[ARVADOS] updated: 1.1.1-120-g2d8d861
Git user
git at public.curoverse.com
Mon Dec 4 11:11:53 EST 2017
Summary of changes:
sdk/R/.RData | Bin 94020 -> 136720 bytes
sdk/R/DESCRIPTION | 4 +-
sdk/R/R/Arvados.R | 9 +-
sdk/R/R/Collection.R | 108 +++++++++++++++++++++++
sdk/R/R/HttpParser.R | 17 ++++
sdk/R/R/arvados_objects.R | 74 ----------------
services/api/app/models/container.rb | 15 ++++
services/api/test/unit/container_request_test.rb | 29 ++++++
8 files changed, 177 insertions(+), 79 deletions(-)
create mode 100644 sdk/R/R/Collection.R
via 2d8d861fadc8f3e0e7d5524c78f980dedc56f759 (commit)
via eb93b9b3b9d05c566f886b9a46bad4043d0a8534 (commit)
via 4ea88c89b61931b2f588461d530b4fa7dcf7487d (commit)
via bc5d3ce17a0b3672b4ff2c24623febc549bdebe5 (commit)
via 77a6645f2a8710a22a43909469077122834c93e6 (commit)
via 8167db395a144238b1702c2bb5a40e4dd7db26ca (commit)
from 02ce18b74c42b34a86208a713e00dfa0e0fe39de (commit)
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commit 2d8d861fadc8f3e0e7d5524c78f980dedc56f759
Merge: eb93b9b 4ea88c8
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date: Mon Dec 4 17:11:07 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 eb93b9b3b9d05c566f886b9a46bad4043d0a8534
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date: Mon Dec 4 16:23:29 2017 +0100
Added a new collection class. Added a method to retrieve list of files
and folders in a collection.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>
diff --git a/sdk/R/.RData b/sdk/R/.RData
index 2b5f989..1e0b193 100644
Binary files a/sdk/R/.RData and b/sdk/R/.RData differ
diff --git a/sdk/R/DESCRIPTION b/sdk/R/DESCRIPTION
index c6afbbb..cc46f65 100644
--- a/sdk/R/DESCRIPTION
+++ b/sdk/R/DESCRIPTION
@@ -13,4 +13,6 @@ RoxygenNote: 6.0.1.9000
Imports:
httr,
stringr,
- jsonlite
+ jsonlite,
+ curl,
+ XML
diff --git a/sdk/R/R/Arvados.R b/sdk/R/R/Arvados.R
index 8b3b40b..d502b8d 100644
--- a/sdk/R/R/Arvados.R
+++ b/sdk/R/R/Arvados.R
@@ -1,5 +1,6 @@
source("./R/HttpRequest.R")
source("./R/HttpParser.R")
+source("./R/custom_classes.R")
#' Arvados SDK Object
#'
@@ -14,16 +15,16 @@ Arvados <- setRefClass(
"Arvados",
fields = list(
- token = "character",
- host = "character"
+ token = "ANY",
+ host = "ANY"
),
methods = list(
- initialize = function(auth_token, host_name)
+ initialize = function(auth_token = NULL, host_name = NULL)
{
version <- "v1"
- #Todo(Fudo): Validate token
+ #Todo(Fudo): Set environment variables
token <<- auth_token
host <<- paste0("https://", host_name, "/arvados/", version, "/")
}
diff --git a/sdk/R/R/Collection.R b/sdk/R/R/Collection.R
new file mode 100644
index 0000000..037f711
--- /dev/null
+++ b/sdk/R/R/Collection.R
@@ -0,0 +1,108 @@
+source("./R/Arvados.R")
+source("./R/HttpParser.R")
+
+#' Collection Object
+#'
+#' @details
+#' Todo: Update description
+#' Collection
+#'
+#' @param uuid Object ID
+#' @param etag Object version
+#' @param owner_uuid No description
+#' @param created_at No description
+#' @param modified_by_client_uuid No description
+#' @param modified_by_user_uuid No description
+#' @param modified_at No description
+#' @param portable_data_hash No description
+#' @param replication_desired No description
+#' @param replication_confirmed_at No description
+#' @param replication_confirmed No description
+#' @param updated_at No description
+#' @param manifest_text No description
+#' @param name No description
+#' @param description No description
+#' @param properties No description
+#' @param delete_at No description
+#' @param file_names No description
+#' @param trash_at No description
+#' @param is_trashed No description
+#'
+#' @export
+Collection <- setRefClass(
+
+ "Collection",
+
+ #NOTE(Fudo): Fix types!
+ fields = list(uuid = "ANY",
+ items = "ANY",
+ etag = "ANY",
+ owner_uuid = "ANY",
+ created_at = "ANY",
+ modified_by_client_uuid = "ANY",
+ modified_by_user_uuid = "ANY",
+ modified_at = "ANY",
+ portable_data_hash = "ANY",
+ replication_desired = "ANY",
+ replication_confirmed_at = "ANY",
+ replication_confirmed = "ANY",
+ updated_at = "ANY",
+ manifest_text = "ANY",
+ name = "ANY",
+ description = "ANY",
+ properties = "ANY",
+ delete_at = "ANY",
+ file_names = "ANY",
+ trash_at = "ANY",
+ is_trashed = "ANY",
+ arvados_api = "Arvados"
+ ),
+
+ methods = list(
+
+ initialize = function(api, uuid)
+ {
+ arvados_api <<- api
+ result <- arvados_api$collection_get(uuid)
+
+ uuid <<- result$uuid
+ etag <<- result$etag
+ owner_uuid <<- result$owner_uuid
+ created_at <<- result$created_at
+ modified_by_client_uuid <<- result$modified_by_client_uuid
+ modified_by_user_uuid <<- result$modified_by_user_uuid
+ modified_at <<- result$modified_at
+ portable_data_hash <<- result$portable_data_hash
+ replication_desired <<- result$replication_desired
+ replication_confirmed_at <<- result$replication_confirmed_at
+ replication_confirmed <<- result$replication_confirmed
+ updated_at <<- result$updated_at
+ manifest_text <<- result$manifest_text
+ name <<- result$name
+ description <<- result$description
+ properties <<- result$properties
+ delete_at <<- result$delete_at
+ file_names <<- result$file_names
+ trash_at <<- result$trash_at
+ is_trashed <<- result$is_trashed
+
+ items <<- getCollectionContent()
+ },
+
+ getCollectionContent = function()
+ {
+ #IMPORTANT(Fudo): This url is hardcoded for now. Fix it later.
+ uri <- URLencode("https://collections.4xphq.arvadosapi.com/c=4xphq-4zz18-9d5b0qm4fgijeyi/_/")
+
+ # fetch directory listing via curl and parse XML response
+ h <- curl::new_handle()
+ curl::handle_setopt(h, customrequest = "PROPFIND")
+
+ #IMPORTANT(Fudo): Token is hardcoded as well. Write it properly.
+ curl::handle_setheaders(h, "Authorization" = paste("OAuth2 4invqy35tf70t7hmvdc83ges8ug9cklhgqq1l8gj2cjn18teuq"))
+ response <- curl::curl_fetch_memory(uri, h)
+
+ HttpParser()$parseWebDAVResponse(response, uri)
+ }
+ )
+)
diff --git a/sdk/R/R/HttpParser.R b/sdk/R/R/HttpParser.R
index 09304fc..ebe7d8c 100644
--- a/sdk/R/R/HttpParser.R
+++ b/sdk/R/R/HttpParser.R
@@ -17,6 +17,23 @@ HttpParser <- setRefClass(
parsed_response <- httr::content(server_response, as = "parsed", type = "application/json")
#Todo(Fudo): Create new Collection object and populate it
+ },
+
+ parseWebDAVResponse = function(response, uri)
+ {
+ #Todo(Fudo): Move this to HttpParser.
+ text <- rawToChar(response$content)
+ doc <- XML::xmlParse(text, asText=TRUE)
+
+ # calculate relative paths
+ base <- paste(paste("/", strsplit(uri, "/")[[1]][-1:-3], sep="", collapse=""), "/", sep="")
+ result <- unlist(
+ XML::xpathApply(doc, "//D:response/D:href", function(node) {
+ sub(base, "", URLdecode(xmlValue(node)), fixed=TRUE)
+ })
+ )
+ result[result != ""]
}
+
)
)
diff --git a/sdk/R/R/arvados_objects.R b/sdk/R/R/arvados_objects.R
index 88fd515..8b13789 100644
--- a/sdk/R/R/arvados_objects.R
+++ b/sdk/R/R/arvados_objects.R
@@ -1,75 +1 @@
-#' Collection Object
-#'
-#' @details
-#' Todo: Update description
-#' Collection
-#'
-#' @param uuid Object ID
-#' @param etag Object version
-#' @param owner_uuid No description
-#' @param created_at No description
-#' @param modified_by_client_uuid No description
-#' @param modified_by_user_uuid No description
-#' @param modified_at No description
-#' @param portable_data_hash No description
-#' @param replication_desired No description
-#' @param replication_confirmed_at No description
-#' @param replication_confirmed No description
-#' @param updated_at No description
-#' @param manifest_text No description
-#' @param name No description
-#' @param description No description
-#' @param properties No description
-#' @param delete_at No description
-#' @param file_names No description
-#' @param trash_at No description
-#' @param is_trashed No description
-#'
-#' @return Collection object
-#'
-#' @family Collection functions
-#' @export
-Collection <- 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)
-{
- structure(list(uuid = uuid,
- etag = etag,
- owner_uuid = owner_uuid,
- created_at = created_at,
- modified_by_client_uuid = modified_by_client_uuid,
- modified_by_user_uuid = modified_by_user_uuid,
- modified_at = modified_at,
- portable_data_hash = portable_data_hash,
- replication_desired = replication_desired,
- replication_confirmed_at = replication_confirmed_at,
- replication_confirmed = replication_confirmed,
- updated_at = updated_at,
- manifest_text = manifest_text,
- name = name,
- description = description,
- properties = properties,
- delete_at = delete_at,
- file_names = file_names,
- trash_at = trash_at,
- is_trashed = is_trashed),
- class = "ArvadosCollection")
-}
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