diff --git a/R/read_study_design_from_DMS.R b/R/read_study_design_from_DMS.R index 831363d..a5c5a21 100644 --- a/R/read_study_design_from_DMS.R +++ b/R/read_study_design_from_DMS.R @@ -104,34 +104,10 @@ read_study_design_from_DMS <- function(data_package_num, ) # Files to search for - study_design_files <- paste0("^", names(required_cols), ".txt$") - - - if(.Platform$OS.type == "unix" | useHTTP){ - local_folder <- "~/temp_study_des" - - remote_folder <- gsub("\\\\","/", dataPkgReport$share_path) - remote_folder <- gsub("(", "\\(", remote_folder, fixed = TRUE) - remote_folder <- gsub(")", "\\)", remote_folder, fixed = TRUE) - - # Get paths to each of the study design tables - file_paths <- lapply(study_design_files, function(file_i) { - get_url_from_dir_and_file(remote_folder, file_i) - }) - - } else if (.Platform$OS.type == "windows") { - local_folder <- dataPkgReport$share_path - - # Get paths to each of the study design tables - file_paths <- lapply(study_design_files, function(file_i) { - list.files(path = local_folder, - pattern = file_i, - full.names = TRUE) - }) - - } else { - stop("Unknown OS type.") - } + file_paths <- file.path( + dataPkgReport$web_path, + glue::glue("{names(required_cols)}.txt") + ) names(file_paths) <- names(required_cols) diff --git a/man/read_MSstats_from_MSFragger_job.Rd b/man/read_MSstats_from_MSFragger_job.Rd index 8db8bf0..f61babf 100644 --- a/man/read_MSstats_from_MSFragger_job.Rd +++ b/man/read_MSstats_from_MSFragger_job.Rd @@ -36,7 +36,7 @@ Function has only been tested with label-free intensity-based if (is_PNNL_DMS_connection_successful()) { msnset <- read_MSstats_from_MSFragger_job( data_package_num = 4938, - param_file = "MSFragger_Tryp_Dyn_MetOx_ProtNTermAcet_StatCysAlk_20ppmParTol.params", + param_file = "MSFragger_Tryp_Dyn_MetOx_ProtNTermAcet_Stat_CysAlk_20ppmParTol.params", settings_file = "MSFragger_MatchBetweenRuns_Java80GB.xml", organism_db = "ID_008026_7A1842EC.fasta") show(msnset)