[ARVADOS] updated: 1.1.2-216-g1178add
Git user
git at public.curoverse.com
Mon Jan 29 06:35:20 EST 2018
Summary of changes:
sdk/R/NAMESPACE | 5 +-
sdk/R/R/Arvados.R | 8 +++
sdk/R/R/ArvadosFile.R | 18 +++++++
sdk/R/R/Collection.R | 22 ++++----
sdk/R/R/CollectionTree.R | 5 +-
sdk/R/R/Subcollection.R | 60 ++++++++++++++++------
sdk/R/R/util.R | 2 +-
sdk/R/README | 4 +-
sdk/R/tests/testthat/test-Collection.R | 2 +-
sdk/R/tests/testthat/test-HttpRequest.R | 2 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 1 +
tools/arvbox/lib/arvbox/docker/Dockerfile.demo | 5 +-
tools/arvbox/lib/arvbox/docker/crunch-setup.sh | 9 +---
tools/arvbox/lib/arvbox/docker/go-setup.sh | 16 ++++++
tools/arvbox/lib/arvbox/docker/keep-setup.sh | 9 +---
.../docker/service/arv-git-httpd/run-service | 9 +---
.../lib/arvbox/docker/service/composer/run-service | 12 ++---
.../service/crunch-dispatch-local/run-service | 15 +++---
.../lib/arvbox/docker/service/keep-web/run-service | 9 +---
.../arvbox/docker/service/keepproxy/run-service | 9 +---
.../arvbox/lib/arvbox/docker/service/postgres/run | 2 +
.../arvbox/docker/service/websockets/run-service | 8 +--
22 files changed, 138 insertions(+), 94 deletions(-)
create mode 100644 tools/arvbox/lib/arvbox/docker/go-setup.sh
via 1178add6cefa51f73dd9a229899ea906d297be5a (commit)
via 44ab8ee44302102a7cd5289ef7336d7a94594558 (commit)
via 5bd7108fed4a87eb7cc5a25844bb8c100977c968 (commit)
from 7471c3fb9752482dccae508c34874f9b3c77dfb1 (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 1178add6cefa51f73dd9a229899ea906d297be5a
Merge: 44ab8ee 5bd7108
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date: Mon Jan 29 12:35:11 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 44ab8ee44302102a7cd5289ef7336d7a94594558
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date: Mon Jan 29 12:33:49 2018 +0100
Implemented custom print functions for all public classes
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>
diff --git a/sdk/R/NAMESPACE b/sdk/R/NAMESPACE
index 1c94e71..d4c143c 100644
--- a/sdk/R/NAMESPACE
+++ b/sdk/R/NAMESPACE
@@ -3,5 +3,8 @@
export(Arvados)
export(ArvadosFile)
export(Collection)
-export(CollectionTree)
export(Subcollection)
+export(print.Arvados)
+export(print.ArvadosFile)
+export(print.Collection)
+export(print.Subcollection)
diff --git a/sdk/R/R/Arvados.R b/sdk/R/R/Arvados.R
index 18b42f6..b21c604 100644
--- a/sdk/R/R/Arvados.R
+++ b/sdk/R/R/Arvados.R
@@ -165,3 +165,11 @@ Arvados <- R6::R6Class(
cloneable = FALSE
)
+
+#' @export print.Arvados
+print.Arvados = function(arvados)
+{
+ cat(paste0("Type: ", "\"", "Arvados", "\""), sep = "\n")
+ cat(paste0("Host: ", "\"", arvados$getHostName(), "\""), sep = "\n")
+ cat(paste0("Token: ", "\"", arvados$getToken(), "\"") , sep = "\n")
+}
diff --git a/sdk/R/R/ArvadosFile.R b/sdk/R/R/ArvadosFile.R
index ffb9a6b..7ffcb29 100644
--- a/sdk/R/R/ArvadosFile.R
+++ b/sdk/R/R/ArvadosFile.R
@@ -202,3 +202,21 @@ ArvadosFile <- R6::R6Class(
cloneable = FALSE
)
+
+#' @export print.ArvadosFile
+print.ArvadosFile = function(arvadosFile)
+{
+ collection <- NULL
+ relativePath <- arvadosFile$getRelativePath()
+
+ if(!is.null(arvadosFile$getCollection()))
+ {
+ collection <- arvadosFile$getCollection()$uuid
+ relativePath <- paste0("/", relativePath)
+ }
+
+ cat(paste0("Type: ", "\"", "ArvadosFile", "\""), sep = "\n")
+ cat(paste0("Name: ", "\"", arvadosFile$getName(), "\""), sep = "\n")
+ cat(paste0("Relative path: ", "\"", relativePath, "\"") , sep = "\n")
+ cat(paste0("Collection: ", "\"", collection, "\""), sep = "\n")
+}
diff --git a/sdk/R/R/Collection.R b/sdk/R/R/Collection.R
index 8d49cd0..2107620 100644
--- a/sdk/R/R/Collection.R
+++ b/sdk/R/R/Collection.R
@@ -50,7 +50,6 @@ Collection <- R6::R6Class(
"Subcollection" %in% class(content))
{
subcollection$add(content)
-
content
}
else
@@ -137,7 +136,7 @@ Collection <- R6::R6Class(
elementToMove <- self$get(content)
if(is.null(elementToMove))
- stop("Element you want to move doesn't exist in the collection.")
+ stop("Content you want to move doesn't exist in the collection.")
elementToMove$move(newLocation)
},
@@ -161,18 +160,15 @@ Collection <- R6::R6Class(
REST = NULL,
tree = NULL,
- fileContent = NULL,
-
- generateTree = function(content)
- {
- treeBranches <- sapply(collectionContent, function(filePath)
- {
- splitPath <- unlist(strsplit(filePath$name, "/", fixed = TRUE))
-
- branch = private$createBranch(splitPath, filePath$fileSize)
- })
- }
+ fileContent = NULL
),
cloneable = FALSE
)
+
+#' @export print.Collection
+print.Collection = function(collection)
+{
+ cat(paste0("Type: ", "\"", "Arvados Collection", "\""), sep = "\n")
+ cat(paste0("uuid: ", "\"", collection$uuid, "\""), sep = "\n")
+}
diff --git a/sdk/R/R/CollectionTree.R b/sdk/R/R/CollectionTree.R
index fcc5dbe..4194be9 100644
--- a/sdk/R/R/CollectionTree.R
+++ b/sdk/R/R/CollectionTree.R
@@ -7,7 +7,6 @@ source("./R/util.R")
#' Update description
#'
#' @examples arv = Collection$new(api, uuid)
-#' @export CollectionTree
CollectionTree <- R6::R6Class(
"CollectionTree",
public = list(
@@ -96,8 +95,8 @@ CollectionTree <- R6::R6Class(
}
else
{
- # Note: REST always returns folder name alone before other folder content
- # (for some reason), so in first iteration we don't know if it's a file
+ # Note: REST always returns folder name alone before other folder
+ # content, so in first iteration we don't know if it's a file
# or folder since its just a name, so we assume it's a file.
# If we encounter that same name again we know
# it's a folder so we need to replace ArvadosFile with Subcollection.
diff --git a/sdk/R/R/Subcollection.R b/sdk/R/R/Subcollection.R
index a1f83f5..7eb4381 100644
--- a/sdk/R/R/Subcollection.R
+++ b/sdk/R/R/Subcollection.R
@@ -13,7 +13,7 @@ Subcollection <- R6::R6Class(
initialize = function(name)
{
- private$name <- name
+ private$name <- name
},
getName = function() private$name,
@@ -101,21 +101,7 @@ Subcollection <- R6::R6Class(
getFileListing = function(fullPath = TRUE)
{
- content <- NULL
-
- if(fullPath)
- {
- for(child in private$children)
- content <- c(content, child$getFileListing())
-
- if(private$name != "")
- content <- unlist(paste0(private$name, "/", content))
- }
- else
- {
- for(child in private$children)
- content <- c(content, child$getName())
- }
+ content <- private$getContentAsCharVector(fullPath)
content[order(tolower(content))]
},
@@ -250,8 +236,50 @@ Subcollection <- R6::R6Class(
parent$remove(private$name)
parent$setCollection(parentsCollection, setRecursively = FALSE)
+ },
+
+ getContentAsCharVector = function(fullPath = TRUE)
+ {
+ content <- NULL
+
+ if(fullPath)
+ {
+ for(child in private$children)
+ content <- c(content, child$getFileListing())
+
+ if(private$name != "")
+ content <- unlist(paste0(private$name, "/", content))
+ }
+ else
+ {
+ for(child in private$children)
+ content <- c(content, child$getName())
+ }
+
+ content
+
}
),
cloneable = FALSE
)
+
+#' @export print.Subcollection
+print.Subcollection = function(subCollection)
+{
+ collection <- NULL
+ relativePath <- subCollection$getRelativePath()
+
+ if(!is.null(subCollection$getCollection()))
+ {
+ collection <- subCollection$getCollection()$uuid
+
+ if(!subCollection$getName() == "")
+ relativePath <- paste0("/", relativePath)
+ }
+
+ cat(paste0("Type: ", "\"", "Arvados Subcollection", "\""), sep = "\n")
+ cat(paste0("Name: ", "\"", subCollection$getName(), "\""), sep = "\n")
+ cat(paste0("Relative path: ", "\"", relativePath, "\"") , sep = "\n")
+ cat(paste0("Collection: ", "\"", collection, "\""), sep = "\n")
+}
diff --git a/sdk/R/R/util.R b/sdk/R/R/util.R
index 65b5a4e..d9af8b0 100644
--- a/sdk/R/R/util.R
+++ b/sdk/R/R/util.R
@@ -49,6 +49,6 @@ splitToPathAndName = function(path)
nameAndPath$name <- components[length(components)]
nameAndPath$path <- trimFromStart(paste0(components[-length(components)], collapse = "/"),
"/")
-
+
nameAndPath
}
diff --git a/sdk/R/README b/sdk/R/README
index 6b8cd3f..8a0c31d 100644
--- a/sdk/R/README
+++ b/sdk/R/README
@@ -57,7 +57,7 @@ deletedCollection <- arv$deleteCollection("uuid")
#Update a collection's metadata:
-updatedCollection <- arv$updateCollection("uuid", list(name = "My new name", description = "a brand new description"))
+updatedCollection <- arv$updateCollection("uuid", list(name = "New name", description = "New description"))
--------------------------------------------------------------------------------------------------------------------------------
@@ -189,7 +189,7 @@ file$move("newDestination/file.cpp")
subcollection <- collection$get("location/to/folder")
subcollection$move("newDestination/folder")
-#Make sure to include file name in new destination
+#Make sure to include new file name in destination
#In second example file$move("newDestination/") will not work
--------------------------------------------------------------------------------------------------------------------------------
diff --git a/sdk/R/tests/testthat/test-Collection.R b/sdk/R/tests/testthat/test-Collection.R
index 0c45958..63a402d 100644
--- a/sdk/R/tests/testthat/test-Collection.R
+++ b/sdk/R/tests/testthat/test-Collection.R
@@ -215,7 +215,7 @@ test_that("move raises exception if new location is not valid", {
collection <- Collection$new(api, "myUUID")
expect_that(collection$move("fish", "object"),
- throws_error("Element you want to move doesn't exist in the collection.",
+ throws_error("Content you want to move doesn't exist in the collection.",
fixed = TRUE))
})
diff --git a/sdk/R/tests/testthat/test-HttpRequest.R b/sdk/R/tests/testthat/test-HttpRequest.R
index 427ec34..e850374 100644
--- a/sdk/R/tests/testthat/test-HttpRequest.R
+++ b/sdk/R/tests/testthat/test-HttpRequest.R
@@ -1,4 +1,4 @@
-context("Http Parser")
+context("Http Request")
test_that(paste("createQuery generates and encodes query portion of http",
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