[ARVADOS] updated: 1.1.2-223-g6459c61
Git user
git at public.curoverse.com
Tue Jan 30 09:02:31 EST 2018
Summary of changes:
sdk/R/R/Arvados.R | 18 +++--
sdk/R/R/ArvadosFile.R | 16 ++---
sdk/R/R/Collection.R | 12 +++-
sdk/R/R/RESTService.R | 2 +-
sdk/R/R/Subcollection.R | 11 ++--
sdk/R/tests/testthat/test-ArvadosFile.R | 8 +++
sdk/R/tests/testthat/test-Collection.R | 80 +++++++++++-----------
sdk/R/tests/testthat/test-Subcollection.R | 9 +++
sdk/go/arvadostest/fixtures.go | 1 +
services/api/test/fixtures/users.yml | 16 +++++
services/crunch-run/crunchrun.go | 106 ++++++++++++++++++------------
tools/sync-groups/sync-groups.go | 21 +++---
tools/sync-groups/sync-groups_test.go | 33 ++++++----
13 files changed, 207 insertions(+), 126 deletions(-)
via 6459c61b9cca7d2382d01c20d1f749a7dc8d21e0 (commit)
via c98c533d5c971efd1d3b122076c5abe0736f8423 (commit)
via 9482a917eef77ef64fc9fee27b0d107727f765ad (commit)
via b4351d725f01431856cbe1ea0e8faf8d4f91dd4e (commit)
via 3a4434f8b767e05456eea248f645422b1ed670d0 (commit)
via 1b7a6c0ca4fa348c313a0862cfca597319cfe08f (commit)
via 90bffaaf5e537608c3a8d2520544bfdd9b98d286 (commit)
from 1178add6cefa51f73dd9a229899ea906d297be5a (commit)
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit 6459c61b9cca7d2382d01c20d1f749a7dc8d21e0
Merge: c98c533 9482a91
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date: Tue Jan 30 15:02:19 2018 +0100
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>
commit c98c533d5c971efd1d3b122076c5abe0736f8423
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date: Tue Jan 30 15:00:40 2018 +0100
Added error checking code to Collection and Subcollection classes
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>
diff --git a/sdk/R/R/Arvados.R b/sdk/R/R/Arvados.R
index b21c604..6493b89 100644
--- a/sdk/R/R/Arvados.R
+++ b/sdk/R/R/Arvados.R
@@ -25,12 +25,12 @@ Arvados <- R6::R6Class(
Sys.setenv(ARVADOS_API_TOKEN = authToken)
hostName <- Sys.getenv("ARVADOS_API_HOST");
- token <- Sys.getenv("ARVADOS_API_TOKEN");
+ token <- Sys.getenv("ARVADOS_API_TOKEN");
if(hostName == "" | token == "")
- stop(paste0("Please provide host name and authentification token",
- " or set ARVADOS_API_HOST and ARVADOS_API_TOKEN",
- " environment variables."))
+ stop(paste("Please provide host name and authentification token",
+ "or set ARVADOS_API_HOST and ARVADOS_API_TOKEN",
+ "environment variables."))
private$REST <- RESTService$new(token, hostName, NULL,
HttpRequest$new(), HttpParser$new())
@@ -119,8 +119,7 @@ Arvados <- R6::R6Class(
names(body) <- c("group")
body$group <- newContent
- updatedProject <- private$REST$updateResource("groups",
- uuid, body)
+ updatedProject <- private$REST$updateResource("groups", uuid, body)
updatedProject
},
@@ -131,8 +130,7 @@ Arvados <- R6::R6Class(
filters[[length(filters) + 1]] <- list("group_class", "=", "project")
- projects <- private$REST$listResources("groups", filters,
- limit, offset)
+ projects <- private$REST$listResources("groups", filters, limit, offset)
projects
},
@@ -169,7 +167,7 @@ Arvados <- R6::R6Class(
#' @export print.Arvados
print.Arvados = function(arvados)
{
- cat(paste0("Type: ", "\"", "Arvados", "\""), sep = "\n")
+ cat(paste0("Type: ", "\"", "Arvados", "\""), sep = "\n")
cat(paste0("Host: ", "\"", arvados$getHostName(), "\""), sep = "\n")
- cat(paste0("Token: ", "\"", arvados$getToken(), "\"") , sep = "\n")
+ cat(paste0("Token: ", "\"", arvados$getToken(), "\""), sep = "\n")
}
diff --git a/sdk/R/R/ArvadosFile.R b/sdk/R/R/ArvadosFile.R
index 7ffcb29..3437933 100644
--- a/sdk/R/R/ArvadosFile.R
+++ b/sdk/R/R/ArvadosFile.R
@@ -13,9 +13,10 @@ ArvadosFile <- R6::R6Class(
initialize = function(name)
{
- private$name <- name
- private$http <- HttpRequest$new()
- private$httpParser <- HttpParser$new()
+ if(name == "")
+ stop("Invalid name.")
+
+ private$name <- name
},
getName = function() private$name,
@@ -132,7 +133,6 @@ ArvadosFile <- R6::R6Class(
if(is.null(private$collection))
stop("ArvadosFile doesn't belong to any collection")
-
newLocation <- trimFromEnd(newLocation, "/")
nameAndPath <- splitToPathAndName(newLocation)
@@ -168,8 +168,6 @@ ArvadosFile <- R6::R6Class(
size = NULL,
parent = NULL,
collection = NULL,
- http = NULL,
- httpParser = NULL,
buffer = NULL,
attachToNewParent = function(newParent)
@@ -215,8 +213,8 @@ print.ArvadosFile = function(arvadosFile)
relativePath <- paste0("/", relativePath)
}
- cat(paste0("Type: ", "\"", "ArvadosFile", "\""), sep = "\n")
+ cat(paste0("Type: ", "\"", "ArvadosFile", "\""), sep = "\n")
cat(paste0("Name: ", "\"", arvadosFile$getName(), "\""), sep = "\n")
- cat(paste0("Relative path: ", "\"", relativePath, "\"") , sep = "\n")
- cat(paste0("Collection: ", "\"", collection, "\""), sep = "\n")
+ cat(paste0("Relative path: ", "\"", relativePath, "\""), sep = "\n")
+ cat(paste0("Collection: ", "\"", collection, "\""), sep = "\n")
}
diff --git a/sdk/R/R/Collection.R b/sdk/R/R/Collection.R
index 2107620..47d88ac 100644
--- a/sdk/R/R/Collection.R
+++ b/sdk/R/R/Collection.R
@@ -49,6 +49,10 @@ Collection <- R6::R6Class(
if("ArvadosFile" %in% class(content) ||
"Subcollection" %in% class(content))
{
+
+ if(content$getName() == "")
+ stop("Content has invalid name.")
+
subcollection$add(content)
content
}
@@ -118,8 +122,14 @@ Collection <- R6::R6Class(
stop(paste("File", filePath, "doesn't exist."))
parent <- file$getParent()
+
+ if(is.null(parent))
+ stop("You can't delete root folder.")
+
parent$remove(file$getName())
})
+
+ "Content removed"
}
else
{
@@ -170,5 +180,5 @@ Collection <- R6::R6Class(
print.Collection = function(collection)
{
cat(paste0("Type: ", "\"", "Arvados Collection", "\""), sep = "\n")
- cat(paste0("uuid: ", "\"", collection$uuid, "\""), sep = "\n")
+ cat(paste0("uuid: ", "\"", collection$uuid, "\""), sep = "\n")
}
diff --git a/sdk/R/R/RESTService.R b/sdk/R/R/RESTService.R
index 65c5302..62356b7 100644
--- a/sdk/R/R/RESTService.R
+++ b/sdk/R/R/RESTService.R
@@ -174,7 +174,7 @@ RESTService <- R6::R6Class(
if(serverResponse$status_code < 200 || serverResponse$status_code >= 300)
stop(paste("Server code:", serverResponse$status_code))
- paste("File deleted:", relativePath)
+ serverResponse
},
move = function(from, to, uuid)
diff --git a/sdk/R/R/Subcollection.R b/sdk/R/R/Subcollection.R
index 7eb4381..d580695 100644
--- a/sdk/R/R/Subcollection.R
+++ b/sdk/R/R/Subcollection.R
@@ -38,7 +38,11 @@ Subcollection <- R6::R6Class(
if("ArvadosFile" %in% class(content) ||
"Subcollection" %in% class(content))
{
+ if(content$getName() == "")
+ stop("Content has invalid name.")
+
childWithSameName <- self$get(content$getName())
+
if(!is.null(childWithSameName))
stop(paste("Subcollection already contains ArvadosFile",
"or Subcollection with same name."))
@@ -83,6 +87,7 @@ Subcollection <- R6::R6Class(
{
REST <- private$collection$getRESTService()
REST$delete(child$getRelativePath(), private$collection$uuid)
+
child$setCollection(NULL)
}
@@ -102,7 +107,6 @@ Subcollection <- R6::R6Class(
getFileListing = function(fullPath = TRUE)
{
content <- private$getContentAsCharVector(fullPath)
-
content[order(tolower(content))]
},
@@ -257,7 +261,6 @@ Subcollection <- R6::R6Class(
}
content
-
}
),
@@ -280,6 +283,6 @@ print.Subcollection = function(subCollection)
cat(paste0("Type: ", "\"", "Arvados Subcollection", "\""), sep = "\n")
cat(paste0("Name: ", "\"", subCollection$getName(), "\""), sep = "\n")
- cat(paste0("Relative path: ", "\"", relativePath, "\"") , sep = "\n")
- cat(paste0("Collection: ", "\"", collection, "\""), sep = "\n")
+ cat(paste0("Relative path: ", "\"", relativePath, "\""), sep = "\n")
+ cat(paste0("Collection: ", "\"", collection, "\""), sep = "\n")
}
diff --git a/sdk/R/tests/testthat/test-ArvadosFile.R b/sdk/R/tests/testthat/test-ArvadosFile.R
index 43c841b..90cc149 100644
--- a/sdk/R/tests/testthat/test-ArvadosFile.R
+++ b/sdk/R/tests/testthat/test-ArvadosFile.R
@@ -2,6 +2,11 @@ source("fakes/FakeRESTService.R")
context("ArvadosFile")
+test_that("constructor raises error if file name is empty string", {
+
+ expect_that(ArvadosFile$new(""), throws_error("Invalid name."))
+})
+
test_that("getFileListing always returns file name", {
dog <- ArvadosFile$new("dog")
@@ -207,6 +212,7 @@ test_that(paste("move raises exception if newLocationInCollection",
"animal/dog",
"animal/fish/shark",
"ball")
+
fakeREST <- FakeRESTService$new(collectionContent)
api <- Arvados$new("myToken", "myHostName")
@@ -227,6 +233,7 @@ test_that("move raises exception if new location contains content with the same
"animal/dog",
"animal/fish/shark",
"dog")
+
fakeREST <- FakeRESTService$new(collectionContent)
api <- Arvados$new("myToken", "myHostName")
@@ -247,6 +254,7 @@ test_that("move moves arvados file inside collection tree", {
"animal/dog",
"animal/fish/shark",
"ball")
+
fakeREST <- FakeRESTService$new(collectionContent)
api <- Arvados$new("myToken", "myHostName")
diff --git a/sdk/R/tests/testthat/test-Collection.R b/sdk/R/tests/testthat/test-Collection.R
index 63a402d..ec00ca3 100644
--- a/sdk/R/tests/testthat/test-Collection.R
+++ b/sdk/R/tests/testthat/test-Collection.R
@@ -5,10 +5,7 @@ context("Collection")
test_that(paste("constructor creates file tree from text content",
"retreived form REST service"), {
-
- collectionContent <- c("animal",
- "animal/fish",
- "ball")
+ collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
api <- Arvados$new("myToken", "myHostName")
@@ -24,9 +21,7 @@ test_that(paste("constructor creates file tree from text content",
test_that(paste("add raises exception if passed argumet is not",
"ArvadosFile or Subcollection"), {
- collectionContent <- c("animal",
- "animal/fish",
- "ball")
+ collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
api <- Arvados$new("myToken", "myHostName")
@@ -42,9 +37,7 @@ test_that(paste("add raises exception if passed argumet is not",
test_that("add raises exception if relative path is not valid", {
- collectionContent <- c("animal",
- "animal/fish",
- "ball")
+ collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
api <- Arvados$new("myToken", "myHostName")
@@ -58,12 +51,25 @@ test_that("add raises exception if relative path is not valid", {
fixed = TRUE))
})
+test_that("add raises exception if content name is empty string", {
+
+ collectionContent <- c("animal", "animal/fish")
+ fakeREST <- FakeRESTService$new(collectionContent)
+
+ api <- Arvados$new("myToken", "myHostName")
+ api$setRESTService(fakeREST)
+ collection <- Collection$new(api, "myUUID")
+
+ rootFolder <- Subcollection$new("")
+
+ expect_that(collection$add(rootFolder),
+ throws_error("Content has invalid name.", fixed = TRUE))
+})
+
test_that(paste("add adds ArvadosFile or Subcollection",
"to local tree structure and remote REST service"), {
- collectionContent <- c("animal",
- "animal/fish",
- "ball")
+ collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
api <- Arvados$new("myToken", "myHostName")
@@ -82,9 +88,7 @@ test_that(paste("add adds ArvadosFile or Subcollection",
test_that("create raises exception if passed argumet is not character vector", {
- collectionContent <- c("animal",
- "animal/fish",
- "ball")
+ collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
api <- Arvados$new("myToken", "myHostName")
@@ -101,6 +105,7 @@ test_that("create raises exception if relative path is not valid", {
collectionContent <- c("animal",
"animal/fish",
"ball")
+
fakeREST <- FakeRESTService$new(collectionContent)
api <- Arvados$new("myToken", "myHostName")
@@ -117,9 +122,7 @@ test_that("create raises exception if relative path is not valid", {
test_that(paste("create adds files specified by fileNames",
"to local tree structure and remote REST service"), {
- collectionContent <- c("animal",
- "animal/fish",
- "ball")
+ collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
api <- Arvados$new("myToken", "myHostName")
@@ -141,9 +144,7 @@ test_that(paste("create adds files specified by fileNames",
test_that("remove raises exception if passed argumet is not character vector", {
- collectionContent <- c("animal",
- "animal/fish",
- "ball")
+ collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
api <- Arvados$new("myToken", "myHostName")
@@ -155,14 +156,23 @@ test_that("remove raises exception if passed argumet is not character vector", {
fixed = TRUE))
})
+test_that("remove raises exception if user tries to remove root folder", {
+
+ collectionContent <- c("animal", "animal/fish")
+ fakeREST <- FakeRESTService$new(collectionContent)
+
+ api <- Arvados$new("myToken", "myHostName")
+ api$setRESTService(fakeREST)
+ collection <- Collection$new(api, "myUUID")
+
+ expect_that(collection$remove(""),
+ throws_error("You can't delete root folder.", fixed = TRUE))
+})
+
test_that(paste("remove removes files specified by paths",
"from local tree structure and from remote REST service"), {
- collectionContent <- c("animal",
- "animal/fish",
- "animal/dog",
- "animal/cat",
- "ball")
+ collectionContent <- c("animal", "animal/fish", "animal/dog", "animal/cat", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
api <- Arvados$new("myToken", "myHostName")
@@ -184,9 +194,7 @@ test_that(paste("remove removes files specified by paths",
test_that(paste("move moves content to a new location inside file tree",
"and on REST service"), {
- collectionContent <- c("animal",
- "animal/dog",
- "ball")
+ collectionContent <- c("animal", "animal/dog", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
api <- Arvados$new("myToken", "myHostName")
@@ -205,9 +213,7 @@ test_that(paste("move moves content to a new location inside file tree",
test_that("move raises exception if new location is not valid", {
- collectionContent <- c("animal",
- "animal/fish",
- "ball")
+ collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
api <- Arvados$new("myToken", "myHostName")
@@ -221,9 +227,7 @@ test_that("move raises exception if new location is not valid", {
test_that("getFileListing returns sorted collection content received from REST service", {
- collectionContent <- c("animal",
- "animal/fish",
- "ball")
+ collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
api <- Arvados$new("myToken", "myHostName")
@@ -241,9 +245,7 @@ test_that("getFileListing returns sorted collection content received from REST s
test_that("get returns arvados file or subcollection from internal tree structure", {
- collectionContent <- c("animal",
- "animal/fish",
- "ball")
+ collectionContent <- c("animal", "animal/fish", "ball")
fakeREST <- FakeRESTService$new(collectionContent)
api <- Arvados$new("myToken", "myHostName")
diff --git a/sdk/R/tests/testthat/test-Subcollection.R b/sdk/R/tests/testthat/test-Subcollection.R
index b155ed4..1b141e1 100644
--- a/sdk/R/tests/testthat/test-Subcollection.R
+++ b/sdk/R/tests/testthat/test-Subcollection.R
@@ -73,6 +73,15 @@ test_that("add adds content to inside collection tree", {
expect_that(animalContainsDog, is_true())
})
+test_that("add raises exception if content name is empty string", {
+
+ animal <- Subcollection$new("animal")
+ rootFolder <- Subcollection$new("")
+
+ expect_that(animal$add(rootFolder),
+ throws_error("Content has invalid name.", fixed = TRUE))
+})
+
test_that(paste("add raises exception if ArvadosFile/Subcollection",
"with same name already exists in the subcollection"), {
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