plumber

It is an API generator in R, which has been tested through Caprion data as follows.

Setup

As noted elsewhere, libsodium is required for installation of the R package.

library(plumber)
library(seqminer)
library(jsonlite)

get_data <- function(filename, region)
{
  query_result <- seqminer::tabix.read(filename, region)
  hdr <- c("Chromosome", "Position",
           "MarkerName", "Allele1", "Allele2", "Freq1", "FreqSE", "MinFreq", "MaxFreq",
           "Effect", "StdErr", "logP",
           "Direction", "HetISq", "HetChiSq", "HetDf", "logHetP", "N")
  df <- read.table(text = paste(query_result, collapse = "\n"), sep = "\t", col.names=hdr)
  return(df)
}

options(width = 200)
filename <- file.path("METAL_dr","ZPI_dr-1.tbl.gz")
region <- "1:10000-20000"
data <- get_data(filename, region)
head(data,1)

plbr <- plumber::Plumber$new()
plbr$handle("GET", "/data", function(req, res) {
  protein <- req$args$protein
  region <- req$args$region
  if (is.null(protein) || is.null(region)) {
    res$status <- 400
    return(list(error = "Both 'protein' and 'region' must be provided"))
  }
  filename <- file.path("METAL_dr",paste0(protein,"_dr-1.tbl.gz"))
  print(filename)
  if (!file.exists(filename)) {
    res$status <- 404
    return(list(error = paste("File for", protein, "not found")))
  }
  data <- get_data(filename, region)
  json_data <- toJSON(data, dataframe = "rows", na = "null")
  res$setHeader("Content-Type", "application/json")
  return(json_data)
})
plbr$run(port = 8001)

We see that,

> head(data,1)
  Chromosome Position   MarkerName Allele1 Allele2  Freq1 FreqSE MinFreq MaxFreq      Effect    StdErr  logP Direction HetISq HetChiSq HetDf logHetP    N
1          1    10352 1:10352_T_TA       t      ta 0.6147 0.0038  0.6122  0.6273 -0.05283738 0.0335632 -0.94    +--???    5.2    2.109     2 -0.4579 2491

and

Running plumber API at http://127.0.0.1:8001
Running swagger Docs at http://127.0.0.1:8001/__docs__/

So we get query results in JSON format from

• browser: http://localhost:8001/data?protein=ZPI&region=1:10000-20000
• curl: curl "http://localhost:8001/data?protein=ZPI&region=1:10000-20000"

Additional work required to get output from curl to a tab-delimited data,

curl "http://localhost:8001/data?protein=APOB&region=1:10000-20000" | \
jq -r '.[0] |
   fromjson |
   .[] |
   [
     .Chromosome, .Position, .MarkerName, .Allele1, .Allele2, .Freq1,
     .Effect, .StdErr, .logP, .Direction, .HetISq, .HetChiSq, .HetDf, .logHetP, .N
   ] |
   @tsv'

where

1. .[0]: Access the first element in the outer array (the string containing the JSON).
2. fromjson: Parse the string into a JSON object.
3. .[]: Iterate over the array inside the parsed JSON.
4. [ ... ]: Create an array of the values needed, each corresponds to a column in the TSV output.
5. @tsv: Convert the array into tab-separated values.

Note also that only selected columns (as in 4) are kept. The simplest way to have the header is add it manually,

(
  echo "Chromosome|Position|MarkerName|Allele1|Allele2|Freq1|Effect|StdErr|logP|Direction|HetISq|HetChiSq|HetDf|logHetP|N" | \
  sed 's/|/\t/g'
  curl command as above.
)

httpuv

This is alternative to plumber,

library(httpuv)
s <- startServer("0.0.0.0", 5000,
  list(
    call = function(req) {
      list(
        status = 200L,
        headers = list(
          'Content-Type' = 'text/html',
          'Access-Control-Allow-Origin' = '*',
          'Access-Control-Allow-Methods' = 'GET, POST, OPTIONS',
          'Access-Control-Allow-Headers' = 'Content-Type'
        ),
        body = "Hello world!"
      )
    },
    staticPaths = list(
      "/assets" = "content/assets/",
      "/lib" = staticPath(
        "content/lib",
        indexhtml = FALSE
      ),
      "/lib/dynamic" = excludeStaticPath()
    ),
    staticPathOptions = staticPathOptions(
      indexhtml = TRUE
    )
  )
)
s$stop()