-#TODO: Some methods do the same thing like collecion.index and collection.list.
-# Make one implementation of the method and make other reference to it.
-
getAPIDocument <- function(){
url <- "https://4xphq.arvadosapi.com/discovery/v1/apis/arvados/v1/rest"
serverResponse <- httr::RETRY("GET", url = url)
#' @export
generateAPI <- function()
{
- #TODO: Consider passing discovery document URL as parameter
+ #TODO: Consider passing discovery document URL as parameter.
#TODO: Consider passing location where to create new files.
- JSONDocument <- getAPIDocument()
+ discoveryDocument <- getAPIDocument()
- generateArvadosClasses(JSONDocument)
- generateArvadosAPIClass(JSONDocument)
-}
+ methodResources <- discoveryDocument$resources
+ resourceNames <- names(methodResources)
-generateArvadosAPIClass <- function(discoveryDocument)
-{
- classMetaData <- discoveryDocument$schemas
- functionResources <- discoveryDocument$resources
- resourceNames <- names(functionResources)
-
- doc <- generateMethodsDocumentation(functionResources, resourceNames)
+ methodDoc <- generateMethodsDocumentation(methodResources, resourceNames)
+ classDoc <- generateAPIClassDocumentation(methodResources, resourceNames)
arvadosAPIHeader <- generateAPIClassHeader()
- arvadosClassMethods <- generateClassContent(functionResources,
- resourceNames, classMetaData)
+ arvadosProjectMethods <- generateProjectMethods()
+ arvadosClassMethods <- generateClassContent(methodResources, resourceNames)
arvadosAPIFooter <- generateAPIClassFooter()
- arvadosClass <- c(doc, arvadosAPIHeader, arvadosClassMethods, arvadosAPIFooter)
+ arvadosClass <- c(methodDoc,
+ classDoc,
+ arvadosAPIHeader,
+ arvadosProjectMethods,
+ arvadosClassMethods,
+ arvadosAPIFooter)
- #TODO: Save to a file or load in memory?
fileConn <- file("./R/Arvados.R", "w")
writeLines(unlist(arvadosClass), fileConn)
close(fileConn)
NULL
}
-generateClassContent <- function(functionResources, resourceNames, classMetaData)
+generateAPIClassHeader <- function()
{
- arvadosMethods <- Map(function(resource, resourceName)
- {
- methodNames <- names(resource$methods)
-
- functions <- Map(function(methodMetaData, methodName)
- {
- methodName <- paste0(resourceName, ".", methodName)
- createFunction(methodName, methodMetaData, classMetaData)
-
- }, resource$methods, methodNames)
-
- unlist(unname(functions))
-
- }, functionResources, resourceNames)
+ c("Arvados <- R6::R6Class(",
+ "",
+ "\t\"Arvados\",",
+ "",
+ "\tpublic = list(",
+ "",
+ "\t\tinitialize = function(authToken = NULL, hostName = NULL, numRetries = 0)",
+ "\t\t{",
+ "\t\t\tif(!is.null(hostName))",
+ "\t\t\t\tSys.setenv(ARVADOS_API_HOST = hostName)",
+ "",
+ "\t\t\tif(!is.null(authToken))",
+ "\t\t\t\tSys.setenv(ARVADOS_API_TOKEN = authToken)",
+ "",
+ "\t\t\thostName <- Sys.getenv(\"ARVADOS_API_HOST\")",
+ "\t\t\ttoken <- Sys.getenv(\"ARVADOS_API_TOKEN\")",
+ "",
+ "\t\t\tif(hostName == \"\" | token == \"\")",
+ "\t\t\t\tstop(paste(\"Please provide host name and authentification token\",",
+ "\t\t\t\t\t\t \"or set ARVADOS_API_HOST and ARVADOS_API_TOKEN\",",
+ "\t\t\t\t\t\t \"environment variables.\"))",
+ "",
+ "\t\t\tprivate$token <- token",
+ "\t\t\tprivate$host <- paste0(\"https://\", hostName, \"/arvados/v1/\")",
+ "\t\t\tprivate$numRetries <- numRetries",
+ "\t\t\tprivate$REST <- RESTService$new(token, hostName,",
+ "\t\t\t HttpRequest$new(), HttpParser$new(),",
+ "\t\t\t numRetries)",
+ "",
+ "\t\t},\n")
+}
- arvadosMethods
+generateProjectMethods <- function()
+{
+ c("\t\tprojects.get = function(uuid)",
+ "\t\t{",
+ "\t\t\tself$groups.get(uuid)",
+ "\t\t},",
+ "",
+ "\t\tprojects.create = function(group, ensure_unique_name = \"false\")",
+ "\t\t{",
+ "\t\t\tgroup <- c(\"group_class\" = \"project\", group)",
+ "\t\t\tself$groups.create(group, ensure_unique_name)",
+ "\t\t},",
+ "",
+ "\t\tprojects.update = function(group, uuid)",
+ "\t\t{",
+ "\t\t\tgroup <- c(\"group_class\" = \"project\", group)",
+ "\t\t\tself$groups.update(group, uuid)",
+ "\t\t},",
+ "",
+ "\t\tprojects.list = function(filters = NULL, where = NULL,",
+ "\t\t\torder = NULL, select = NULL, distinct = NULL,",
+ "\t\t\tlimit = \"100\", offset = \"0\", count = \"exact\",",
+ "\t\t\tinclude_trash = NULL)",
+ "\t\t{",
+ "\t\t\tfilters[[length(filters) + 1]] <- list(\"group_class\", \"=\", \"project\")",
+ "\t\t\tself$groups.list(filters, where, order, select, distinct,",
+ "\t\t\t limit, offset, count, include_trash)",
+ "\t\t},",
+ "",
+ "\t\tprojects.delete = function(uuid)",
+ "\t\t{",
+ "\t\t\tself$groups.delete(uuid)",
+ "\t\t},",
+ "")
}
-generateMethodsDocumentation <- function(functionResources, resourceNames)
+generateClassContent <- function(methodResources, resourceNames)
{
- arvadosMethods <- unlist(unname(Map(function(resource, resourceName)
+ arvadosMethods <- Map(function(resource, resourceName)
{
methodNames <- names(resource$methods)
functions <- Map(function(methodMetaData, methodName)
{
+ #NOTE: Index, show and destroy are aliases for the preferred names
+ # "list", "get" and "delete". Until they are removed from discovery
+ # document we will filter them here.
+ if(methodName %in% c("index", "show", "destroy"))
+ return(NULL)
+
methodName <- paste0(resourceName, ".", methodName)
- getMethodDocumentation(methodName, methodMetaData)
+ createMethod(methodName, methodMetaData)
}, resource$methods, methodNames)
unlist(unname(functions))
- }, functionResources, resourceNames)))
-
- arvadosMethods
-}
-
-getMethodDocumentation <- function(methodName, methodMetaData)
-{
- name <- paste("#' @name", methodName)
- usage <- getMethodUsage(methodName, methodMetaData)
- description <- paste("#'", methodName, "is a method defined in Arvados class.")
- params <- getMethodDescription(methodMetaData)
- returnValue <- paste("#' @return", methodMetaData$response[["$ref"]], "object.")
+ }, methodResources, resourceNames)
- c(description,
- "#' ",
- usage,
- params,
- returnValue,
- name,
- "NULL",
- "")
+ arvadosMethods
}
-getMethodUsage <- function(methodName, methodMetaData)
+generateAPIClassFooter <- function()
{
- args <- getFunctionArguments(methodMetaData)
- c(formatArgs(paste0("#' @usage arv$", methodName, "("), "#' \t", args, ")", 40))
+ c("\t\tgetHostName = function() private$host,",
+ "\t\tgetToken = function() private$token,",
+ "\t\tsetRESTService = function(newREST) private$REST <- newREST,",
+ "\t\tgetRESTService = function() private$REST",
+ "\t),",
+ "",
+ "\tprivate = list(",
+ "",
+ "\t\ttoken = NULL,",
+ "\t\thost = NULL,",
+ "\t\tREST = NULL,",
+ "\t\tnumRetries = NULL",
+ "\t),",
+ "",
+ "\tcloneable = FALSE",
+ ")")
}
-getMethodDescription <- function(methodMetaData)
+createMethod <- function(name, methodMetaData)
{
- request <- methodMetaData$request
- requestDoc <- NULL
-
- if(!is.null(request))
- {
- requestDoc <- unname(unlist(sapply(request$properties, function(prop)
- {
- className <- sapply(prop, function(ref) ref)
- objectName <- paste0(tolower(substr(className, 1, 1)),
- substr(className, 2, nchar(className)))
- paste("#' @param", objectName, className, "object.")
- })))
- }
-
- argNames <- names(methodMetaData$parameters)
+ args <- getMethodArguments(methodMetaData)
+ signature <- getMethodSignature(name, args)
+ body <- getMethodBody(methodMetaData)
- argsDoc <- unname(unlist(sapply(argNames, function(argName)
- {
- arg <- methodMetaData$parameters[[argName]]
- argDescription <- arg$description
- paste("#' @param", argName, argDescription)
- })))
-
- c(requestDoc, argsDoc)
-}
-
-getFunctionName <- function(functionMetaData)
-{
- stringr::str_replace(functionMetaData$id, "arvados.", "")
+ c(signature,
+ "\t\t{",
+ body,
+ "\t\t},\n")
}
-#TODO: Make sure that arguments that are required always go first.
-# This is not the case if request$required is false.
-getFunctionArguments <- function(functionMetaData)
+getMethodArguments <- function(methodMetaData)
{
- request <- functionMetaData$request
+ request <- methodMetaData$request
requestArgs <- NULL
if(!is.null(request))
{
+ resourceName <- tolower(request$properties[[1]][[1]])
+
if(request$required)
- requestArgs <- names(request$properties)
+ requestArgs <- resourceName
else
- requestArgs <- paste(names(request$properties), "=", "NULL")
+ requestArgs <- paste(resourceName, "=", "NULL")
}
- argNames <- names(functionMetaData$parameters)
+ argNames <- names(methodMetaData$parameters)
args <- sapply(argNames, function(argName)
{
- arg <- functionMetaData$parameters[[argName]]
+ arg <- methodMetaData$parameters[[argName]]
if(!arg$required)
{
c(requestArgs, args)
}
-getFunctionBody <- function(functionMetaData, classMetaData)
+getMethodSignature <- function(methodName, args)
{
- url <- getRequestURL(functionMetaData)
- headers <- getRequestHeaders()
- requestQueryList <- getRequestQueryList(functionMetaData)
- requestBody <- getRequestBody(functionMetaData)
- request <- getRequest(functionMetaData)
- response <- getResponse(functionMetaData)
- errorCheck <- getErrorCheckingCode()
- returnObject <- getReturnObject(functionMetaData, classMetaData)
- returnStatement <- getReturnObjectValidationCode()
+ collapsedArgs <- paste0(args, collapse = ", ")
+ lineLengthLimit <- 40
+
+ if(nchar(collapsedArgs) > lineLengthLimit)
+ {
+ return(paste0("\t\t",
+ formatArgs(paste(methodName, "= function("),
+ "\t", args, ")", lineLengthLimit)))
+ }
+ else
+ {
+ return(paste0("\t\t", methodName, " = function(", collapsedArgs, ")"))
+ }
+}
+
+getMethodBody <- function(methodMetaData)
+{
+ url <- getRequestURL(methodMetaData)
+ headers <- getRequestHeaders()
+ requestQueryList <- getRequestQueryList(methodMetaData)
+ requestBody <- getRequestBody(methodMetaData)
+ request <- getRequest(methodMetaData)
+ response <- getResponse(methodMetaData)
+ errorCheck <- getErrorCheckingCode()
+ returnStatement <- getReturnObject()
body <- c(url,
headers,
- requestQueryList,
+ requestQueryList, "",
requestBody, "",
request, response, "",
errorCheck, "",
- returnObject, "",
returnStatement)
paste0("\t\t\t", body)
}
-getReturnObjectValidationCode <- function()
-{
- c("if(result$isEmpty())",
- "\tresource",
- "else",
- "\tresult")
-}
-
-getErrorCheckingCode <- function()
-{
- c("if(!is.null(resource$errors))", "\tstop(resource$errors)")
-}
-
-getRequestBody <- function(functionMetaData)
+getRequestURL <- function(methodMetaData)
{
- request <- functionMetaData$request
-
- if(is.null(request) || !request$required)
- return("body <- NULL")
-
- requestParameterName <- names(request$properties)[1]
- paste0("body <- ", requestParameterName, "$toJSON()")
+ endPoint <- methodMetaData$path
+ endPoint <- stringr::str_replace_all(endPoint, "\\{", "${")
+ url <- c(paste0("endPoint <- stringr::str_interp(\"", endPoint, "\")"),
+ paste0("url <- paste0(private$host, endPoint)"))
+ url
}
getRequestHeaders <- function()
" \"Content-Type\" = \"application/json\")")
}
-getReturnObject <- function(functionMetaData, classMetaData)
+getRequestQueryList <- function(methodMetaData)
{
- returnClass <- functionMetaData$response[["$ref"]]
- classArguments <- getReturnClassArguments(returnClass, classMetaData)
+ queryArgs <- names(Filter(function(arg) arg$location == "query",
+ methodMetaData$parameters))
- if(returnClass == "Collection")
- return(c(formatArgs("result <- Collection$new(", "\t",
- classArguments, ")", 40),
- "",
- "result$setRESTService(private$REST)"))
+ if(length(queryArgs) == 0)
+ return("queryArgs <- NULL")
+
+ queryArgs <- sapply(queryArgs, function(arg) paste0(arg, " = ", arg))
+ collapsedArgs <- paste0(queryArgs, collapse = ", ")
+
+ lineLengthLimit <- 40
- formatArgs(paste0("result <- ", returnClass, "$new("),
- "\t", classArguments, ")", 40)
+ if(nchar(collapsedArgs) > lineLengthLimit)
+ return(formatArgs("queryArgs <- list(", "\t\t\t\t ", queryArgs, ")",
+ lineLengthLimit))
+ else
+ return(paste0("queryArgs <- list(", collapsedArgs, ")"))
}
-getReturnClassArguments <- function(className, classMetaData)
+getRequestBody <- function(methodMetaData)
{
- classArguments <- unique(names(classMetaData[[className]]$properties))
+ request <- methodMetaData$request
- arguments <- sapply(classArguments, function(arg)
- {
- paste0(arg, " = resource$", arg)
- })
+ if(is.null(request) || !request$required)
+ return("body <- NULL")
+
+ resourceName <- tolower(request$properties[[1]][[1]])
- arguments
+ requestParameterName <- names(request$properties)[1]
+
+ c(paste0("if(length(", resourceName, ") > 0)"),
+ paste0("\tbody <- jsonlite::toJSON(list(", resourceName, " = ", resourceName, "), "),
+ "\t auto_unbox = TRUE)",
+ "else",
+ "\tbody <- NULL")
}
-getRequest <- function(functionMetaData)
+getRequest <- function(methodMetaData)
{
- method <- functionMetaData$httpMethod
+ method <- methodMetaData$httpMethod
c(paste0("response <- private$REST$http$exec(\"", method, "\", url, headers, body,"),
" queryArgs, private$numRetries)")
}
-getResponse <- function(functionMetaData)
+getResponse <- function(methodMetaData)
{
"resource <- private$REST$httpParser$parseJSONResponse(response)"
}
-getRequestURL <- function(functionMetaData)
+getErrorCheckingCode <- function()
{
- endPoint <- functionMetaData$path
- endPoint <- stringr::str_replace_all(endPoint, "\\{", "${")
- url <- c(paste0("endPoint <- stringr::str_interp(\"", endPoint, "\")"),
- paste0("url <- paste0(private$host, endPoint)"))
- url
+ c("if(!is.null(resource$errors))",
+ "\tstop(resource$errors)")
}
-getRequestQueryList <- function(functionMetaData)
+getReturnObject <- function()
{
- args <- names(functionMetaData$parameters)
+ "resource"
+}
- if(length(args) == 0)
- return("queryArgs <- NULL")
+#NOTE: Arvados class documentation:
- args <- sapply(args, function(arg) paste0(arg, " = ", arg))
- collapsedArgs <- paste0(args, collapse = ", ")
- if(nchar(collapsedArgs) > 40)
- return(formatArgs("queryArgs <- list(", "\t", args, ")", 40))
- else
- return(paste0("queryArgs <- list(", collapsedArgs, ")"))
-}
-
-createFunction <- function(functionName, functionMetaData, classMetaData)
+generateMethodsDocumentation <- function(methodResources, resourceNames)
{
- args <- getFunctionArguments(functionMetaData)
- body <- getFunctionBody(functionMetaData, classMetaData)
- funSignature <- getFunSignature(functionName, args)
+ methodsDoc <- unlist(unname(Map(function(resource, resourceName)
+ {
+ methodNames <- names(resource$methods)
- c(funSignature,
- "\t\t{",
- body,
- "\t\t},\n")
-}
+ methodDoc <- Map(function(methodMetaData, methodName)
+ {
+ #NOTE: Index, show and destroy are aliases for the preferred names
+ # "list", "get" and "delete". Until they are removed from discovery
+ # document we will filter them here.
+ if(methodName %in% c("index", "show", "destroy"))
+ return(NULL)
-getFunSignature <- function(funName, args)
-{
- collapsedArgs <- paste0(args, collapse = ", ")
+ methodName <- paste0(resourceName, ".", methodName)
+ getMethodDocumentation(methodName, methodMetaData)
- if(nchar(collapsedArgs) > 40)
- {
- return(paste0("\t\t",
- formatArgs(paste(funName, "= function("),
- "\t", args, ")", 40)))
- }
- else
- {
- return(paste0("\t\t", funName, " = function(", collapsedArgs, ")"))
- }
-}
+ }, resource$methods, methodNames)
-generateAPIClassHeader <- function()
-{
- c("#' @export",
- "Arvados <- R6::R6Class(",
- "",
- "\t\"Arvados\",",
- "",
- "\tpublic = list(",
- "",
- "\t\tinitialize = function(authToken = NULL, hostName = NULL, numRetries = 0)",
- "\t\t{",
- "\t\t\tif(!is.null(hostName))",
- "\t\t\t\tSys.setenv(ARVADOS_API_HOST = hostName)",
- "",
- "\t\t\tif(!is.null(authToken))",
- "\t\t\t\tSys.setenv(ARVADOS_API_TOKEN = authToken)",
- "",
- "\t\t\thostName <- Sys.getenv(\"ARVADOS_API_HOST\")",
- "\t\t\ttoken <- Sys.getenv(\"ARVADOS_API_TOKEN\")",
- "",
- "\t\t\tif(hostName == \"\" | token == \"\")",
- "\t\t\t\tstop(paste(\"Please provide host name and authentification token\",",
- "\t\t\t\t\t\t \"or set ARVADOS_API_HOST and ARVADOS_API_TOKEN\",",
- "\t\t\t\t\t\t \"environment variables.\"))",
- "",
- "\t\t\tprivate$token <- token",
- "\t\t\tprivate$host <- paste0(\"https://\", hostName, \"/arvados/v1/\")",
- "\t\t\tprivate$numRetries <- numRetries",
- "\t\t\tprivate$REST <- RESTService$new(token, hostName,",
- "\t\t\t HttpRequest$new(), HttpParser$new(),",
- "\t\t\t numRetries)",
- "",
- "\t\t},\n")
+ unlist(unname(methodDoc))
+
+ }, methodResources, resourceNames)))
+
+ methodsDoc
}
-generateAPIClassFooter <- function()
+generateAPIClassDocumentation <- function(methodResources, resourceNames)
{
- c("\t\tgetHostName = function() private$host,",
- "\t\tgetToken = function() private$token,",
- "\t\tsetRESTService = function(newREST) private$REST <- newREST",
- "\t),",
- "",
- "\tprivate = list(",
- "",
- "\t\ttoken = NULL,",
- "\t\thost = NULL,",
- "\t\tREST = NULL,",
- "\t\tnumRetries = NULL",
- "\t),",
+ c("#' Arvados",
+ "#'",
+ "#' Arvados class gives users ability to manipulate collections and projects.",
+ "#'" ,
+ "#' @section Usage:",
+ "#' \\preformatted{arv = Arvados$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$collections.create(list(name = \"Example\",",
+ "#' description = \"This is a test collection\"))",
+ "#' }",
+ "NULL",
"",
- "\tcloneable = FALSE",
- ")")
+ "#' @export")
}
-generateArvadosClasses <- function(resources)
+getAPIClassMethodList <- function(methodResources, resourceNames)
{
- classes <- sapply(resources$schemas, function(classSchema)
+ methodList <- unlist(unname(Map(function(resource, resourceName)
{
- #NOTE: Collection is implemented manually.
- if(classSchema$id != "Collection")
- getArvadosClass(classSchema)
-
- }, USE.NAMES = TRUE)
-
- unlist(unname(classes))
+ methodNames <- names(resource$methods)
+ paste0(resourceName,
+ ".",
+ methodNames[!(methodNames %in% c("index", "show", "destroy"))])
- fileConn <- file("./R/ArvadosClasses.R", "w")
- writeLines(unlist(classes), fileConn)
- close(fileConn)
- NULL
+ }, methodResources, resourceNames)))
+
+ hardcodedMethods <- c("projects.create", "projects.get",
+ "projects.list", "projects.update", "projects.delete")
+ paste0("#' \t\\item{}{\\code{\\link{", sort(c(methodList, hardcodedMethods)), "}}}")
}
-getArvadosClass <- function(classSchema)
+getMethodDocumentation <- function(methodName, methodMetaData)
{
- name <- classSchema$id
- fields <- unique(names(classSchema$properties))
- constructorArgs <- paste(fields, "= NULL")
- documentation <- getClassDocumentation(classSchema, constructorArgs)
-
- classString <- c(documentation,
- paste0(name, " <- R6::R6Class("),
- "",
- paste0("\t\"", name, "\","),
- "",
- "\tpublic = list(",
- paste0("\t\t", fields, " = NULL,"),
- "",
- paste0("\t\t", formatArgs("initialize = function(", "\t\t",
- constructorArgs, ")", 40)),
- "\t\t{",
- paste0("\t\t\tself$", fields, " <- ", fields),
- "\t\t\t",
- paste0("\t\t\t", formatArgs("private$classFields <- c(", "\t",
- paste0("\"", fields, "\""), ")", 40)),
- "\t\t},",
- "",
- "\t\ttoJSON = function() {",
- "\t\t\tfields <- sapply(private$classFields, function(field)",
- "\t\t\t{",
- "\t\t\t\tself[[field]]",
- "\t\t\t}, USE.NAMES = TRUE)",
- "\t\t\t",
- paste0("\t\t\tjsonlite::toJSON(list(\"", tolower(name), "\" =
- Filter(Negate(is.null), fields)), auto_unbox = TRUE)"),
- "\t\t},",
- "",
- "\t\tisEmpty = function() {",
- "\t\t\tfields <- sapply(private$classFields,",
- "\t\t\t function(field) self[[field]])",
- "",
- paste0("\t\t\tif(any(sapply(fields, function(field) !is.null(field)",
- " && field != \"\")))"),
- "\t\t\t\tFALSE",
- "\t\t\telse",
- "\t\t\t\tTRUE",
- "\t\t}",
- "\t),",
- "",
- "\tprivate = list(",
- "\t\tclassFields = NULL",
- "\t),",
- "",
- "\tcloneable = FALSE",
- ")",
- "")
+ name <- paste("#' @name", methodName)
+ usage <- getMethodUsage(methodName, methodMetaData)
+ description <- paste("#'", methodName, "is a method defined in Arvados class.")
+ params <- getMethodDescription(methodMetaData)
+ returnValue <- paste("#' @return", methodMetaData$response[["$ref"]], "object.")
+
+ c(description,
+ "#' ",
+ usage,
+ params,
+ returnValue,
+ name,
+ "NULL",
+ "")
}
-getClassDocumentation <- function(classSchema, constructorArgs)
+getMethodUsage <- function(methodName, methodMetaData)
{
- name <- classSchema$id
- description <- classSchema$description
- nameLowercaseFirstLetter <- paste0(tolower(substr(name, 1, 1)),
- substr(name, 2, nchar(name)))
- c(paste0("#' ", name),
- "#' ",
- paste0("#' ", description),
- "#' ",
- "#' @section Usage:",
- formatArgs(paste0("#' \\preformatted{",
- nameLowercaseFirstLetter, " -> ", name, "$new("),
- "#' \t", constructorArgs, ")", 50),
-
- "#' }",
- "#' ",
- paste0("#' @section Arguments:"),
- "#' \\describe{",
- paste0("#' ", getClassArgumentDescription(classSchema)),
- "#' }",
- "#' ",
- paste0("#' @name ", name),
- "NULL",
- "",
- "#' @export")
+ lineLengthLimit <- 40
+ args <- getMethodArguments(methodMetaData)
+ c(formatArgs(paste0("#' @usage arv$", methodName,
+ "("), "#' \t", args, ")", lineLengthLimit))
}
-getClassArgumentDescription <- function(classSchema)
+getMethodDescription <- function(methodMetaData)
{
- argDoc <- sapply(classSchema$properties, function(arg)
- {
- paste0("{", arg$description, "}")
- }, USE.NAMES = TRUE)
+ request <- methodMetaData$request
+ requestDoc <- NULL
+
+ if(!is.null(request))
+ {
+ requestDoc <- unname(unlist(sapply(request$properties, function(prop)
+ {
+ className <- sapply(prop, function(ref) ref)
+ objectName <- paste0(tolower(substr(className, 1, 1)),
+ substr(className, 2, nchar(className)))
+ paste("#' @param", objectName, className, "object.")
+ })))
+ }
+
+ argNames <- names(methodMetaData$parameters)
- paste0("\\item{", names(classSchema$properties), "}", argDoc)
+ argsDoc <- unname(unlist(sapply(argNames, function(argName)
+ {
+ arg <- methodMetaData$parameters[[argName]]
+ argDescription <- arg$description
+ paste("#' @param", argName, argDescription)
+ })))
+
+ c(requestDoc, argsDoc)
}
+#NOTE: Utility functions:
+
+# This function is used to split very long lines of code into smaller chunks.
+# This is usually the case when we pass a lot of named argumets to a function.
formatArgs <- function(prependAtStart, prependToEachSplit,
args, appendAtEnd, lineLength)
{
projects / arvados.git / blobdiff