compose_io_v1.4.2 {biocompute}

Compose BioCompute Object - Input and Output Domain (v1.4.2)

Description

This domain contains the list of global input and output files created by the computational workflow, excluding the intermediate files.

Usage

compose_io_v1.4.2(input = NULL, output = NULL)

compose_io(input = NULL, output = NULL)

Arguments

input

Data frame. Variables include filename, uri, and access_time. Each row is one item in the input subdomain.

output

Data frame. Variables include mediatype, uri, and access_time. Each row is one item in the output subdomain.

Value

A list of class bco.domain

Examples

input_subdomain <- data.frame(
  "filename" = c(
    "Hepatitis C virus genotype 1",
    "Hepatitis C virus type 1b complete genome"
  ),
  "uri" = c(
    "https://www.ncbi.nlm.nih.gov/nuccore/22129792",
    "https://www.ncbi.nlm.nih.gov/nuccore/5420376"
  ),
  "access_time" = c(
    as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
    as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST")
  ),
  stringsAsFactors = FALSE
)

output_subdomain <- data.frame(
  "mediatype" = c("text/csv", "text/csv"),
  "uri" = c(
    "https://example.com/data/514769/dnaAccessionBased.csv",
    "https://example.com/data/514801/SNPProfile*.csv"
  ),
  "access_time" = c(
    as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
    as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST")
  ),
  stringsAsFactors = FALSE
)

compose_io(input_subdomain, output_subdomain) %>% convert_json()