2021-09-28_sammi_ovarian_sample_in_brca.R

# Description: Determine if ovarian sample in BrCa cohort that should have been removed is 
#     is present in clinical files and original data upload. 
# Author: Haley Hunter-Zinck
# Date: 2021-09-28
# Request: 
#     Source: Sammi in Freedcamp task https://freedcamp.com/view/2995682/tasks/42253884
#     Date of request: 2021-09-28
#     Message: Hi, I see that the ovarian sample (cpt_oncotree_code = LGSOC) is still 
#               included in the breast data in today's data cut (9/28/2021)

# setup ----------------------------

tic = as.double(Sys.time())

library(glue)
library(dplyr)
library(synapser)
synLogin()

# synapse
synid_folder_clinical <- "syn26253353"
synid_file_ca <- "syn26253370"
synid_file_vicc_brca_upload <- "syn24201984"
code_ovarian <- 'LGSOC'
sample_id_ovarian <- "GENIE-VICC-508075-unk-1"

# functions ----------------------------

get_synapse_entity_data_in_csv <- function(synapse_id, sep = ",", na.strings = c("NA")) {
  
  data <- read.csv(synGet(synapse_id)$path, stringsAsFactors = F, 
                   na.strings = na.strings, sep = sep)
  return(data)
}

save_to_synapse <- function(path, 
                            parent_id, 
                            file_name = NA, 
                            prov_name = NA, 
                            prov_desc = NA, 
                            prov_used = NA, 
                            prov_exec = NA) {
  
  if (is.na(file_name)) {
    file_name = path
  } 
  file <- File(path = path, parentId = parent_id, name = file_name)
  
  if (!is.na(prov_name) || !is.na(prov_desc) || !is.na(prov_used) || !is.na(prov_exec)) {
    act <- Activity(name = prov_name,
                    description = prov_desc,
                    used = prov_used,
                    executed = prov_exec)
    file <- synStore(file, activity = act)
  } else {
    file <- synStore(file)
  }
  
  return(T)
}

get_synapse_entity_name <- function(synapse_id) {
  return(synGet(synapse_id, downloadFile = F)$properties$name)
}


# read ----------------------------

data_clinical <- get_synapse_entity_data_in_csv(synid_file_ca)
data_upload <- get_synapse_entity_data_in_csv(synid_file_vicc_brca_upload)

# check for sample  ----------------------------

data_clinical %>% 
  filter(cpt_oncotree_code == code_ovarian) %>%
  select(cohort, record_id, institution, cpt_number, cpt_genie_sample_id, cpt_oncotree_code)

data_upload %>% 
  filter(cpt_oncotree_code == code_ovarian) %>%
  select(record_id, cpt_genie_sample_id, cpt_oncotree_code)

# remove sample  ----------------------------

mod <- data_clinical %>% 
  filter(cpt_oncotree_code != code_ovarian) 

dim(data_clinical)
dim(mod)

file_output <- get_synapse_entity_name(synid_file_ca)
write.csv(mod, row.names = F, file = file_output)
save_to_synapse(file_output, parent_id = synid_folder_clinical)

# close out ----------------------------

toc = as.double(Sys.time())
print(glue("Runtime: {round(toc - tic)} s"))