[ARVADOS] updated: 1.1.3-88-g4df7d22
Git user
git at public.curoverse.com
Thu Feb 22 10:27:23 EST 2018
Summary of changes:
sdk/R/NAMESPACE | 48 ++++-
sdk/R/R/Arvados.R | 236 ---------------------
sdk/R/R/Collection.R | 105 +++++++--
sdk/R/R/RESTService.R | 107 +---------
sdk/R/R/autoGenAPI.R | 52 +++--
sdk/R/man/Arvados.Rd | 62 ------
sdk/R/man/print.Arvados.Rd | 16 --
sdk/R/tests/testthat/test-Arvados.R | 306 ---------------------------
sdk/R/tests/testthat/test-ArvadosFile.R | 51 ++---
sdk/R/tests/testthat/test-Collection.R | 75 +++----
sdk/R/tests/testthat/test-RESTService.R | 230 --------------------
sdk/R/tests/testthat/test-Subcollection.R | 31 ++-
sdk/go/arvados/collection_fs_test.go | 2 +-
sdk/python/arvados/keep.py | 180 ++++++++--------
sdk/python/tests/test_keep_client.py | 28 ++-
services/keepstore/azure_blob_volume.go | 6 +
services/keepstore/azure_blob_volume_test.go | 13 ++
services/keepstore/mounts_test.go | 12 +-
services/keepstore/s3_volume.go | 6 +
services/keepstore/s3_volume_test.go | 13 ++
services/keepstore/volume.go | 31 +--
services/keepstore/volume_test.go | 4 +
services/keepstore/volume_unix.go | 6 +
services/keepstore/volume_unix_test.go | 13 ++
tools/sync-groups/sync-groups.go | 2 +-
25 files changed, 446 insertions(+), 1189 deletions(-)
delete mode 100644 sdk/R/R/Arvados.R
delete mode 100644 sdk/R/man/Arvados.Rd
delete mode 100644 sdk/R/man/print.Arvados.Rd
delete mode 100644 sdk/R/tests/testthat/test-Arvados.R
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commit 4df7d22706adfd8654b87d22c3400a9dc33035a9
Merge: 6c786c2 b77a0df
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date: Thu Feb 22 16:27:08 2018 +0100
Merge branch 'master' of git.curoverse.com:arvados into 13076-r-autogen-api
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>
commit 6c786c23b5b44ac27570be617d79d5cf5f9e2c7f
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date: Thu Feb 22 16:22:49 2018 +0100
Integrated autogenerated classes with existing content
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>
diff --git a/sdk/R/NAMESPACE b/sdk/R/NAMESPACE
index fcee910..e6cf09b 100644
--- a/sdk/R/NAMESPACE
+++ b/sdk/R/NAMESPACE
@@ -1,11 +1,57 @@
# Generated by roxygen2: do not edit by hand
-S3method(print,Arvados)
S3method(print,ArvadosFile)
S3method(print,Collection)
S3method(print,Subcollection)
+export(ApiClient)
+export(ApiClientAuthorization)
+export(ApiClientAuthorizationList)
+export(ApiClientList)
export(Arvados)
export(ArvadosFile)
+export(AuthorizedKey)
+export(AuthorizedKeyList)
export(Collection)
+export(CollectionList)
+export(Container)
+export(ContainerList)
+export(ContainerRequest)
+export(ContainerRequestList)
+export(Group)
+export(GroupList)
+export(Human)
+export(HumanList)
+export(Job)
+export(JobList)
+export(JobTask)
+export(JobTaskList)
+export(KeepDisk)
+export(KeepDiskList)
+export(KeepService)
+export(KeepServiceList)
+export(Link)
+export(LinkList)
+export(Log)
+export(LogList)
+export(Node)
+export(NodeList)
+export(PipelineInstance)
+export(PipelineInstanceList)
+export(PipelineTemplate)
+export(PipelineTemplateList)
+export(Repository)
+export(RepositoryList)
+export(Specimen)
+export(SpecimenList)
export(Subcollection)
+export(Trait)
+export(TraitList)
+export(User)
+export(UserAgreement)
+export(UserAgreementList)
+export(UserList)
+export(VirtualMachine)
+export(VirtualMachineList)
+export(Workflow)
+export(WorkflowList)
export(generateAPI)
diff --git a/sdk/R/R/Arvados.R b/sdk/R/R/Arvados.R
deleted file mode 100644
index 8b0e92b..0000000
--- a/sdk/R/R/Arvados.R
+++ /dev/null
@@ -1,236 +0,0 @@
-source("./R/RESTService.R")
-source("./R/HttpRequest.R")
-source("./R/HttpParser.R")
-
-#' 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{
-#' \item{authToken}{Authentification token. If not specified ARVADOS_API_TOKEN environment variable will be used.}
-#' \item{hostName}{Host name. If not specified ARVADOS_API_HOST environment variable will be used.}
-#' \item{numRetries}{Number which specifies how many times to retry failed service requests.}
-#' }
-#'
-#' @section Methods:
-#' \describe{
-#' \item{getToken()}{Returns authentification token currently in use.}
-#' \item{getHostName()}{Returns host name currently in use.}
-#' \item{getNumRetries()}{Returns number which specifies how many times to retry failed service requests.}
-#' \item{setNumRetries(newNumOfRetries)}{Sets number which specifies how many times to retry failed service requests.}
-#' \item{getCollection(uuid)}{Get collection with specified UUID.}
-#' \item{listCollections(filters = NULL, limit = 100, offset = 0)}{Returns list of collections based on filters parameter.}
-#' \item{listAllCollections(filters = NULL)}{Lists all collections, based on filters parameter, even if the number of items is greater than maximum API limit.}
-#' \item{deleteCollection(uuid)}{Deletes collection with specified UUID.}
-#' \item{updateCollection(uuid, newContent)}{Updates collection with specified UUID.}
-#' \item{createCollection(content)}{Creates new collection.}
-#' \item{getProject(uuid)}{Get project with specified UUID.}
-#' \item{listProjects(filters = NULL, limit = 100, offset = 0)}{Returns list of projects based on filters parameter.}
-#' \item{listAllProjects(filters = NULL)}{Lists all projects, based on filters parameter, even if the number of items is greater than maximum API limit.}
-#' \item{deleteProject(uuid)}{Deletes project with specified UUID.}
-#' \item{updateProject(uuid, newContent)}{Updates project with specified UUID.}
-#' \item{createProject(content)}{Creates new project.}
-#' }
-#'
-#' @name Arvados
-#' @examples
-#' \dontrun{
-#' arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
-#'
-#' collection <- arv$getCollection("uuid")
-#'
-#' collectionList <- arv$listCollections(list(list("name", "like", "Test%")))
-#' collectionList <- arv$listAllCollections(list(list("name", "like", "Test%")))
-#'
-#' deletedCollection <- arv$deleteCollection("uuid")
-#'
-#' updatedCollection <- arv$updateCollection("uuid", list(name = "New name",
-#' description = "New description"))
-#'
-#' createdCollection <- arv$createCollection(list(name = "Example",
-#' description = "This is a test collection"))
-#' }
-NULL
-
-#' @export
-Arvados <- R6::R6Class(
-
- "Arvados",
-
- public = list(
-
- initialize = function(authToken = NULL, hostName = NULL, numRetries = 0)
- {
- if(!is.null(hostName))
- Sys.setenv(ARVADOS_API_HOST = hostName)
-
- if(!is.null(authToken))
- Sys.setenv(ARVADOS_API_TOKEN = authToken)
-
- hostName <- Sys.getenv("ARVADOS_API_HOST");
- token <- Sys.getenv("ARVADOS_API_TOKEN");
-
- if(hostName == "" | token == "")
- stop(paste("Please provide host name and authentification token",
- "or set ARVADOS_API_HOST and ARVADOS_API_TOKEN",
- "environment variables."))
-
- private$numRetries <- numRetries
- private$REST <- RESTService$new(token, hostName,
- HttpRequest$new(), HttpParser$new(),
- numRetries)
-
- private$token <- private$REST$token
- private$host <- private$REST$hostName
- },
-
- getToken = function() private$REST$token,
- getHostName = function() private$REST$hostName,
- getWebDavHostName = function() private$REST$getWebDavHostName(),
- getRESTService = function() private$REST,
- setRESTService = function(newRESTService) private$REST <- newRESTService,
-
- getNumRetries = function() private$REST$numRetries,
- setNumRetries = function(newNumOfRetries)
- {
- private$REST$setNumRetries(newNumOfRetries)
- },
-
- getCollection = function(uuid)
- {
- collection <- private$REST$getResource("collections", uuid)
- collection
- },
-
- listCollections = function(filters = NULL, limit = 100, offset = 0)
- {
- if(!is.null(filters))
- names(filters) <- c("collection")
-
- collections <- private$REST$listResources("collections", filters,
- limit, offset)
- collections
- },
-
- listAllCollections = function(filters = NULL)
- {
- if(!is.null(filters))
- names(filters) <- c("collection")
-
- collectionURL <- paste0(private$host, "collections")
- allCollection <- private$REST$fetchAllItems(collectionURL, filters)
- allCollection
- },
-
- deleteCollection = function(uuid)
- {
- removedCollection <- private$REST$deleteResource("collections", uuid)
- removedCollection
- },
-
- updateCollection = function(uuid, newContent)
- {
- body <- list(list())
- names(body) <- c("collection")
- body$collection <- newContent
-
- updatedCollection <- private$REST$updateResource("collections",
- uuid, body)
- updatedCollection
- },
-
- createCollection = function(content)
- {
- body <- list(list())
- names(body) <- c("collection")
- body$collection <- content
-
- newCollection <- private$REST$createResource("collections", body)
- newCollection
- },
-
- getProject = function(uuid)
- {
- project <- private$REST$getResource("groups", uuid)
- project
- },
-
- createProject = function(content)
- {
- body <- list(list())
- names(body) <- c("group")
- body$group <- c("group_class" = "project", content)
-
- newProject <- private$REST$createResource("groups", body)
- newProject
- },
-
- updateProject = function(uuid, newContent)
- {
- body <- list(list())
- names(body) <- c("group")
- body$group <- newContent
-
- updatedProject <- private$REST$updateResource("groups", uuid, body)
- updatedProject
- },
-
- listProjects = function(filters = NULL, limit = 100, offset = 0)
- {
- if(!is.null(filters))
- names(filters) <- c("groups")
-
- filters[[length(filters) + 1]] <- list("group_class", "=", "project")
-
- projects <- private$REST$listResources("groups", filters, limit, offset)
- projects
- },
-
- listAllProjects = function(filters = NULL)
- {
- if(!is.null(filters))
- names(filters) <- c("groups")
-
- filters[[length(filters) + 1]] <- list("group_class", "=", "project")
-
- projectURL <- paste0(private$host, "groups")
-
- result <- private$REST$fetchAllItems(projectURL, filters)
- result
- },
-
- deleteProject = function(uuid)
- {
- removedProject <- private$REST$deleteResource("groups", uuid)
- removedProject
- }
- ),
-
- private = list(
-
- token = NULL,
- host = NULL,
- REST = NULL,
- numRetries = NULL
- ),
-
- cloneable = FALSE
-)
-
-#' print.Arvados
-#'
-#' Custom print function for Arvados class
-#'
-#' @param x Instance of Arvados class
-#' @param ... Optional arguments.
-#' @export
-print.Arvados = function(x, ...)
-{
- cat(paste0("Type: ", "\"", "Arvados", "\""), sep = "\n")
- cat(paste0("Host: ", "\"", x$getHostName(), "\""), sep = "\n")
- cat(paste0("Token: ", "\"", x$getToken(), "\""), sep = "\n")
-}
diff --git a/sdk/R/R/Collection.R b/sdk/R/R/Collection.R
index ed5b4f4..37b2fb9 100644
--- a/sdk/R/R/Collection.R
+++ b/sdk/R/R/Collection.R
@@ -53,22 +53,74 @@ Collection <- R6::R6Class(
public = list(
- api = NULL,
- uuid = NULL,
-
- initialize = function(api, uuid)
+ uuid = NULL,
+ etag = NULL,
+ owner_uuid = NULL,
+ created_at = NULL,
+ modified_by_client_uuid = NULL,
+ modified_by_user_uuid = NULL,
+ modified_at = NULL,
+ portable_data_hash = NULL,
+ replication_desired = NULL,
+ replication_confirmed_at = NULL,
+ replication_confirmed = NULL,
+ updated_at = NULL,
+ manifest_text = NULL,
+ name = NULL,
+ description = NULL,
+ properties = NULL,
+ delete_at = NULL,
+ file_names = NULL,
+ trash_at = NULL,
+ is_trashed = NULL,
+
+ initialize = function(uuid = NULL, etag = NULL, owner_uuid = NULL,
+ created_at = NULL, modified_by_client_uuid = NULL,
+ modified_by_user_uuid = NULL, modified_at = NULL,
+ portable_data_hash = NULL, replication_desired = NULL,
+ replication_confirmed_at = NULL,
+ replication_confirmed = NULL, updated_at = NULL,
+ manifest_text = NULL, name = NULL, description = NULL,
+ properties = NULL, delete_at = NULL, file_names = NULL,
+ trash_at = NULL, is_trashed = NULL)
{
- self$api <- api
- private$REST <- api$getRESTService()
-
- self$uuid <- uuid
-
- private$fileContent <- private$REST$getCollectionContent(uuid)
- private$tree <- CollectionTree$new(private$fileContent, self)
+ self$uuid <- uuid
+ self$etag <- etag
+ self$owner_uuid <- owner_uuid
+ self$created_at <- created_at
+ self$modified_by_client_uuid <- modified_by_client_uuid
+ self$modified_by_user_uuid <- modified_by_user_uuid
+ self$modified_at <- modified_at
+ self$portable_data_hash <- portable_data_hash
+ self$replication_desired <- replication_desired
+ self$replication_confirmed_at <- replication_confirmed_at
+ self$replication_confirmed <- replication_confirmed
+ self$updated_at <- updated_at
+ self$manifest_text <- manifest_text
+ self$name <- name
+ self$description <- description
+ self$properties <- properties
+ self$delete_at <- delete_at
+ self$file_names <- file_names
+ self$trash_at <- trash_at
+ self$is_trashed <- is_trashed
+
+ private$classFields <- c("uuid", "etag", "owner_uuid",
+ "created_at", "modified_by_client_uuid",
+ "modified_by_user_uuid", "modified_at",
+ "portable_data_hash", "replication_desired",
+ "replication_confirmed_at",
+ "replication_confirmed", "updated_at",
+ "manifest_text", "name", "description",
+ "properties", "delete_at", "file_names",
+ "trash_at", "is_trashed")
},
add = function(content, relativePath = "")
{
+ if(is.null(private$tree))
+ private$genereateCollectionTreeStructure()
+
if(relativePath == "" ||
relativePath == "." ||
relativePath == "./")
@@ -87,7 +139,6 @@ Collection <- R6::R6Class(
if("ArvadosFile" %in% class(content) ||
"Subcollection" %in% class(content))
{
-
if(content$getName() == "")
stop("Content has invalid name.")
@@ -104,6 +155,9 @@ Collection <- R6::R6Class(
create = function(fileNames, relativePath = "")
{
+ if(is.null(private$tree))
+ private$genereateCollectionTreeStructure()
+
if(relativePath == "" ||
relativePath == "." ||
relativePath == "./")
@@ -149,6 +203,9 @@ Collection <- R6::R6Class(
remove = function(paths)
{
+ if(is.null(private$tree))
+ private$genereateCollectionTreeStructure()
+
if(is.character(paths))
{
sapply(paths, function(filePath)
@@ -179,6 +236,9 @@ Collection <- R6::R6Class(
move = function(content, newLocation)
{
+ if(is.null(private$tree))
+ private$genereateCollectionTreeStructure()
+
content <- trimFromEnd(content, "/")
elementToMove <- self$get(content)
@@ -191,12 +251,18 @@ Collection <- R6::R6Class(
getFileListing = function()
{
+ if(is.null(private$tree))
+ private$genereateCollectionTreeStructure()
+
content <- private$REST$getCollectionContent(self$uuid)
content[order(tolower(content))]
},
get = function(relativePath)
{
+ if(is.null(private$tree))
+ private$genereateCollectionTreeStructure()
+
private$tree$getElement(relativePath)
},
@@ -208,7 +274,20 @@ Collection <- R6::R6Class(
REST = NULL,
tree = NULL,
- fileContent = NULL
+ fileContent = NULL,
+ classFields = NULL,
+
+ genereateCollectionTreeStructure = function()
+ {
+ if(is.null(self$uuid))
+ stop("Collection uuid is not defined.")
+
+ if(is.null(private$REST))
+ stop("REST service is not defined.")
+
+ private$fileContent <- private$REST$getCollectionContent(self$uuid)
+ private$tree <- CollectionTree$new(private$fileContent, self)
+ }
),
cloneable = FALSE
diff --git a/sdk/R/R/RESTService.R b/sdk/R/R/RESTService.R
index 12e6591..b87310e 100644
--- a/sdk/R/R/RESTService.R
+++ b/sdk/R/R/RESTService.R
@@ -4,27 +4,22 @@ RESTService <- R6::R6Class(
public = list(
- hostName = NULL,
token = NULL,
http = NULL,
httpParser = NULL,
numRetries = NULL,
- initialize = function(token, hostName,
+ initialize = function(token, rawHost,
http, httpParser,
numRetries = 0,
webDavHostName = NULL)
{
- version <- "v1"
+ self$token <- token
+ self$http <- http
+ self$httpParser <- httpParser
+ self$numRetries <- numRetries
- self$token <- token
- self$hostName <- paste0("https://", hostName,
- "/arvados/", version, "/")
- self$http <- http
- self$httpParser <- httpParser
- self$numRetries <- numRetries
-
- private$rawHostName <- hostName
+ private$rawHostName <- rawHost
private$webDavHostName <- webDavHostName
},
@@ -55,40 +50,7 @@ RESTService <- R6::R6Class(
private$webDavHostName
},
- getResource = function(resource, uuid)
- {
- resourceURL <- paste0(self$hostName, resource, "/", uuid)
- headers <- list(Authorization = paste("OAuth2", self$token))
-
- serverResponse <- self$http$execute("GET", resourceURL, headers,
- retryTimes = self$numRetries)
-
- resource <- self$httpParser$parseJSONResponse(serverResponse)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- listResources = function(resource, filters = NULL, limit = 100, offset = 0)
- {
- resourceURL <- paste0(self$hostName, resource)
- headers <- list(Authorization = paste("OAuth2", self$token))
- body <- NULL
-
- serverResponse <- self$http$execute("GET", resourceURL, headers, body,
- filters, limit, offset,
- self$numRetries)
-
- resources <- self$httpParser$parseJSONResponse(serverResponse)
-
- if(!is.null(resources$errors))
- stop(resources$errors)
-
- resources
- },
-
+ #Move this to utility
fetchAllItems = function(resourceURL, filters)
{
headers <- list(Authorization = paste("OAuth2", self$token))
@@ -120,61 +82,6 @@ RESTService <- R6::R6Class(
items
},
- deleteResource = function(resource, uuid)
- {
- collectionURL <- paste0(self$hostName, resource, "/", uuid)
- headers <- list("Authorization" = paste("OAuth2", self$token),
- "Content-Type" = "application/json")
-
- serverResponse <- self$http$execute("DELETE", collectionURL, headers,
- retryTimes = self$numRetries)
-
- removedResource <- self$httpParser$parseJSONResponse(serverResponse)
-
- if(!is.null(removedResource$errors))
- stop(removedResource$errors)
-
- removedResource
- },
-
- updateResource = function(resource, uuid, newContent)
- {
- resourceURL <- paste0(self$hostName, resource, "/", uuid)
- headers <- list("Authorization" = paste("OAuth2", self$token),
- "Content-Type" = "application/json")
-
- newContent <- jsonlite::toJSON(newContent, auto_unbox = T)
-
- serverResponse <- self$http$execute("PUT", resourceURL, headers, newContent,
- retryTimes = self$numRetries)
-
- updatedResource <- self$httpParser$parseJSONResponse(serverResponse)
-
- if(!is.null(updatedResource$errors))
- stop(updatedResource$errors)
-
- updatedResource
- },
-
- createResource = function(resource, content)
- {
- resourceURL <- paste0(self$hostName, resource)
- headers <- list("Authorization" = paste("OAuth2", self$token),
- "Content-Type" = "application/json")
-
- content <- jsonlite::toJSON(content, auto_unbox = T)
-
- serverResponse <- self$http$execute("POST", resourceURL, headers, content,
- retryTimes = self$numRetries)
-
- newResource <- self$httpParser$parseJSONResponse(serverResponse)
-
- if(!is.null(newResource$errors))
- stop(newResource$errors)
-
- newResource
- },
-
create = function(files, uuid)
{
sapply(files, function(filePath)
diff --git a/sdk/R/R/autoGenAPI.R b/sdk/R/R/autoGenAPI.R
index c7bf4b3..95206a4 100644
--- a/sdk/R/R/autoGenAPI.R
+++ b/sdk/R/R/autoGenAPI.R
@@ -44,7 +44,7 @@ generateArvadosAPIClass <- function(discoveryDocument)
arvadosClass <- c(arvadosAPIHeader, arvadosMethods, arvadosAPIFooter)
#TODO: Save to a file or load in memory?
- fileConn <- file("ArvadosAPI.R", "w")
+ fileConn <- file("./R/Arvados.R", "w")
writeLines(unlist(arvadosClass), fileConn)
close(fileConn)
NULL
@@ -93,7 +93,6 @@ getFunctionBody <- function(functionMetaData, classMetaData)
url <- getRequestURL(functionMetaData)
headers <- getRequestHeaders()
requestQueryList <- getRequestQueryList(functionMetaData)
- requestQueryList <- getRequestQueryList(functionMetaData)
requestBody <- getRequestBody(functionMetaData)
request <- getRequest(functionMetaData)
response <- getResponse(functionMetaData)
@@ -116,7 +115,7 @@ getRequestBody <- function(functionMetaData)
getRequestHeaders <- function()
{
- paste0("headers <- list(Authorization = paste(\"OAuth2\", private$token),",
+ paste0("headers <- list(Authorization = paste(\"OAuth2\", private$token), ",
"\"Content-Type\" = \"application/json\")")
}
@@ -125,6 +124,11 @@ getReturnObject <- function(functionMetaData, classMetaData)
returnClass <- functionMetaData$response[["$ref"]]
classArguments <- getReturnClassArguments(returnClass, classMetaData)
+ if(returnClass == "Collection")
+ return(c(paste0("collection <- ", returnClass, "$new(", classArguments, ")"),
+ "collection$setRESTService(private$REST)",
+ "collection"))
+
c(paste0(returnClass, "$new(", classArguments, ")"))
}
@@ -143,12 +147,12 @@ getReturnClassArguments <- function(className, classMetaData)
getRequest <- function(functionMetaData)
{
method <- functionMetaData$httpMethod
- paste0("response <- private$http$exec(\"", method, "\", url, headers, body, queryArgs)")
+ paste0("response <- private$REST$http$exec(\"", method, "\", url, headers, body, queryArgs)")
}
getResponse <- function(functionMetaData)
{
- "resource <- private$httpParser$parseJSONResponse(response)"
+ "resource <- private$REST$httpParser$parseJSONResponse(response)"
}
getRequestURL <- function(functionMetaData)
@@ -189,9 +193,9 @@ createFunction <- function(functionName, functionMetaData, classMetaData)
generateAPIClassHeader <- function()
{
c("#' @export",
- "ArvadosAPI <- R6::R6Class(",
+ "Arvados <- R6::R6Class(",
"",
- "\t\"ArvadosAPI\",",
+ "\t\"Arvados\",",
"",
"\tpublic = list(",
"",
@@ -203,33 +207,36 @@ generateAPIClassHeader <- function()
"\t\t\tif(!is.null(authToken))",
"\t\t\t\tSys.setenv(ARVADOS_API_TOKEN = authToken)",
"",
- "\t\t\tprivate$rawHost <- Sys.getenv(\"ARVADOS_API_HOST\")",
- "\t\t\tprivate$host <- paste0(\"https://\", private$rawHost, \"/arvados/v1/\")",
- "\t\t\tprivate$token <- Sys.getenv(\"ARVADOS_API_TOKEN\")",
- "\t\t\tprivate$numRetries <- numRetries",
- "\t\t\tprivate$http <- ArvadosR:::HttpRequest$new()",
- "\t\t\tprivate$httpParser <- ArvadosR:::HttpParser$new()",
+ "\t\t\thostName <- Sys.getenv(\"ARVADOS_API_HOST\")",
+ "\t\t\ttoken <- Sys.getenv(\"ARVADOS_API_TOKEN\")",
"",
- "\t\t\tif(private$rawHost == \"\" | private$token == \"\")",
+ "\t\t\tif(hostName == \"\" | token == \"\")",
"\t\t\t\tstop(paste(\"Please provide host name and authentification token\",",
"\t\t\t\t\t\t \"or set ARVADOS_API_HOST and ARVADOS_API_TOKEN\",",
"\t\t\t\t\t\t \"environment variables.\"))",
+ "",
+ "\t\t\tprivate$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")
}
generateAPIClassFooter <- function()
{
c("\t\tgetHostName = function() private$host,",
- "\t\tgetToken = function() private$token",
+ "\t\tgetToken = function() private$token,",
+ "\t\tsetRESTService = function(newREST) private$REST <- newREST",
"\t),",
"",
"\tprivate = list(",
"",
"\t\ttoken = NULL,",
- "\t\trawHost = NULL,",
"\t\thost = NULL,",
- "\t\thttp = NULL,",
- "\t\thttpParser = NULL,",
+ "\t\tREST = NULL,",
"\t\tnumRetries = NULL",
"\t),",
"",
@@ -241,13 +248,15 @@ generateArvadosClasses <- function(resources)
{
classes <- sapply(resources$schemas, function(classSchema)
{
- getArvadosClass(classSchema)
+ #NOTE: Collection is implemented manually.
+ if(classSchema$id != "Collection")
+ getArvadosClass(classSchema)
}, USE.NAMES = TRUE)
unlist(unname(classes))
- fileConn <- file("ArvadosClasses.R", "w")
+ fileConn <- file("./R/ArvadosClasses.R", "w")
writeLines(unlist(classes), fileConn)
close(fileConn)
NULL
@@ -260,7 +269,8 @@ getArvadosClass <- function(classSchema)
fieldsList <- paste0("c(", paste0("\"", fields, "\"", collapse = ", "), ")")
constructorArgs <- paste0(fields, " = NULL", collapse = ", ")
- classString <- c(paste0(name, " <- R6::R6Class("),
+ classString <- c("#' @export",
+ paste0(name, " <- R6::R6Class("),
"",
paste0("\t\"", name, "\","),
"",
diff --git a/sdk/R/man/Arvados.Rd b/sdk/R/man/Arvados.Rd
deleted file mode 100644
index 3c66437..0000000
--- a/sdk/R/man/Arvados.Rd
+++ /dev/null
@@ -1,62 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{Arvados}
-\alias{Arvados}
-\title{Arvados}
-\description{
-Arvados class gives users ability to manipulate collections and projects.
-}
-\section{Usage}{
-
-\preformatted{arv = Arvados$new(authToken = NULL, hostName = NULL, numRetries = 0)}
-}
-
-\section{Arguments}{
-
-\describe{
- \item{authToken}{Authentification token. If not specified ARVADOS_API_TOKEN environment variable will be used.}
- \item{hostName}{Host name. If not specified ARVADOS_API_HOST environment variable will be used.}
- \item{numRetries}{Number which specifies how many times to retry failed service requests.}
-}
-}
-
-\section{Methods}{
-
-\describe{
- \item{getToken()}{Returns authentification token currently in use.}
- \item{getHostName()}{Returns host name currently in use.}
- \item{getNumRetries()}{Returns number which specifies how many times to retry failed service requests.}
- \item{setNumRetries(newNumOfRetries)}{Sets number which specifies how many times to retry failed service requests.}
- \item{getCollection(uuid)}{Get collection with specified UUID.}
- \item{listCollections(filters = NULL, limit = 100, offset = 0)}{Returns list of collections based on filters parameter.}
- \item{listAllCollections(filters = NULL)}{Lists all collections, based on filters parameter, even if the number of items is greater than maximum API limit.}
- \item{deleteCollection(uuid)}{Deletes collection with specified UUID.}
- \item{updateCollection(uuid, newContent)}{Updates collection with specified UUID.}
- \item{createCollection(content)}{Creates new collection.}
- \item{getProject(uuid)}{Get project with specified UUID.}
- \item{listProjects(filters = NULL, limit = 100, offset = 0)}{Returns list of projects based on filters parameter.}
- \item{listAllProjects(filters = NULL)}{Lists all projects, based on filters parameter, even if the number of items is greater than maximum API limit.}
- \item{deleteProject(uuid)}{Deletes project with specified UUID.}
- \item{updateProject(uuid, newContent)}{Updates project with specified UUID.}
- \item{createProject(content)}{Creates new project.}
-}
-}
-
-\examples{
-\dontrun{
-arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
-
-collection <- arv$getCollection("uuid")
-
-collectionList <- arv$listCollections(list(list("name", "like", "Test\%")))
-collectionList <- arv$listAllCollections(list(list("name", "like", "Test\%")))
-
-deletedCollection <- arv$deleteCollection("uuid")
-
-updatedCollection <- arv$updateCollection("uuid", list(name = "New name",
- description = "New description"))
-
-createdCollection <- arv$createCollection(list(name = "Example",
- description = "This is a test collection"))
-}
-}
diff --git a/sdk/R/man/print.Arvados.Rd b/sdk/R/man/print.Arvados.Rd
deleted file mode 100644
index 0833d15..0000000
--- a/sdk/R/man/print.Arvados.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{print.Arvados}
-\alias{print.Arvados}
-\title{print.Arvados}
-\usage{
-\method{print}{Arvados}(x, ...)
-}
-\arguments{
-\item{x}{Instance of Arvados class}
-
-\item{...}{Optional arguments.}
-}
-\description{
-Custom print function for Arvados class
-}
diff --git a/sdk/R/tests/testthat/test-Arvados.R b/sdk/R/tests/testthat/test-Arvados.R
deleted file mode 100644
index 25cf88f..0000000
--- a/sdk/R/tests/testthat/test-Arvados.R
+++ /dev/null
@@ -1,306 +0,0 @@
-context("Arvados API")
-
-source("fakes/FakeRESTService.R")
-
-test_that("Constructor will use environment variables if no parameters are passed to it", {
-
- Sys.setenv(ARVADOS_API_HOST = "environment_api_host")
- Sys.setenv(ARVADOS_API_TOKEN = "environment_api_token")
-
- arv <- Arvados$new()
-
- Sys.unsetenv("ARVADOS_API_HOST")
- Sys.unsetenv("ARVADOS_API_TOKEN")
-
- expect_that("https://environment_api_host/arvados/v1/",
- equals(arv$getHostName()))
-
- expect_that("environment_api_token",
- equals(arv$getToken()))
-})
-
-test_that("Constructor preferes constructor fields over environment variables", {
-
- Sys.setenv(ARVADOS_API_HOST = "environment_api_host")
- Sys.setenv(ARVADOS_API_TOKEN = "environment_api_token")
-
- arv <- Arvados$new("constructor_api_token", "constructor_api_host")
-
- Sys.unsetenv("ARVADOS_API_HOST")
- Sys.unsetenv("ARVADOS_API_TOKEN")
-
- expect_that("https://constructor_api_host/arvados/v1/",
- equals(arv$getHostName()))
-
- expect_that("constructor_api_token",
- equals(arv$getToken()))
-})
-
-test_that("Constructor raises exception if fields and environment variables are not provided", {
-
- expect_that(Arvados$new(),
- throws_error(paste0("Please provide host name and authentification token",
- " or set ARVADOS_API_HOST and ARVADOS_API_TOKEN",
- " environment variables.")))
-})
-
-test_that("getCollection delegates operation to RESTService class", {
-
- arv <- Arvados$new("token", "hostName")
- fakeREST <- FakeRESTService$new()
- arv$setRESTService(fakeREST)
- collectionUUID <- "aaaaa-j7d0g-ccccccccccccccc"
-
- arv$getCollection(collectionUUID)
-
- expect_that(fakeREST$getResourceCallCount, equals(1))
-})
-
-test_that("listCollections delegates operation to RESTService class", {
-
- arv <- Arvados$new("token", "hostName")
- fakeREST <- FakeRESTService$new()
- arv$setRESTService(fakeREST)
-
- arv$listCollections()
-
- expect_that(fakeREST$listResourcesCallCount, equals(1))
-})
-
-test_that("listCollections filter paramerter must be named 'collection'", {
-
- filters <- list(list("name", "like", "MyCollection"))
- names(filters) <- c("collection")
- fakeREST <- FakeRESTService$new(expectedFilterContent = filters)
- arv <- Arvados$new("token", "hostName")
- arv$setRESTService(fakeREST)
-
- arv$listCollections(list(list("name", "like", "MyCollection")))
-
- expect_that(fakeREST$filtersAreConfiguredCorrectly, is_true())
-})
-
-test_that("listAllCollections delegates operation to RESTService class", {
-
- arv <- Arvados$new("token", "hostName")
- fakeREST <- FakeRESTService$new()
- arv$setRESTService(fakeREST)
-
- arv$listAllCollections()
-
- expect_that(fakeREST$fetchAllItemsCallCount, equals(1))
-})
-
-test_that("listAllCollections filter paramerter must be named 'collection'", {
-
- filters <- list(list("name", "like", "MyCollection"))
- names(filters) <- c("collection")
- fakeREST <- FakeRESTService$new(expectedFilterContent = filters)
- arv <- Arvados$new("token", "hostName")
- arv$setRESTService(fakeREST)
-
- arv$listAllCollections(list(list("name", "like", "MyCollection")))
-
- expect_that(fakeREST$filtersAreConfiguredCorrectly, is_true())
-})
-
-test_that("deleteCollection delegates operation to RESTService class", {
-
- arv <- Arvados$new("token", "hostName")
- fakeREST <- FakeRESTService$new()
- arv$setRESTService(fakeREST)
- collectionUUID <- "aaaaa-j7d0g-ccccccccccccccc"
-
- arv$deleteCollection(collectionUUID)
-
- expect_that(fakeREST$deleteResourceCallCount, equals(1))
-})
-
-test_that("updateCollection delegates operation to RESTService class", {
-
- arv <- Arvados$new("token", "hostName")
- fakeREST <- FakeRESTService$new()
- arv$setRESTService(fakeREST)
- newCollectionContent <- list(newName = "Brand new shiny name")
- collectionUUID <- "aaaaa-j7d0g-ccccccccccccccc"
-
- arv$updateCollection(collectionUUID, newCollectionContent)
-
- expect_that(fakeREST$updateResourceCallCount, equals(1))
-})
-
-test_that("updateCollection adds content to request parameter named 'collection'", {
-
- collectionUUID <- "aaaaa-j7d0g-ccccccccccccccc"
- body <- list(list())
- names(body) <- c("collection")
- body$collection <- list(name = "MyCollection", desc = "No description")
- fakeREST <- FakeRESTService$new(returnContent = body)
- arv <- Arvados$new("token", "hostName")
- arv$setRESTService(fakeREST)
-
- arv$updateCollection(collectionUUID,
- list(name = "MyCollection", desc = "No description"))
-
- expect_that(fakeREST$bodyIsConfiguredCorrectly, is_true())
-})
-
-test_that("createCollection delegates operation to RESTService class", {
-
- arv <- Arvados$new("token", "hostName")
- fakeREST <- FakeRESTService$new()
- arv$setRESTService(fakeREST)
- collectionContent <- list(newName = "Brand new shiny name")
-
- arv$createCollection(collectionContent)
-
- expect_that(fakeREST$createResourceCallCount, equals(1))
-})
-
-test_that("createCollection adds content to request parameter named 'collection'", {
-
- body <- list(list())
- names(body) <- c("collection")
- body$collection <- list(name = "MyCollection", desc = "No description")
- fakeREST <- FakeRESTService$new(returnContent = body)
- arv <- Arvados$new("token", "hostName")
- arv$setRESTService(fakeREST)
-
- arv$createCollection(list(name = "MyCollection", desc = "No description"))
-
- expect_that(fakeREST$bodyIsConfiguredCorrectly, is_true())
-})
-
-test_that("getProject delegates operation to RESTService class", {
-
- arv <- Arvados$new("token", "hostName")
- fakeREST <- FakeRESTService$new()
- arv$setRESTService(fakeREST)
- projectUUID <- "aaaaa-j7d0g-ccccccccccccccc"
-
- arv$getCollection(projectUUID)
-
- expect_that(fakeREST$getResourceCallCount, equals(1))
-})
-
-test_that("listProjects delegates operation to RESTService class", {
-
- arv <- Arvados$new("token", "hostName")
- fakeREST <- FakeRESTService$new()
- arv$setRESTService(fakeREST)
-
- arv$listCollections()
-
- expect_that(fakeREST$listResourcesCallCount, equals(1))
-})
-
-test_that("listProjects filter contains additional 'group_class' field by default", {
-
- filters <- list(list("name", "like", "MyProject"))
- names(filters) <- c("groups")
- filters[[length(filters) + 1]] <- list("group_class", "=", "project")
-
- fakeREST <- FakeRESTService$new(expectedFilterContent = filters)
- arv <- Arvados$new("token", "hostName")
- arv$setRESTService(fakeREST)
-
- arv$listProjects(list(list("name", "like", "MyProject")))
-
- expect_that(fakeREST$filtersAreConfiguredCorrectly, is_true())
-})
-
-test_that("listAllProjects delegates operation to RESTService class", {
-
- arv <- Arvados$new("token", "hostName")
- fakeREST <- FakeRESTService$new()
- arv$setRESTService(fakeREST)
-
- arv$listAllProjects()
-
- expect_that(fakeREST$fetchAllItemsCallCount, equals(1))
-})
-
-test_that("listAllProjects filter contains additional 'group_class' field by default", {
-
- filters <- list(list("name", "like", "MyProject"))
- names(filters) <- c("groups")
- filters[[length(filters) + 1]] <- list("group_class", "=", "project")
-
- fakeREST <- FakeRESTService$new(expectedFilterContent = filters)
- arv <- Arvados$new("token", "hostName")
- arv$setRESTService(fakeREST)
-
- arv$listAllProjects(list(list("name", "like", "MyProject")))
-
- expect_that(fakeREST$filtersAreConfiguredCorrectly, is_true())
-})
-
-test_that("deleteProject delegates operation to RESTService class", {
-
- arv <- Arvados$new("token", "hostName")
- fakeREST <- FakeRESTService$new()
- arv$setRESTService(fakeREST)
- projectUUID <- "aaaaa-j7d0g-ccccccccccccccc"
-
- arv$deleteCollection(projectUUID)
-
- expect_that(fakeREST$deleteResourceCallCount, equals(1))
-})
-
-test_that("updateProject delegates operation to RESTService class", {
-
- arv <- Arvados$new("token", "hostName")
- fakeREST <- FakeRESTService$new()
- arv$setRESTService(fakeREST)
- newProjectContent <- list(newName = "Brand new shiny name")
- projectUUID <- "aaaaa-j7d0g-ccccccccccccccc"
-
- arv$updateCollection(projectUUID, newProjectContent)
-
- expect_that(fakeREST$updateResourceCallCount, equals(1))
-})
-
-test_that("updateProject adds content to request parameter named 'group'", {
-
- projectUUID <- "aaaaa-j7d0g-ccccccccccccccc"
- body <- list(list())
- names(body) <- c("group")
- body$group <- list(name = "MyProject", desc = "No description")
-
- fakeREST <- FakeRESTService$new(returnContent = body)
- arv <- Arvados$new("token", "hostName")
- arv$setRESTService(fakeREST)
-
- arv$updateProject(projectUUID,
- list(name = "MyProject", desc = "No description"))
-
- expect_that(fakeREST$bodyIsConfiguredCorrectly, is_true())
-})
-
-test_that("createProject delegates operation to RESTService class", {
-
- arv <- Arvados$new("token", "hostName")
- fakeREST <- FakeRESTService$new()
- arv$setRESTService(fakeREST)
- projectContent <- list(newName = "Brand new shiny name")
-
- arv$createCollection(projectContent)
-
- expect_that(fakeREST$createResourceCallCount, equals(1))
-})
-
-test_that("createProject request body contains 'goup_class' filed", {
-
- body <- list(list())
- names(body) <- c("group")
- body$group <- c("group_class" = "project",
- list(name = "MyProject", desc = "No description"))
-
- fakeREST <- FakeRESTService$new(returnContent = body)
- arv <- Arvados$new("token", "hostName")
- arv$setRESTService(fakeREST)
-
- arv$createProject(list(name = "MyProject", desc = "No description"))
-
- expect_that(fakeREST$bodyIsConfiguredCorrectly, is_true())
-})
diff --git a/sdk/R/tests/testthat/test-ArvadosFile.R b/sdk/R/tests/testthat/test-ArvadosFile.R
index 90cc149..67ed0f6 100644
--- a/sdk/R/tests/testthat/test-ArvadosFile.R
+++ b/sdk/R/tests/testthat/test-ArvadosFile.R
@@ -45,9 +45,8 @@ test_that(paste("getSizeInBytes delegates size calculation",
returnSize <- 100
fakeREST <- FakeRESTService$new(collectionContent, returnSize)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
fish <- collection$get("animal/fish")
resourceSize <- fish$getSizeInBytes()
@@ -81,9 +80,8 @@ test_that("read raises exception offset or length is negative number", {
collectionContent <- c("animal", "animal/fish")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
fish <- collection$get("animal/fish")
expect_that(fish$read(contentType = "text", offset = -1),
@@ -100,9 +98,8 @@ test_that("read delegates reading operation to REST service class", {
readContent <- "my file"
fakeREST <- FakeRESTService$new(collectionContent, readContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
fish <- collection$get("animal/fish")
fileContent <- fish$read("text")
@@ -118,9 +115,8 @@ test_that(paste("connection delegates connection creation ro RESTService class",
collectionContent <- c("animal", "animal/fish")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
fish <- collection$get("animal/fish")
connection <- fish$connection("r")
@@ -134,9 +130,8 @@ test_that(paste("connection returns textConnection opened",
collectionContent <- c("animal", "animal/fish")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
fish <- collection$get("animal/fish")
connection <- fish$connection("w")
@@ -156,9 +151,8 @@ test_that("flush sends data stored in a connection to a REST server", {
collectionContent <- c("animal", "animal/fish")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
fish <- collection$get("animal/fish")
connection <- fish$connection("w")
@@ -184,9 +178,8 @@ test_that("write delegates writing operation to REST service class", {
collectionContent <- c("animal", "animal/fish")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
fish <- collection$get("animal/fish")
fileContent <- fish$write("new file content")
@@ -215,10 +208,8 @@ test_that(paste("move raises exception if newLocationInCollection",
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
-
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
dog <- collection$get("animal/dog")
expect_that(dog$move("objects/dog"),
@@ -236,9 +227,8 @@ test_that("move raises exception if new location contains content with the same
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
dog <- collection$get("animal/dog")
expect_that(dog$move("dog"),
@@ -257,9 +247,8 @@ test_that("move moves arvados file inside collection tree", {
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
dog <- collection$get("animal/dog")
dog$move("dog")
diff --git a/sdk/R/tests/testthat/test-Collection.R b/sdk/R/tests/testthat/test-Collection.R
index ec00ca3..56e09f8 100644
--- a/sdk/R/tests/testthat/test-Collection.R
+++ b/sdk/R/tests/testthat/test-Collection.R
@@ -8,9 +8,8 @@ test_that(paste("constructor creates file tree from text content",
collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
root <- collection$get("")
@@ -24,9 +23,8 @@ test_that(paste("add raises exception if passed argumet is not",
collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
newNumber <- 10
@@ -40,9 +38,8 @@ test_that("add raises exception if relative path is not valid", {
collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
newPen <- ArvadosFile$new("pen")
@@ -56,9 +53,8 @@ test_that("add raises exception if content name is empty string", {
collectionContent <- c("animal", "animal/fish")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
rootFolder <- Subcollection$new("")
@@ -72,9 +68,8 @@ test_that(paste("add adds ArvadosFile or Subcollection",
collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
newDog <- ArvadosFile$new("dog")
collection$add(newDog, "animal")
@@ -91,9 +86,8 @@ test_that("create raises exception if passed argumet is not character vector", {
collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
expect_that(collection$create(10),
throws_error("Expected character vector, got (numeric).",
@@ -108,9 +102,8 @@ test_that("create raises exception if relative path is not valid", {
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
newPen <- ArvadosFile$new("pen")
@@ -125,9 +118,8 @@ test_that(paste("create adds files specified by fileNames",
collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
files <- c("dog", "cat")
collection$create(files, "animal")
@@ -147,9 +139,8 @@ test_that("remove raises exception if passed argumet is not character vector", {
collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
expect_that(collection$remove(10),
throws_error("Expected character vector, got (numeric).",
@@ -161,9 +152,8 @@ test_that("remove raises exception if user tries to remove root folder", {
collectionContent <- c("animal", "animal/fish")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
expect_that(collection$remove(""),
throws_error("You can't delete root folder.", fixed = TRUE))
@@ -175,9 +165,8 @@ test_that(paste("remove removes files specified by paths",
collectionContent <- c("animal", "animal/fish", "animal/dog", "animal/cat", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
collection$remove(c("animal/dog", "animal/cat"))
@@ -197,9 +186,8 @@ test_that(paste("move moves content to a new location inside file tree",
collectionContent <- c("animal", "animal/dog", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
collection$move("animal/dog", "dog")
@@ -216,9 +204,8 @@ test_that("move raises exception if new location is not valid", {
collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
expect_that(collection$move("fish", "object"),
throws_error("Content you want to move doesn't exist in the collection.",
@@ -230,9 +217,8 @@ test_that("getFileListing returns sorted collection content received from REST s
collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
contentMatchExpected <- all(collection$getFileListing() ==
c("animal", "animal/fish", "ball"))
@@ -248,9 +234,8 @@ test_that("get returns arvados file or subcollection from internal tree structur
collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
fish <- collection$get("animal/fish")
fishIsNotNull <- !is.null(fish)
diff --git a/sdk/R/tests/testthat/test-RESTService.R b/sdk/R/tests/testthat/test-RESTService.R
index d4f3c2c..ef4a114 100644
--- a/sdk/R/tests/testthat/test-RESTService.R
+++ b/sdk/R/tests/testthat/test-RESTService.R
@@ -31,92 +31,6 @@ test_that("getWebDavHostName returns webDAV host name properly", {
expect_that("https://myWebDavServer.com", equals(REST$getWebDavHostName()))
})
-test_that("getResource calls REST service properly", {
-
- serverResponse <- NULL
- resourceUUID <- "aaaaa-j7d0g-ccccccccccccccc"
- expectedURL <- paste0("https://host/arvados/v1/collections/", resourceUUID)
-
- httpRequest <- FakeHttpRequest$new(expectedURL, serverResponse)
-
- REST <- RESTService$new("token", "host",
- httpRequest, FakeHttpParser$new(),
- 0, "webDavHost")
-
- REST$getResource("collections", resourceUUID)
-
- expect_that(httpRequest$URLIsProperlyConfigured, is_true())
- expect_that(httpRequest$requestHeaderContainsAuthorizationField, is_true())
- expect_that(httpRequest$numberOfGETRequests, equals(1))
-})
-
-test_that("getResource parses server response", {
-
- resourceUUID <- "aaaaa-j7d0g-ccccccccccccccc"
- httpParser <- FakeHttpParser$new()
- REST <- RESTService$new("token", "host",
- FakeHttpRequest$new(), httpParser,
- 0, "webDavHost")
-
- REST$getResource("collections", resourceUUID)
-
- expect_that(httpParser$parserCallCount, equals(1))
-})
-
-test_that("getResource raises exception if response contains errors field", {
-
- resourceUUID <- "aaaaa-j7d0g-ccccccccccccccc"
- serverResponse <- list(errors = 404)
-
- REST <- RESTService$new("token", "host",
- FakeHttpRequest$new(NULL, serverResponse),
- FakeHttpParser$new(),
- 0, "webDavHost")
-
- expect_that(REST$getResource("collections", resourceUUID), throws_error("404", fixed = TRUE))
-})
-
-test_that("listResources calls REST service properly", {
-
- serverResponse <- NULL
- expectedURL <- paste0("https://host/arvados/v1/collections")
- httpRequest <- FakeHttpRequest$new(expectedURL, serverResponse)
-
- REST <- RESTService$new("token", "host",
- httpRequest, FakeHttpParser$new(),
- 0, "webDavHost")
-
- REST$listResources("collections")
-
- expect_that(httpRequest$URLIsProperlyConfigured, is_true())
- expect_that(httpRequest$requestHeaderContainsAuthorizationField, is_true())
- expect_that(httpRequest$numberOfGETRequests, equals(1))
-})
-
-test_that("listResources parses server response", {
-
- httpParser <- FakeHttpParser$new()
- REST <- RESTService$new("token", "host",
- FakeHttpRequest$new(), httpParser,
- 0, "webDavHost")
-
- REST$listResources("collections")
-
- expect_that(httpParser$parserCallCount, equals(1))
-})
-
-test_that("listResources raises exception if response contains errors field", {
-
- serverResponse <- list(errors = 404)
-
- REST <- RESTService$new("token", "host",
- FakeHttpRequest$new(NULL, serverResponse),
- FakeHttpParser$new(),
- 0, "webDavHost")
-
- expect_that(REST$listResources("collections"), throws_error("404", fixed = TRUE))
-})
-
test_that("fetchAllItems always returns all resource items from server", {
expectedURL <- NULL
@@ -145,150 +59,6 @@ test_that("fetchAllItems always returns all resource items from server", {
expect_that(httpParser$parserCallCount, equals(3))
})
-test_that("deleteResource calls REST service properly", {
-
- serverResponse <- NULL
- resourceUUID <- "aaaaa-j7d0g-ccccccccccccccc"
- expectedURL <- paste0("https://host/arvados/v1/collections/", resourceUUID)
-
- httpRequest <- FakeHttpRequest$new(expectedURL, serverResponse)
-
- REST <- RESTService$new("token", "host",
- httpRequest, FakeHttpParser$new(),
- 0, "webDavHost")
-
- REST$deleteResource("collections", resourceUUID)
-
- expect_that(httpRequest$URLIsProperlyConfigured, is_true())
- expect_that(httpRequest$requestHeaderContainsAuthorizationField, is_true())
- expect_that(httpRequest$numberOfDELETERequests, equals(1))
-})
-
-test_that("deleteCollection parses server response", {
-
- resourceUUID <- "aaaaa-j7d0g-ccccccccccccccc"
- httpParser <- FakeHttpParser$new()
- REST <- RESTService$new("token", "host",
- FakeHttpRequest$new(), httpParser,
- 0, "webDavHost")
-
- REST$deleteResource("collections", resourceUUID)
-
- expect_that(httpParser$parserCallCount, equals(1))
-})
-
-test_that("deleteCollection raises exception if response contains errors field", {
-
- resourceUUID <- "aaaaa-j7d0g-ccccccccccccccc"
- serverResponse <- list(errors = 404)
-
- REST <- RESTService$new("token", "host",
- FakeHttpRequest$new(NULL, serverResponse),
- FakeHttpParser$new(),
- 0, "webDavHost")
-
- expect_that(REST$deleteResource("collections", resourceUUID), throws_error("404", fixed = TRUE))
-})
-
-test_that("updateResource calls REST service properly", {
-
- serverResponse <- NULL
- resourceUUID <- "aaaaa-j7d0g-ccccccccccccccc"
- expectedURL <- paste0("https://host/arvados/v1/collections/", resourceUUID)
- newResourceContent <- list(newName = "Brand new shiny name")
-
- httpRequest <- FakeHttpRequest$new(expectedURL, serverResponse)
-
- REST <- RESTService$new("token", "host",
- httpRequest, FakeHttpParser$new(),
- 0, "webDavHost")
-
- REST$updateResource("collections", resourceUUID, newResourceContent)
-
- expect_that(httpRequest$URLIsProperlyConfigured, is_true())
- expect_that(httpRequest$requestHeaderContainsAuthorizationField, is_true())
- expect_that(httpRequest$JSONEncodedBodyIsProvided, is_true())
- expect_that(httpRequest$numberOfPUTRequests, equals(1))
-})
-
-test_that("updateResource parses server response", {
-
- newResourceContent <- list(newName = "Brand new shiny name")
- resourceUUID <- "aaaaa-j7d0g-ccccccccccccccc"
- httpParser <- FakeHttpParser$new()
- REST <- RESTService$new("token", "host",
- FakeHttpRequest$new(), httpParser,
- 0, "webDavHost")
-
- REST$updateResource("collections", resourceUUID, newResourceContent)
-
- expect_that(httpParser$parserCallCount, equals(1))
-})
-
-test_that("updateResource raises exception if response contains errors field", {
-
- resourceUUID <- "aaaaa-j7d0g-ccccccccccccccc"
- serverResponse <- list(errors = 404)
- newResourceContent <- list(newName = "Brand new shiny name")
- REST <- RESTService$new("token", "host",
- FakeHttpRequest$new(NULL, serverResponse),
- FakeHttpParser$new(),
- 0, "webDavHost")
-
- expect_that(REST$updateResource("collections", resourceUUID, newResourceContent),
- throws_error("404", fixed = TRUE))
-})
-
-test_that("createResource calls REST service properly", {
-
- resourceContent <- list(name = "My favorite collection")
- serverResponse <- NULL
- resourceUUID <- "aaaaa-j7d0g-ccccccccccccccc"
- expectedURL <- "https://host/arvados/v1/collections"
- newResourceContent <- list(newName = "Brand new shiny name")
-
- httpRequest <- FakeHttpRequest$new(expectedURL, serverResponse)
-
- REST <- RESTService$new("token", "host",
- httpRequest, FakeHttpParser$new(),
- 0, "webDavHost")
-
- REST$createResource("collections", resourceContent)
-
- expect_that(httpRequest$URLIsProperlyConfigured, is_true())
- expect_that(httpRequest$requestHeaderContainsAuthorizationField, is_true())
- expect_that(httpRequest$JSONEncodedBodyIsProvided, is_true())
- expect_that(httpRequest$numberOfPOSTRequests, equals(1))
-})
-
-test_that("createResource parses server response", {
-
- resourceContent <- list(newName = "Brand new shiny name")
- resourceUUID <- "aaaaa-j7d0g-ccccccccccccccc"
- httpParser <- FakeHttpParser$new()
- REST <- RESTService$new("token", "host",
- FakeHttpRequest$new(), httpParser,
- 0, "webDavHost")
-
- REST$createResource("collections", resourceContent)
-
- expect_that(httpParser$parserCallCount, equals(1))
-})
-
-test_that("createResource raises exception if response contains errors field", {
-
- resourceUUID <- "aaaaa-j7d0g-ccccccccccccccc"
- serverResponse <- list(errors = 404)
- resourceContent <- list(newName = "Brand new shiny name")
- REST <- RESTService$new("token", "host",
- FakeHttpRequest$new(NULL, serverResponse),
- FakeHttpParser$new(),
- 0, "webDavHost")
-
- expect_that(REST$createResource("collections", resourceContent),
- throws_error("404", fixed = TRUE))
-})
-
test_that("create calls REST service properly", {
uuid <- "aaaaa-j7d0g-ccccccccccccccc"
diff --git a/sdk/R/tests/testthat/test-Subcollection.R b/sdk/R/tests/testthat/test-Subcollection.R
index 1b141e1..eafc747 100644
--- a/sdk/R/tests/testthat/test-Subcollection.R
+++ b/sdk/R/tests/testthat/test-Subcollection.R
@@ -117,10 +117,9 @@ test_that(paste("add post content to a REST service",
collectionContent <- c("animal", "animal/fish")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
animal <- collection$get("animal")
dog <- ArvadosFile$new("dog")
@@ -168,9 +167,8 @@ test_that(paste("remove removes content from REST service",
collectionContent <- c("animal", "animal/fish", "animal/dog")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
animal <- collection$get("animal")
animal$remove("fish")
@@ -278,9 +276,8 @@ test_that("move raises exception if new location contains content with the same
"fish")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
fish <- collection$get("animal/fish")
expect_that(fish$move("fish"),
@@ -298,10 +295,8 @@ test_that(paste("move raises exception if newLocationInCollection",
"ball")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
-
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
fish <- collection$get("animal/fish")
expect_that(fish$move("objects/dog"),
@@ -317,9 +312,8 @@ test_that("move moves subcollection inside collection tree", {
"ball")
fakeREST <- FakeRESTService$new(collectionContent)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
fish <- collection$get("animal/fish")
fish$move("fish")
@@ -345,9 +339,8 @@ test_that(paste("getSizeInBytes delegates size calculation",
returnSize <- 100
fakeREST <- FakeRESTService$new(collectionContent, returnSize)
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
+ collection <- Collection$new("fakeUUID")
+ collection$setRESTService(fakeREST)
animal <- collection$get("animal")
resourceSize <- animal$getSizeInBytes()
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