## ----style, echo = FALSE, results = 'asis', message=FALSE---------------------
BiocStyle::markdown()

## ----echo = FALSE, message = FALSE--------------------------------------------
library(Spectra)
library(BiocStyle)

## ----eval = FALSE-------------------------------------------------------------
# if (!requireNamespace("BiocManager", quietly = TRUE))
#     install.packages("BiocManager")
# 
# BiocManager::install("MsBackendMassIVE")

## -----------------------------------------------------------------------------
library(MsBackendMassIVE)

#' List files of a MassIVE data set
all_files <- massive_list_files("MSV000080547")
head(all_files)

## -----------------------------------------------------------------------------
massive_ftp_path("MSV000080547", mustWork = FALSE)

## -----------------------------------------------------------------------------
library(Spectra)

#' Load MS data files of one data set
s <- Spectra("MSV000080547", filePattern = "1.mzML$",
             source = MsBackendMassIVE())
s

## -----------------------------------------------------------------------------
spectraVariables(s)

## -----------------------------------------------------------------------------
spectraData(s, c("massive_id", "data_file"))
basename(s$data_file) |> head()

## -----------------------------------------------------------------------------
massive_sync(s@backend)

## -----------------------------------------------------------------------------
res <- massive_sync_data_files("MSV000080547",
                               fileName = "AG_spiked_sample11.mzML")
res

## -----------------------------------------------------------------------------
massive_cached_data_files()

## -----------------------------------------------------------------------------
prm <- massive_param_file("MSV000080547")
head(prm)

## -----------------------------------------------------------------------------
massive_number_files("MSV000080547")

## -----------------------------------------------------------------------------
massive_list_files("MSV000083058") |> head()
massive_download_file("MSV000083058",
                      fileName = "README_Histones_P108_VS3.docx",
                      path = tempdir())

## -----------------------------------------------------------------------------
res <- gnps2_query("MSV000083058")
head(res)

## -----------------------------------------------------------------------------
files_info <- gnps2_query("MSV000083058", filepath_pattern = "mzML$")
size_gb <- round(sum(files_info$size)/(2^30), 2)
message("Total size of mzML files in data set MSV000083058: ", size_gb, " GB")

## -----------------------------------------------------------------------------
gnps2_usi_download_link(res$usi[4])

## -----------------------------------------------------------------------------
sessionInfo()