+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
getAPIDocument <- function(){
- url <- "https://4xphq.arvadosapi.com/discovery/v1/apis/arvados/v1/rest"
+ url <- "https://jutro.arvadosapi.com/discovery/v1/apis/arvados/v1/rest"
serverResponse <- httr::RETRY("GET", url = url)
httr::content(serverResponse, as = "parsed", type = "application/json")
}
+#' generateAPI
+#'
+#' Autogenerate classes to interact with Arvados from the Arvados discovery document.
+#'
#' @export
generateAPI <- function()
{
discoveryDocument <- getAPIDocument()
methodResources <- discoveryDocument$resources
+
+ # Don't emit deprecated APIs
+ methodResources <- methodResources[!(names(methodResources) %in% c("jobs", "job_tasks", "pipeline_templates", "pipeline_instances",
+ "keep_disks", "nodes", "humans", "traits", "specimens"))]
resourceNames <- names(methodResources)
- doc <- generateMethodsDocumentation(methodResources, resourceNames)
- arvadosAPIHeader <- generateAPIClassHeader()
- arvadosProjectMethods <- generateProjectMethods()
- arvadosClassMethods <- generateClassContent(methodResources, resourceNames)
- arvadosAPIFooter <- generateAPIClassFooter()
+ methodDoc <- genMethodsDoc(methodResources, resourceNames)
+ classDoc <- genAPIClassDoc(methodResources, resourceNames)
+ arvadosAPIHeader <- genAPIClassHeader()
+ arvadosProjectMethods <- genProjectMethods()
+ arvadosClassMethods <- genClassContent(methodResources, resourceNames)
+ arvadosAPIFooter <- genAPIClassFooter()
- arvadosClass <- c(doc,
+ arvadosClass <- c(methodDoc,
+ classDoc,
arvadosAPIHeader,
arvadosProjectMethods,
arvadosClassMethods,
arvadosAPIFooter)
fileConn <- file("./R/Arvados.R", "w")
+ writeLines(c(
+ "# Copyright (C) The Arvados Authors. All rights reserved.",
+ "#",
+ "# SPDX-License-Identifier: Apache-2.0", ""), fileConn)
writeLines(unlist(arvadosClass), fileConn)
close(fileConn)
NULL
}
-generateAPIClassHeader <- function()
+genAPIClassHeader <- function()
{
- c("#' @export",
- "Arvados <- R6::R6Class(",
+ c("Arvados <- R6::R6Class(",
"",
"\t\"Arvados\",",
"",
"\t\t},\n")
}
-generateProjectMethods <- function()
+genProjectMethods <- function()
{
c("\t\tprojects.get = function(uuid)",
"\t\t{",
"")
}
-generateClassContent <- function(methodResources, resourceNames)
+genClassContent <- function(methodResources, resourceNames)
{
arvadosMethods <- Map(function(resource, resourceName)
{
arvadosMethods
}
-generateAPIClassFooter <- function()
+genAPIClassFooter <- function()
{
c("\t\tgetHostName = function() private$host,",
"\t\tgetToken = function() private$token,",
getRequestHeaders <- function()
{
- c("headers <- list(Authorization = paste(\"OAuth2\", private$token), ",
+ c("headers <- list(Authorization = paste(\"Bearer\", private$token), ",
" \"Content-Type\" = \"application/json\")")
}
#NOTE: Arvados class documentation:
-generateMethodsDocumentation <- function(methodResources, resourceNames)
+genMethodsDoc <- function(methodResources, resourceNames)
{
methodsDoc <- unlist(unname(Map(function(resource, resourceName)
{
return(NULL)
methodName <- paste0(resourceName, ".", methodName)
- getMethodDocumentation(methodName, methodMetaData)
+ getMethodDoc(methodName, methodMetaData)
}, resource$methods, methodNames)
unlist(unname(methodDoc))
}, methodResources, resourceNames)))
-
- methodsDoc
+
+ projectDoc <- genProjectMethodsDoc()
+
+ c(methodsDoc, projectDoc)
+}
+
+genAPIClassDoc <- function(methodResources, resourceNames)
+{
+ c("#' Arvados",
+ "#'",
+ "#' Arvados class gives users ability to access Arvados REST API.",
+ "#'" ,
+ "#' @section Usage:",
+ "#' \\preformatted{arv = Arvados$new(authToken = NULL, hostName = NULL, numRetries = 0)}",
+ "#'",
+ "#' @section Arguments:",
+ "#' \\describe{",
+ "#' \t\\item{authToken}{Authentification token. If not specified ARVADOS_API_TOKEN environment variable will be used.}",
+ "#' \t\\item{hostName}{Host name. If not specified ARVADOS_API_HOST environment variable will be used.}",
+ "#' \t\\item{numRetries}{Number which specifies how many times to retry failed service requests.}",
+ "#' }",
+ "#'",
+ "#' @section Methods:",
+ "#' \\describe{",
+ getAPIClassMethodList(methodResources, resourceNames),
+ "#' }",
+ "#'",
+ "#' @name Arvados",
+ "#' @examples",
+ "#' \\dontrun{",
+ "#' arv <- Arvados$new(\"your Arvados token\", \"example.arvadosapi.com\")",
+ "#'",
+ "#' collection <- arv$collections.get(\"uuid\")",
+ "#'",
+ "#' collectionList <- arv$collections.list(list(list(\"name\", \"like\", \"Test%\")))",
+ "#' collectionList <- listAll(arv$collections.list, list(list(\"name\", \"like\", \"Test%\")))",
+ "#'",
+ "#' deletedCollection <- arv$collections.delete(\"uuid\")",
+ "#'",
+ "#' updatedCollection <- arv$collections.update(list(name = \"New name\", description = \"New description\"),",
+ "#' \"uuid\")",
+ "#'",
+ "#' createdCollection <- arv$collections.create(list(name = \"Example\",",
+ "#' description = \"This is a test collection\"))",
+ "#' }",
+ "NULL",
+ "",
+ "#' @export")
+}
+
+getAPIClassMethodList <- function(methodResources, resourceNames)
+{
+ methodList <- unlist(unname(Map(function(resource, resourceName)
+ {
+ methodNames <- names(resource$methods)
+ paste0(resourceName,
+ ".",
+ methodNames[!(methodNames %in% c("index", "show", "destroy"))])
+
+ }, methodResources, resourceNames)))
+
+ hardcodedMethods <- c("projects.create", "projects.get",
+ "projects.list", "projects.update", "projects.delete")
+ paste0("#' \t\\item{}{\\code{\\link{", sort(c(methodList, hardcodedMethods)), "}}}")
}
-getMethodDocumentation <- function(methodName, methodMetaData)
+getMethodDoc <- function(methodName, methodMetaData)
{
name <- paste("#' @name", methodName)
usage <- getMethodUsage(methodName, methodMetaData)
params <- getMethodDescription(methodMetaData)
returnValue <- paste("#' @return", methodMetaData$response[["$ref"]], "object.")
- c(description,
+ c(paste("#'", methodName),
+ "#' ",
+ description,
"#' ",
usage,
params,
className <- sapply(prop, function(ref) ref)
objectName <- paste0(tolower(substr(className, 1, 1)),
substr(className, 2, nchar(className)))
- paste("#' @param", objectName, className, "object.")
+ paste("#' @param", objectName, className, "object.")
})))
}
{
arg <- methodMetaData$parameters[[argName]]
argDescription <- arg$description
- paste("#' @param", argName, argDescription)
+ paste("#' @param", argName, argDescription)
})))
c(requestDoc, argsDoc)
}
+genProjectMethodsDoc <- function()
+{
+ #TODO: Manually update this documentation to reflect changes in discovery document.
+ c("#' project.get",
+ "#' ",
+ "#' projects.get is equivalent to groups.get method.",
+ "#' ",
+ "#' @usage arv$projects.get(uuid)",
+ "#' @param uuid The UUID of the Group in question.",
+ "#' @return Group object.",
+ "#' @name projects.get",
+ "NULL",
+ "",
+ "#' project.create",
+ "#' ",
+ "#' projects.create wrapps groups.create method by setting group_class attribute to \"project\".",
+ "#' ",
+ "#' @usage arv$projects.create(group, ensure_unique_name = \"false\")",
+ "#' @param group Group object.",
+ "#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.",
+ "#' @return Group object.",
+ "#' @name projects.create",
+ "NULL",
+ "",
+ "#' project.update",
+ "#' ",
+ "#' projects.update wrapps groups.update method by setting group_class attribute to \"project\".",
+ "#' ",
+ "#' @usage arv$projects.update(group, uuid)",
+ "#' @param group Group object.",
+ "#' @param uuid The UUID of the Group in question.",
+ "#' @return Group object.",
+ "#' @name projects.update",
+ "NULL",
+ "",
+ "#' project.delete",
+ "#' ",
+ "#' projects.delete is equivalent to groups.delete method.",
+ "#' ",
+ "#' @usage arv$project.delete(uuid)",
+ "#' @param uuid The UUID of the Group in question.",
+ "#' @return Group object.",
+ "#' @name projects.delete",
+ "NULL",
+ "",
+ "#' project.list",
+ "#' ",
+ "#' projects.list wrapps groups.list method by setting group_class attribute to \"project\".",
+ "#' ",
+ "#' @usage arv$projects.list(filters = NULL,",
+ "#' where = NULL, order = NULL, distinct = NULL,",
+ "#' limit = \"100\", offset = \"0\", count = \"exact\",",
+ "#' include_trash = NULL, uuid = NULL, recursive = NULL)",
+ "#' @param filters ",
+ "#' @param where ",
+ "#' @param order ",
+ "#' @param distinct ",
+ "#' @param limit ",
+ "#' @param offset ",
+ "#' @param count ",
+ "#' @param include_trash Include items whose is_trashed attribute is true.",
+ "#' @param uuid ",
+ "#' @param recursive Include contents from child groups recursively.",
+ "#' @return Group object.",
+ "#' @name projects.list",
+ "NULL",
+ "")
+}
+
#NOTE: Utility functions:
# This function is used to split very long lines of code into smaller chunks.
{
if(length(args) > 1)
{
- args[1:(length(args) - 1)] <- paste0(args[1:(length(args) - 1)], ",")
+ args[1:(length(args) - 1)] <- paste0(args[1:(length(args) - 1)], ",")
}
args[1] <- paste0(prependAtStart, args[1])
argLines <- c(argLines, line)
}
-
+
argLines <- unlist(argLines)
argLinesLen <- length(argLines)
if(argLinesLen > 1)
- argLines[2:argLinesLen] <- paste0(prependToEachSplit, argLines[2:argLinesLen])
+ argLines[2:argLinesLen] <- paste0(prependToEachSplit, argLines[2:argLinesLen])
argLines
}
projects / arvados.git / blobdiff