Code for extracting data from mousedb

mousedb_access.R

#To use this you must supply:
#a cohort_id number
#an output datafile ('something.csv')
#the api_key to access the database

#for example:

#raw_data_file <- "Raw MRI Data.csv"
#cohort_id <- 35
#api_key <- 'SEE SLACK FOR THE API KEY'

#update.data(cohort_id=cohort_id, datafile=raw_data_file,api_key=api_key)



update.data <- function(cohort_id, datafile, api_key){

library(RCurl)
library(jsonlite)
  #get data from this cohort
cohort.url <- paste('http://bridgeslab.sph.umich.edu/mousedb/api/v1/data/?format=json&',api_key,'&limit=1000&animal__cohort=',cohort_id, sep="")

cohort.json <- fromJSON(getURL(cohort.url))
data_values <- cohort.json$meta$total_count


if(data_values <1000) {
  data <- fromJSON(getURL(cohort.url), flatten=T)$objects 
} else{
    offsets <- seq(1000,ceiling(data_values / 1000) * 1000,by=1000) #get integers from 2000 to x000 rounding up from data_values
  data <- fromJSON(getURL(cohort.url), flatten=T)$objects 
  for (offset in offsets){
    bigger.cohort.url <- paste('http://bridgeslab.sph.umich.edu/mousedb/api/v1/data/?format=json&',api_key,'&limit=1000&&offset=',offset,'&animal__cohort=',cohort_id, sep="")
    data <- bind_rows(data, fromJSON(getURL(bigger.cohort.url), flatten=T)$objects)
  }
}

data <-
  data %>%
  rename(MouseID = animal.MouseID,
         assay = assay.assay,
         Sex = animal.Gender,
         Genotype = animal.Genotype) %>%
  select(age,animal.id,MouseID,Sex,Genotype,values, assay, experiment.date)

write_csv(x=data, path=datafile)
}