Compose BioCompute Object - Provenance Domain (v1.4.2)

compose_provenance_v1.4.2(
  name = NULL,
  version = NULL,
  review = NULL,
  derived_from = NULL,
  obsolete_after = NULL,
  embargo = NULL,
  created = NULL,
  modified = NULL,
  contributors = NULL,
  license = NULL
)

compose_provenance(
  name = NULL,
  version = NULL,
  review = NULL,
  derived_from = NULL,
  obsolete_after = NULL,
  embargo = NULL,
  created = NULL,
  modified = NULL,
  contributors = NULL,
  license = NULL
)

Arguments

name: Character string. Name for the BCO.
version: Character string. Version of this BCO instance object. Should follow the Semantic Versioning format (MAJOR.MINOR.PATCH).
review: Data frame. Reviewer identifiers and descriptions of the status of an object in the review process.
derived_from: Character string. Inheritance/derivation description.
obsolete_after: Date-time object. Expiration date of the object (optional).
embargo: Vector of date-time objects start_time and end_time. If the object has a period of time that it is not public, that range can be specified with this.
created: Date-time object. Initial creation time of the object.
modified: Date-time object. The most recent modification time of the object.
contributors: Data frame. Contributor identifiers and descriptions of their contribution types.
license: Character string. Licence URL or other licence information (text).

Value

A list of class bco.domain

Examples

name <- "HCV1a ledipasvir resistance SNP detection"
version <- "1.0.0"
review <- data.frame(
  "status" = c("approved", "approved"),
  "reviewer_comment" = c(
    "Approved by [company name] staff. Waiting for approval from FDA Reviewer",
    "The revised BCO looks fine"
  ),
  "date" = c(
    as.POSIXct("2017-11-12T12:30:48", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
    as.POSIXct("2017-12-12T12:30:48", format = "%Y-%m-%dT%H:%M:%S", tz = "America/Los_Angeles")
  ),
  "reviewer_name" = c("Jane Doe", "John Doe"),
  "reviewer_affiliation" = c("Seven Bridges Genomics", "U.S. Food and Drug Administration"),
  "reviewer_email" = c("example@sevenbridges.com", "example@fda.gov"),
  "reviewer_contribution" = c("curatedBy", "curatedBy"),
  "reviewer_orcid" = c("https://orcid.org/0000-0000-0000-0000", NA),
  stringsAsFactors = FALSE
)

derived_from <- "https://github.com/biocompute-objects/BCO_Specification/blob/1.2.1-beta/HCV1a.json"
obsolete_after <- as.POSIXct("2018-11-12T12:30:48", format = "%Y-%m-%dT%H:%M:%S", tz = "EST")

embargo <- c(
  "start_time" = as.POSIXct("2017-10-12T12:30:48", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
  "end_time" = as.POSIXct("2017-11-12T12:30:48", format = "%Y-%m-%dT%H:%M:%S", tz = "EST")
)

created <- as.POSIXct("2017-01-20T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST")

modified <- as.POSIXct("2019-05-10T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST")

contributors <- data.frame(
  "name" = c("Jane Doe", "John Doe"),
  "affiliation" = c("Seven Bridges Genomics", "U.S. Food and Drug Administration"),
  "email" = c("example@sevenbridges.com", "example@fda.gov"),
  "contribution" = I(list(c("createdBy", "curatedBy"), c("authoredBy"))),
  "orcid" = c("https://orcid.org/0000-0000-0000-0000", NA),
  stringsAsFactors = FALSE
)

license <- "https://creativecommons.org/licenses/by/4.0/"

compose_provenance(
  name, version, review, derived_from, obsolete_after,
  embargo, created, modified, contributors, license
) %>% convert_json()
#> {
#>   "name": "HCV1a ledipasvir resistance SNP detection",
#>   "version": "1.0.0",
#>   "review": [
#>     {
#>       "status": "approved",
#>       "reviewer_comment": "Approved by [company name] staff. Waiting for approval from FDA Reviewer",
#>       "date": 1510507848,
#>       "reviewer": [
#>         {
#>           "reviewer_name": "Jane Doe",
#>           "reviewer_affiliation": "Seven Bridges Genomics",
#>           "reviewer_email": "example@sevenbridges.com",
#>           "reviewer_contribution": "curatedBy",
#>           "reviewer_orcid": "https://orcid.org/0000-0000-0000-0000"
#>         }
#>       ]
#>     },
#>     {
#>       "status": "approved",
#>       "reviewer_comment": "The revised BCO looks fine",
#>       "date": 1513110648,
#>       "reviewer": [
#>         {
#>           "reviewer_name": "John Doe",
#>           "reviewer_affiliation": "U.S. Food and Drug Administration",
#>           "reviewer_email": "example@fda.gov",
#>           "reviewer_contribution": "curatedBy",
#>           "reviewer_orcid": "NA"
#>         }
#>       ]
#>     }
#>   ],
#>   "derived_from": "https://github.com/biocompute-objects/BCO_Specification/blob/1.2.1-beta/HCV1a.json",
#>   "obsolete_after": "2018-11-12T12:30:48-0500",
#>   "embargo": ["2017-10-12T12:30:48-0500", "2017-11-12T12:30:48-0500"],
#>   "created": "2017-01-20T09:40:17-0500",
#>   "modified": "2019-05-10T09:40:17-0500",
#>   "contributors": [
#>     {
#>       "name": "Jane Doe",
#>       "affiliation": "Seven Bridges Genomics",
#>       "email": "example@sevenbridges.com",
#>       "contribution": ["createdBy", "curatedBy"],
#>       "orcid": "https://orcid.org/0000-0000-0000-0000"
#>     },
#>     {
#>       "name": "John Doe",
#>       "affiliation": "U.S. Food and Drug Administration",
#>       "email": "example@fda.gov",
#>       "contribution": "authoredBy",
#>       "orcid": "NA"
#>     }
#>   ],
#>   "license": "https://creativecommons.org/licenses/by/4.0/"
#> }