quiet_library <- function(...) { suppressPackageStartupMessages(library(...)) }
quiet_library(hise)
quiet_library(dplyr)
quiet_library(purrr)

BR1_rna_desc <- getFileDescriptors(
    fileType = "scRNA-seq-labeled", 
    filter = list(cohort.cohortGuid = "BR1"))
BR2_rna_desc <- getFileDescriptors(
    fileType = "scRNA-seq-labeled", 
    filter = list(cohort.cohortGuid = "BR2"))
UP1_rna_desc <- getFileDescriptors(
    fileType = "scRNA-seq-labeled", 
    filter = list(cohort.cohortGuid = "UP1"))

BR1_rna_desc <- fileDescToDataframe(BR1_rna_desc)
BR2_rna_desc <- fileDescToDataframe(BR2_rna_desc)
UP1_rna_desc <- fileDescToDataframe(UP1_rna_desc)

meta_data <- plyr::rbind.fill(BR1_rna_desc , BR2_rna_desc )

meta_data <- meta_data %>%
  filter(!grepl("EXP",file.batchID)) %>%
  filter(!file.batchID == "B004") %>%
  mutate(file.batch_num = as.numeric(sub("B","",file.batchID))) %>%
  filter(file.batch_num <= 145) %>%
  select(-file.batch_num)

non_healthy <- meta_data %>%
  filter(sample.diseaseStatesRecordedAtVisit != "") %>%
  select(subject.subjectGuid, sample.diseaseStatesRecordedAtVisit) %>%
  unique()

non_healthy

meta_data <- meta_data %>%
  filter(!subject.subjectGuid %in% non_healthy$subject.subjectGuid)

meta_data$pbmc_sample_id <- gsub("_","",paste0("PB0",substr(sub(".*PB0", "", meta_data$file.name),1,8)))
meta_data <- meta_data %>% 
  arrange(pbmc_sample_id) %>%
  filter(!duplicated(sample.sampleKitGuid, fromLast = TRUE)) %>%
  filter(sample.visitName == 'Flu Year 1 Day 0') %>%
  arrange(sample.sampleKitGuid)

table(meta_data$cohort.cohortGuid)

UP_Sample_kits <- c("KT00809","KT00811","KT00193","KT00841",
                    "KT00842","KT00833","KT00910","KT00884",
                    "KT00892","KT00914","KT00913","KT00927",
                    "KT00928","KT02391","KT02392","KT03223")

UP1_rna_desc <- UP1_rna_desc %>% 
  filter(sample.sampleKitGuid %in% UP_Sample_kits)

meta_data <- plyr::rbind.fill(meta_data, UP1_rna_desc)

if(!dir.exists("output")) {
    dir.create("output")
}

out_file <- file.path(
    "output",
    paste0("ref_h5_meta_data_",Sys.Date(),".csv")
)

write.csv(
    meta_data,
    out_file,
    row.names = FALSE,
    quote = FALSE
)

res <- cacheFiles(list(meta_data$file.id))

study_space_uuid <- "64097865-486d-43b3-8f94-74994e0a72e0"
title <- paste("PBMC Ref. Metadata", Sys.Date())

in_list <- as.list(meta_data$file.id)

out_list <- list(out_file)

uploadFiles(
    files = out_list,
    studySpaceId = study_space_uuid,
    title = title,
    inputFileIds = in_list,
    store = "project",
    doPrompt = FALSE
)

sessionInfo()