version())

    }

    omnipath_init_db(pkgname)
    .load_magic_bytes(pkgname)
    .load_urls(pkgname)
    .load_id_types(pkgname)
    .load_organisms(pkgname)

    if(buildserver){

        omnipath_unlock_cache_db()

        logger::log_trace(
            'Cache locked: %s',
            file.exists(omnipath_cache_lock_path())
        )

    }

}