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

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

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()
#> {
#>   "input_subdomain": [
#>     {
#>       "uri": [
#>         {
#>           "filename": "Hepatitis C virus genotype 1",
#>           "uri": "https://www.ncbi.nlm.nih.gov/nuccore/22129792",
#>           "access_time": "2017-01-24T09:40:17-0500"
#>         }
#>       ]
#>     },
#>     {
#>       "uri": [
#>         {
#>           "filename": "Hepatitis C virus type 1b complete genome",
#>           "uri": "https://www.ncbi.nlm.nih.gov/nuccore/5420376",
#>           "access_time": "2017-01-24T09:40:17-0500"
#>         }
#>       ]
#>     }
#>   ],
#>   "output_subdomain": [
#>     {
#>       "mediatype": "text/csv",
#>       "uri": [
#>         {
#>           "uri": "https://example.com/data/514769/dnaAccessionBased.csv",
#>           "access_time": "2017-01-24T09:40:17-0500"
#>         }
#>       ]
#>     },
#>     {
#>       "mediatype": "text/csv",
#>       "uri": [
#>         {
#>           "uri": "https://example.com/data/514801/SNPProfile*.csv",
#>           "access_time": "2017-01-24T09:40:17-0500"
#>         }
#>       ]
#>     }
#>   ]
#> }