X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/6eeb2b1a7b30e356514f1f842c5d7ecafd126732..8e43dcf899a3322e66c709b149ce557f5255bf18:/sdk/R/R/autoGenAPI.R

diff --git a/sdk/R/R/autoGenAPI.R b/sdk/R/R/autoGenAPI.R
index e0ad551e1e..c86684f8b0 100644
--- a/sdk/R/R/autoGenAPI.R
+++ b/sdk/R/R/autoGenAPI.R
@@ -1,5 +1,9 @@
+# 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")
@@ -13,14 +17,18 @@ 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)
 
-    methodDoc <- generateMethodsDocumentation(methodResources, resourceNames)
-    classDoc <- generateAPIClassDocumentation(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(methodDoc,
                       classDoc,
@@ -30,12 +38,16 @@ generateAPI <- function()
                       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("Arvados <- R6::R6Class(",
       "",
@@ -69,7 +81,7 @@ generateAPIClassHeader <- function()
       "\t\t},\n")
 }
 
-generateProjectMethods <- function()
+genProjectMethods <- function()
 {
     c("\t\tprojects.get = function(uuid)",
       "\t\t{",
@@ -105,7 +117,7 @@ generateProjectMethods <- function()
       "")
 }
 
-generateClassContent <- function(methodResources, resourceNames)
+genClassContent <- function(methodResources, resourceNames)
 {
     arvadosMethods <- Map(function(resource, resourceName)
     {
@@ -131,7 +143,7 @@ generateClassContent <- function(methodResources, resourceNames)
     arvadosMethods
 }
 
-generateAPIClassFooter <- function()
+genAPIClassFooter <- function()
 {
     c("\t\tgetHostName = function() private$host,",
       "\t\tgetToken = function() private$token,",
@@ -248,7 +260,7 @@ getRequestURL <- function(methodMetaData)
 
 getRequestHeaders <- function()
 {
-    c("headers <- list(Authorization = paste(\"OAuth2\", private$token), ",
+    c("headers <- list(Authorization = paste(\"Bearer\", private$token), ",
       "                \"Content-Type\" = \"application/json\")")
 }
 
@@ -315,8 +327,7 @@ getReturnObject <- function()
 
 #NOTE: Arvados class documentation:
 
-
-generateMethodsDocumentation <- function(methodResources, resourceNames)
+genMethodsDoc <- function(methodResources, resourceNames)
 {
     methodsDoc <- unlist(unname(Map(function(resource, resourceName)
     {
@@ -331,22 +342,24 @@ generateMethodsDocumentation <- function(methodResources, resourceNames)
                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)
 }
 
-generateAPIClassDocumentation <- function(methodResources, resourceNames)
+genAPIClassDoc <- function(methodResources, resourceNames)
 {
     c("#' Arvados",
       "#'",
-      "#' Arvados class gives users ability to manipulate collections and projects.",
+      "#' Arvados class gives users ability to access Arvados REST API.",
       "#'" ,
       "#' @section Usage:",
       "#' \\preformatted{arv = Arvados$new(authToken = NULL, hostName = NULL, numRetries = 0)}",
@@ -396,13 +409,13 @@ getAPIClassMethodList <- function(methodResources, resourceNames)
                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)), "}}}") 
+    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)
@@ -410,7 +423,9 @@ getMethodDocumentation <- function(methodName, methodMetaData)
     params      <- getMethodDescription(methodMetaData)
     returnValue <- paste("#' @return", methodMetaData$response[["$ref"]], "object.")
 
-    c(description,
+    c(paste("#'", methodName),
+      "#' ",
+      description,
       "#' ",
       usage,
       params,
@@ -440,7 +455,7 @@ getMethodDescription <- function(methodMetaData)
                                  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.")
                              })))
     }
 
@@ -450,12 +465,81 @@ getMethodDescription <- function(methodMetaData)
     {
         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.
@@ -465,7 +549,7 @@ formatArgs <- function(prependAtStart, prependToEachSplit,
 {
     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])
@@ -488,12 +572,12 @@ formatArgs <- function(prependAtStart, prependToEachSplit,
 
         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
 }