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Code for extracting data from mousedb
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| #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) | |
| } |
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