[ARVADOS] updated: 1.1.1-205-gf2a79e0
Git user
git at public.curoverse.com
Fri Dec 8 11:23:07 EST 2017
Summary of changes:
build/run-tests.sh | 10 +
sdk/R/.RData | Bin 162592 -> 190002 bytes
sdk/R/R/Arvados.R | 20 +-
sdk/R/R/ArvadosFile.R | 31 ++-
sdk/R/R/Collection.R | 21 +-
sdk/R/R/HttpParser.R | 12 +-
sdk/R/R/HttpRequest.R | 5 +-
sdk/python/tests/run_test_server.py | 15 --
services/api/Gemfile | 1 +
services/api/Gemfile.lock | 2 +
.../api/app/controllers/application_controller.rb | 2 +-
.../controllers/arvados/v1/schema_controller.rb | 11 +-
.../app/controllers/user_sessions_controller.rb | 6 +-
services/api/app/middlewares/arvados_api_token.rb | 45 ++---
.../api/app/models/api_client_authorization.rb | 118 ++++++++++++
services/api/config/application.default.yml | 29 ++-
.../arvados/v1/groups_controller_test.rb | 1 -
services/api/test/integration/remote_user_test.rb | 214 +++++++++++++++++++++
services/api/test/integration/users_test.rb | 1 -
services/api/test/test_helper.rb | 8 +
20 files changed, 472 insertions(+), 80 deletions(-)
create mode 100644 services/api/test/integration/remote_user_test.rb
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commit f2a79e0cc9bffcbe941d9a05b78f102fa6f09d03
Merge: eb95e18 e21d1ca
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date: Fri Dec 8 17:22:53 2017 +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 eb95e18a3f2686762a99723ba4d7f0803f9d3c5d
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date: Fri Dec 8 17:20:12 2017 +0100
Added ability to read file from a collection and made minor fixes to
collection content tree.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>
diff --git a/sdk/R/.RData b/sdk/R/.RData
index 626630b..21c7024 100644
Binary files a/sdk/R/.RData and b/sdk/R/.RData differ
diff --git a/sdk/R/R/Arvados.R b/sdk/R/R/Arvados.R
index 82f3aba..ab38763 100644
--- a/sdk/R/R/Arvados.R
+++ b/sdk/R/R/Arvados.R
@@ -64,11 +64,11 @@ Arvados <- setRefClass(
collection_get <<- function(uuid)
{
- collection_url <- paste0(host, "collections/", uuid)
+ collectionURL <- paste0(host, "collections/", uuid)
headers <- list(Authorization = paste("OAuth2", token))
http <- HttpRequest()
- serverResponse <- http$GET(collection_url, headers)
+ serverResponse <- http$GET(collectionURL, headers)
httpParser <- HttpParser()
collection <- httpParser$parseJSONResponse(serverResponse)
@@ -81,11 +81,11 @@ Arvados <- setRefClass(
collection_list <<- function(filters = NULL, limit = 100, offset = 0)
{
- collection_url <- paste0(host, "collections")
+ collectionURL <- paste0(host, "collections")
headers <- list(Authorization = paste("OAuth2", token))
http <- HttpRequest()
- serverResponse <- http$GET(collection_url, headers, NULL, filters, limit, offset)
+ serverResponse <- http$GET(collectionURL, headers, NULL, filters, limit, offset)
httpParser <- HttpParser()
collection <- httpParser$parseJSONResponse(serverResponse)
@@ -98,12 +98,12 @@ Arvados <- setRefClass(
collection_delete <<- function(uuid)
{
- collection_url <- paste0(host, "collections/", uuid)
+ collectionURL <- paste0(host, "collections/", uuid)
headers <- list("Authorization" = paste("OAuth2", token),
"Content-Type" = "application/json")
http <- HttpRequest()
- serverResponse <- http$DELETE(collection_url, headers)
+ serverResponse <- http$DELETE(collectionURL, headers)
httpParser <- HttpParser()
collection <- httpParser$parseJSONResponse(serverResponse)
@@ -116,13 +116,13 @@ Arvados <- setRefClass(
collection_update <<- function(uuid, body)
{
- collection_url <- paste0(host, "collections/", uuid)
+ collectionURL <- paste0(host, "collections/", uuid)
headers <- list("Authorization" = paste("OAuth2", token),
"Content-Type" = "application/json")
body <- jsonlite::toJSON(body, auto_unbox = T)
http <- HttpRequest()
- serverResponse <- http$PUT(collection_url, headers, body)
+ serverResponse <- http$PUT(collectionURL, headers, body)
httpParser <- HttpParser()
collection <- httpParser$parseJSONResponse(serverResponse)
@@ -135,13 +135,13 @@ Arvados <- setRefClass(
collection_create <<- function(body)
{
- collection_url <- paste0(host, "collections")
+ collectionURL <- paste0(host, "collections")
headers <- list("Authorization" = paste("OAuth2", token),
"Content-Type" = "application/json")
body <- jsonlite::toJSON(body, auto_unbox = T)
http <- HttpRequest()
- serverResponse <- http$POST(collection_url, headers, body)
+ serverResponse <- http$POST(collectionURL, headers, body)
httpParser <- HttpParser()
collection <- httpParser$parseJSONResponse(serverResponse)
diff --git a/sdk/R/R/ArvadosFile.R b/sdk/R/R/ArvadosFile.R
index 45aee1e..067e70a 100644
--- a/sdk/R/R/ArvadosFile.R
+++ b/sdk/R/R/ArvadosFile.R
@@ -1,3 +1,4 @@
+source("./R/HttpRequest.R")
#' ArvadosFile Class
#'
#' @details
@@ -10,12 +11,38 @@ ArvadosFile <- setRefClass(
"ArvadosFile",
fields = list(
name = "character",
- relativePath = "character"
+ relativePath = "character",
+
+ read = "function"
+
+
),
methods = list(
- initialize = function(subcollectionName)
+ initialize = function(subcollectionName, api)
{
name <<- subcollectionName
+
+ read <<- function(offset = 0, length = 0)
+ {
+ if(offset < 0 || length < 0)
+ stop("Offset and length must be positive values.")
+
+ range = paste0("bytes=", offset, "-")
+
+ if(length > 0)
+ range = paste0(range, offset + length - 1)
+
+ fileURL = paste0(api$getWebDavHostName(), relativePath);
+ headers <- list(Authorization = paste("OAuth2", api$getWebDavToken()),
+ Range = range)
+
+ #TODO(Fudo): Move this to HttpRequest.R
+ # serverResponse <- httr::GET(url = fileURL,
+ # config = httr::add_headers(unlist(headers)))
+ http <- HttpRequest()
+ serverResponse <- http$GET(fileURL, headers)
+ parsed_response <- httr::content(serverResponse, "raw")
+ }
}
)
)
diff --git a/sdk/R/R/Collection.R b/sdk/R/R/Collection.R
index bd6bd3f..29afadc 100644
--- a/sdk/R/R/Collection.R
+++ b/sdk/R/R/Collection.R
@@ -128,7 +128,7 @@ Collection <- setRefClass(
}
}
- nodeToCheck = .self$items
+ nodeToCheck = .self$fileContent
for(fileNameIndex in 1:length(fileWithPath))
{
nodeToCheck <- findFileIfExists(fileWithPath[fileNameIndex], nodeToCheck)
@@ -143,15 +143,16 @@ Collection <- setRefClass(
# Private methods
.createCollectionContentTree <- function(fileStructure)
{
- #TODO(Fudo): Refactot this.
+ #TODO(Fudo): Refactor this.
+ #TODO(Fudo): Find a way to link children to parents. (R has no pointers or references).
treeBranches <- sapply(fileStructure, function(filePath)
{
- fileWithPath <- unlist(str_split(filePath, "/"))
+ fileWithPath <- unlist(stringr::str_split(filePath, "/"))
file <- fileWithPath[length(fileWithPath), drop = T]
if(file != "")
{
- file <- ArvadosFile(file)
+ file <- ArvadosFile(file, api)
file$relativePath <- filePath
}
else
@@ -212,13 +213,13 @@ Collection <- setRefClass(
}
#Todo(Fudo): This is dummy data. Real content will come from WebDAV server.
- testFileStructure <- c("math.h", "main.cpp", "emptyFolder/",
- "java/render.java", "java/test/observer.java",
- "java/test/observable.java",
- "csharp/this.cs", "csharp/is.cs",
- "csharp/dummy.cs", "csharp/file.cs")
+ # testFileStructure <- c("math.h", "main.cpp", "emptyFolder/",
+ # "java/render.java", "java/test/observer.java",
+ # "java/test/observable.java",
+ # "csharp/this.cs", "csharp/is.cs",
+ # "csharp/dummy.cs", "csharp/file.cs")
items <<- getCollectionContent()
- fileContent <<- .createCollectionContentTree(testFileStructure)
+ fileContent <<- .createCollectionContentTree(items)
}
)
)
diff --git a/sdk/R/R/HttpParser.R b/sdk/R/R/HttpParser.R
index bbe0a60..fb895be 100644
--- a/sdk/R/R/HttpParser.R
+++ b/sdk/R/R/HttpParser.R
@@ -12,16 +12,16 @@ HttpParser <- setRefClass(
{
},
- parseCollectionGet = function(server_response)
+ parseCollectionGet = function(serverResponse)
{
- parsed_response <- httr::content(server_response, as = "parsed", type = "application/json")
+ parsed_response <- httr::content(serverResponse, as = "parsed", type = "application/json")
#Todo(Fudo): Create new Collection object and populate it
},
- parseJSONResponse = function(server_response)
+ parseJSONResponse = function(serverResponse)
{
- parsed_response <- httr::content(server_response, as = "parsed", type = "application/json")
+ parsed_response <- httr::content(serverResponse, as = "parsed", type = "application/json")
#Todo(Fudo): Create new Collection object and populate it
},
@@ -39,7 +39,9 @@ HttpParser <- setRefClass(
sub(base, "", URLdecode(XML::xmlValue(node)), fixed=TRUE)
})
)
- result[result != ""]
+ result <- result[result != ""]
+ #Todo(Fudo): Test this.
+ result[-1]
}
)
diff --git a/sdk/R/R/HttpRequest.R b/sdk/R/R/HttpRequest.R
index eecf0c1..ddb8f71 100644
--- a/sdk/R/R/HttpRequest.R
+++ b/sdk/R/R/HttpRequest.R
@@ -17,9 +17,8 @@ HttpRequest <- setRefClass(
{
# Public methods
GET <<- function(url, headers = NULL, body = NULL,
- queryFilters = NULL, limit = 100, offset = 0)
+ queryFilters = NULL, limit = NULL, offset = NULL)
{
- print(limit)
headers <- httr::add_headers(unlist(headers))
query <- .createQuery(queryFilters, limit, offset)
url <- paste0(url, query)
@@ -49,7 +48,7 @@ HttpRequest <- setRefClass(
}
DELETE <<- function(url, headers = NULL, body = NULL,
- queryFilters = NULL, limit = 100, offset = 0)
+ queryFilters = NULL, limit = NULL, offset = NULL)
{
headers <- httr::add_headers(unlist(headers))
query <- .createQuery(queryFilters, limit, offset)
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