Merge pull request #1 from sbg/dev

Merge dev to master branch
sbg · Oct 21, 2021 · 37e6a16 · 37e6a16
2 parents 3d18af6 + 45632ec
commit 37e6a16
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diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,5 @@
-.DS_Store
 .Rproj.user
 .Rhistory
 .RData
 .Ruserdata
+.DS_store
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: biocompute
 Type: Package
 Title: Create and Manipulate BioCompute Objects
-Version: 1.0.6
+Version: 1.1.0
 Authors@R: c(
     person("Jeffrey", "Grover", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-6246-1767")),
     person("Soner", "Koc", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0000-0002-0772-6600")),

diff --git a/NAMESPACE b/NAMESPACE
@@ -3,28 +3,28 @@
 export("%>%")
 export(compose)
 export(compose_description)
-export(compose_description_v1.3.0)
+export(compose_description_v1.4.2)
 export(compose_error)
-export(compose_error_v1.3.0)
+export(compose_error_v1.4.2)
 export(compose_execution)
-export(compose_execution_v1.3.0)
+export(compose_execution_v1.4.2)
 export(compose_extension)
-export(compose_extension_v1.3.0)
+export(compose_extension_v1.4.2)
 export(compose_fhir)
-export(compose_fhir_v1.3.0)
+export(compose_fhir_v1.4.2)
 export(compose_io)
-export(compose_io_v1.3.0)
+export(compose_io_v1.4.2)
 export(compose_parametric)
-export(compose_parametric_v1.3.0)
+export(compose_parametric_v1.4.2)
 export(compose_provenance)
-export(compose_provenance_v1.3.0)
+export(compose_provenance_v1.4.2)
 export(compose_scm)
-export(compose_scm_v1.3.0)
+export(compose_scm_v1.4.2)
 export(compose_tlf)
-export(compose_tlf_v1.3.0)
+export(compose_tlf_v1.4.2)
 export(compose_usability)
-export(compose_usability_v1.3.0)
-export(compose_v1.3.0)
+export(compose_usability_v1.4.2)
+export(compose_v1.4.2)
 export(convert_json)
 export(convert_yaml)
 export(export_html)
@@ -36,10 +36,11 @@ export(generate_example)
 export(generate_id)
 export(is_bco)
 export(is_domain)
+export(read_bco)
 export(validate_checksum)
-export(validate_checksum_v1.3.0)
+export(validate_checksum_v1.4.2)
 export(validate_schema)
-export(validate_schema_v1.3.0)
+export(validate_schema_v1.4.2)
 export(versions)
 importFrom(curl,curl_escape)
 importFrom(digest,digest)

diff --git a/NEWS.md b/NEWS.md
@@ -1,14 +1,15 @@
-# biocompute 1.0.6
+# biocompute 1.1.0
 
 ## Improvements
 
-- Fixed broken links to BCO specification in documentation
+- Update to BCO spec v1.4.2
+- Added ability to read BCOs from json.
 
-# biocompute 1.0.5
+# biocompute 1.0.6
 
 ## Improvements
 
-- Update package maintainer.
+- Fixed broken links to BCO specification in documentation.
 
 # biocompute 1.0.4
 

diff --git a/R/compose-description.R b/R/compose-description.R
@@ -1,10 +1,10 @@
-#' Compose BioCompute Object - Description Domain (v1.3.0)
+#' Compose BioCompute Object - Description Domain (v1.4.2)
 #'
 #' @param keywords Character vector. A list of keywords to aid in
 #' searchability and description of the experiment.
 #' @param xref Data frame. A list of the databases and/or ontology IDs
 #' that are cross-referenced in the BCO.
-#' @param platform Character string. Reference to a particular deployment
+#' @param platform Character string or list. Reference to a particular deployment
 #' of an existing platform where this BCO can be reproduced.
 #' @param pipeline_meta Data frame. Pipeline metadata.
 #' Variables include \code{step_number}, \code{name}, \code{description},
@@ -20,7 +20,7 @@
 #' @return A list of class \code{bco.domain}
 #'
 #' @rdname compose_description
-#' @export compose_description_v1.3.0
+#' @export compose_description_v1.4.2
 #'
 #' @examples
 #' keywords <- c("HCV1a", "Ledipasvir", "antiviral resistance", "SNP", "amino acid substitutions")
@@ -108,9 +108,9 @@
 #'   keywords, xref, platform,
 #'   pipeline_meta, pipeline_prerequisite, pipeline_input, pipeline_output
 #' ) %>% convert_json()
-compose_description_v1.3.0 <-
+compose_description_v1.4.2 <-
   function(
-           keywords = NULL, xref = NULL, platform = "Seven Bridges Platform",
+           keywords = NULL, xref = NULL, platform = list("Seven Bridges Platform"),
            pipeline_meta = NULL, pipeline_prerequisite = NULL,
            pipeline_input = NULL, pipeline_output = NULL) {
     if (is.null(keywords)) keywords <- character()
@@ -210,7 +210,7 @@ compose_description_v1.3.0 <-
     domain <- list(
       "keywords" = keywords,
       "xref" = xref_lst,
-      "platform" = platform,
+      "platform" = as.list(platform),
       "pipeline_steps" = ps_lst
     )
     class(domain) <- c(class(domain), "bco.domain")
@@ -220,4 +220,4 @@ compose_description_v1.3.0 <-
 
 #' @rdname compose_description
 #' @export compose_description
-compose_description <- compose_description_v1.3.0
+compose_description <- compose_description_v1.4.2
diff --git a/R/compose-error.R b/R/compose-error.R
@@ -1,9 +1,9 @@
-#' Compose BioCompute Object - Error Domain (v1.3.0)
+#' Compose BioCompute Object - Error Domain (v1.4.2)
 #'
 #' The error domain can be used to determine what range of input
 #' returns outputs that are within the tolerance level defined
 #' in this subdomain and therefore can be used to optimize algorithm
-#' (\href{https://github.com/biocompute-objects/BCO_Specification/blob/1.3.0/error-domain.md}{domain definition}).
+#' (\href{https://github.com/biocompute-objects/BCO_Specification/blob/1.4.2/docs/error-domain.md}{domain definition}).
 #'
 #' @param empirical Data frame. Variables include \code{key} and \code{value}.
 #' Each row is one item in the empirical error subdomain.
@@ -13,7 +13,7 @@
 #' @return A list of class \code{bco.domain}
 #'
 #' @rdname compose_error
-#' @export compose_error_v1.3.0
+#' @export compose_error_v1.4.2
 #'
 #' @examples
 #' empirical <- data.frame(
@@ -29,7 +29,7 @@
 #' )
 #'
 #' compose_error(empirical, algorithmic) %>% convert_json()
-compose_error_v1.3.0 <- function(empirical = NULL, algorithmic = NULL) {
+compose_error_v1.4.2 <- function(empirical = NULL, algorithmic = NULL) {
   empirical_lst <- if (!is.null(empirical)) as.list(setNames(as.character(empirical$value), as.character(empirical$key))) else list()
   algorithmic_lst <- if (!is.null(algorithmic)) as.list(setNames(as.character(algorithmic$value), as.character(algorithmic$key))) else list()
 
@@ -41,4 +41,4 @@ compose_error_v1.3.0 <- function(empirical = NULL, algorithmic = NULL) {
 
 #' @rdname compose_error
 #' @export compose_error
-compose_error <- compose_error_v1.3.0
+compose_error <- compose_error_v1.4.2
diff --git a/R/compose-execution.R b/R/compose-execution.R
@@ -1,6 +1,6 @@
-#' Compose BioCompute Object - Execution Domain (v1.3.0)
+#' Compose BioCompute Object - Execution Domain (v1.4.2)
 #'
-#' @param script Character string. Points to internal or external
+#' @param script Character string or list. Points to internal or external
 #' references to an object that was used to perform computations
 #' for this BCO instance.
 #' @param script_driver Character string. Indicate what kind of
@@ -26,7 +26,7 @@
 #' @importFrom stats setNames
 #'
 #' @rdname compose_execution
-#' @export compose_execution_v1.3.0
+#' @export compose_execution_v1.4.2
 #'
 #' @examples
 #' script <- "https://example.com/workflows/antiviral_resistance_detection_hive.py"
@@ -62,7 +62,7 @@
 #' compose_execution(
 #'   script, script_driver, software_prerequisites, external_data_endpoints, environment_variables
 #' ) %>% convert_json()
-compose_execution_v1.3.0 <-
+compose_execution_v1.4.2 <-
   function(
            script = NULL, script_driver = NULL, software_prerequisites = NULL,
            external_data_endpoints = NULL, environment_variables = NULL) {
@@ -101,7 +101,7 @@ compose_execution_v1.3.0 <-
     }
 
     domain <- list(
-      "script" = script,
+      "script" = as.list(script),
       "script_driver" = script_driver,
       "software_prerequisites" = sp_lst,
       "external_data_endpoints" = ede_lst,
@@ -114,4 +114,4 @@ compose_execution_v1.3.0 <-
 
 #' @rdname compose_execution
 #' @export compose_execution
-compose_execution <- compose_execution_v1.3.0
+compose_execution <- compose_execution_v1.4.2
diff --git a/R/compose-extension-fhir.R b/R/compose-extension-fhir.R
@@ -1,4 +1,4 @@
-#' Compose BioCompute Object - FHIR Extension (v1.3.0)
+#' Compose BioCompute Object - FHIR Extension (v1.4.2)
 #'
 #' @param endpoint Character string. The URL of the endpoint of the
 #' FHIR server containing the resource.
@@ -9,7 +9,7 @@
 #' @return A list of class \code{bco.domain}
 #'
 #' @rdname compose_fhir
-#' @export compose_fhir_v1.3.0
+#' @export compose_fhir_v1.4.2
 #'
 #' @examples
 #' fhir_endpoint <- "https://fhirtest.uhn.ca/baseDstu3"
@@ -24,7 +24,7 @@
 #' )
 #'
 #' compose_fhir(fhir_endpoint, fhir_version, fhir_resources) %>% convert_json()
-compose_fhir_v1.3.0 <- function(endpoint = NULL, version = NULL, resources = NULL) {
+compose_fhir_v1.4.2 <- function(endpoint = NULL, version = NULL, resources = NULL) {
   if (!is.null(resources)) {
     names(resources)[which(names(resources) == "id")] <- "fhir_id"
     names(resources)[which(names(resources) == "resource")] <- "fhir_resource"
@@ -41,4 +41,4 @@ compose_fhir_v1.3.0 <- function(endpoint = NULL, version = NULL, resources = NUL
 
 #' @rdname compose_fhir
 #' @export compose_fhir
-compose_fhir <- compose_fhir_v1.3.0
+compose_fhir <- compose_fhir_v1.4.2
diff --git a/R/compose-extension-scm.R b/R/compose-extension-scm.R
@@ -1,4 +1,4 @@
-#' Compose BioCompute Object - SCM Extension (v1.3.0)
+#' Compose BioCompute Object - SCM Extension (v1.4.2)
 #'
 #' @param scm_repository Character string. Base URL of the SCM repository.
 #' @param scm_type Character string. Type of SCM database. Must be one of
@@ -14,7 +14,7 @@
 #' @return A list of class \code{bco.domain}
 #'
 #' @rdname compose_scm
-#' @export compose_scm_v1.3.0
+#' @export compose_scm_v1.4.2
 #'
 #' @examples
 #' scm_repository <- "https://github.com/example/repo"
@@ -24,7 +24,7 @@
 #' scm_preview <- "https://github.com/example/repo/blob/master/mutation-detection.cwl"
 #'
 #' compose_scm(scm_repository, scm_type, scm_commit, scm_path, scm_preview) %>% convert_json()
-compose_scm_v1.3.0 <-
+compose_scm_v1.4.2 <-
   function(
            scm_repository = NULL, scm_type = c("git", "svn", "hg", "other"),
            scm_commit = NULL, scm_path = NULL, scm_preview = NULL) {
@@ -50,4 +50,4 @@ compose_scm_v1.3.0 <-
 
 #' @rdname compose_scm
 #' @export compose_scm
-compose_scm <- compose_scm_v1.3.0
+compose_scm <- compose_scm_v1.4.2
diff --git a/R/compose-extension.R b/R/compose-extension.R
@@ -1,12 +1,12 @@
-#' Compose BioCompute Object - Extension Domain (v1.3.0)
+#' Compose BioCompute Object - Extension Domain (v1.4.2)
 #'
 #' @param fhir FHIR extension domain composed by \code{\link{compose_fhir}}.
 #' @param scm SCM extension domain composed by \code{\link{compose_scm}}.
 #'
 #' @return A list of class \code{bco.domain}
 #'
 #' @rdname compose_extension
-#' @export compose_extension_v1.3.0
+#' @export compose_extension_v1.4.2
 #'
 #' @examples
 #' fhir_endpoint <- "https://fhirtest.uhn.ca/baseDstu3"
@@ -31,7 +31,7 @@
 #' scm <- compose_scm(scm_repository, scm_type, scm_commit, scm_path, scm_preview)
 #'
 #' compose_extension(fhir, scm) %>% convert_json()
-compose_extension_v1.3.0 <- function(fhir = NULL, scm = NULL) {
+compose_extension_v1.4.2 <- function(fhir = NULL, scm = NULL) {
   if (is.null(fhir)) fhir_lst <- list() else fhir_lst <- fhir
   if (is.null(scm)) scm_lst <- list() else scm_lst <- scm
 
@@ -46,4 +46,4 @@ compose_extension_v1.3.0 <- function(fhir = NULL, scm = NULL) {
 
 #' @rdname compose_extension
 #' @export compose_extension
-compose_extension <- compose_extension_v1.3.0
+compose_extension <- compose_extension_v1.4.2
diff --git a/R/compose-io.R b/R/compose-io.R
@@ -1,4 +1,4 @@
-#' Compose BioCompute Object - Input and Output Domain (v1.3.0)
+#' 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.
@@ -13,7 +13,7 @@
 #' @return A list of class \code{bco.domain}
 #'
 #' @rdname compose_io
-#' @export compose_io_v1.3.0
+#' @export compose_io_v1.4.2
 #'
 #' @examples
 #' input_subdomain <- data.frame(
@@ -46,7 +46,7 @@
 #' )
 #'
 #' compose_io(input_subdomain, output_subdomain) %>% convert_json()
-compose_io_v1.3.0 <- function(input = NULL, output = NULL) {
+compose_io_v1.4.2 <- function(input = NULL, output = NULL) {
   if (!is.null(input)) {
     input$access_time <- as.character(input$access_time, format = "%Y-%m-%dT%H:%M:%S%z")
     input_lst <- df2list(input)
@@ -79,4 +79,4 @@ compose_io_v1.3.0 <- function(input = NULL, output = NULL) {
 
 #' @rdname compose_io
 #' @export compose_io
-compose_io <- compose_io_v1.3.0
+compose_io <- compose_io_v1.4.2
diff --git a/R/compose-parametric.R b/R/compose-parametric.R
@@ -1,8 +1,8 @@
-#' Compose BioCompute Object - Parametric Domain (v1.3.0)
+#' Compose BioCompute Object - Parametric Domain (v1.4.2)
 #'
 #' Non-default parameters customizing the computational flow
 #' which can affect the output of the calculations
-#' (\href{https://github.com/biocompute-objects/BCO_Specification/blob/1.3.0/parametric-domain.md}{domain definition}).
+#' (\href{https://github.com/biocompute-objects/BCO_Specification/blob/1.4.2/docs/parametric-domain.md}{domain definition}).
 #'
 #' @param df Data frame. Variables include \code{param} (parameter names),
 #' \code{value} (value of the parameters), and \code{step}
@@ -13,7 +13,7 @@
 #' @importFrom jsonlite toJSON
 #'
 #' @rdname compose_parametric
-#' @export compose_parametric_v1.3.0
+#' @export compose_parametric_v1.4.2
 #'
 #' @examples
 #' df_parametric <- data.frame(
@@ -27,7 +27,7 @@
 #' )
 #'
 #' compose_parametric(df_parametric) %>% convert_json()
-compose_parametric_v1.3.0 <- function(df = NULL) {
+compose_parametric_v1.4.2 <- function(df = NULL) {
   if (!is.null(df)) {
     # mix types in values under the same key is probably bad practice
     # so we consciously choose to be more strict and make everything character
@@ -47,4 +47,4 @@ compose_parametric_v1.3.0 <- function(df = NULL) {
 
 #' @rdname compose_parametric
 #' @export compose_parametric
-compose_parametric <- compose_parametric_v1.3.0
+compose_parametric <- compose_parametric_v1.4.2