[ARVADOS] updated: 1.1.2-98-g2d3726d
Git user
git at public.curoverse.com
Tue Jan 9 11:22:06 EST 2018
Summary of changes:
README.md | 14 +-
build/check-copyright-notices | 301 ++++++++--------
build/run-build-docker-jobs-image.sh | 20 +-
build/run-build-packages-one-target.sh | 6 +-
build/run-build-packages.sh | 2 +
build/run-library.sh | 9 +-
build/run-tests.sh | 19 +-
cmd/arvados-client/.gitignore | 1 +
cmd/arvados-client/cmd.go | 79 +++++
cmd/arvados-client/cmd_test.go | 41 +++
doc/api/methods/users.html.textile.liquid | 13 +
.../install-slurm.html.textile.liquid | 2 +
doc/user/cwl/bwa-mem/bwa-mem.cwl | 4 +-
lib/cli/external.go | 124 +++++++
lib/cli/flags.go | 33 ++
lib/cli/get.go | 75 ++++
lib/cli/get_test.go | 33 ++
lib/cmd/cmd.go | 116 +++++++
lib/cmd/cmd_test.go | 62 ++++
lib/cmdtest/leakcheck.go | 54 +++
sdk/R/DESCRIPTION | 1 +
sdk/R/R/Arvados.R | 34 +-
sdk/R/R/ArvadosFile.R | 83 +++--
sdk/R/R/Collection.R | 84 ++---
sdk/R/R/CollectionTree.R | 28 +-
sdk/R/R/HttpRequest.R | 8 +-
sdk/R/R/Subcollection.R | 173 +++++-----
sdk/R/tests/testthat.R | 4 +
sdk/R/tests/testthat/HttpRequestStub.R | 52 +++
sdk/R/tests/testthat/test-Arvados.R | 35 ++
sdk/cwl/arvados_cwl/arvworkflow.py | 5 +-
sdk/cwl/arvados_cwl/runner.py | 15 +-
sdk/cwl/tests/arvados-tests.yml | 5 +
.../cwl/tests/secondary/dir/hg19.fa | 0
.../cwl/tests/secondary/dir/hg19.fa.amb | 0
.../cwl/tests/secondary/dir/hg19.fa.ann | 0
.../cwl/tests/secondary/dir/hg19.fa.fai | 0
sdk/cwl/tests/secondary/ls.cwl | 11 +
sdk/cwl/tests/secondary/sub.cwl | 17 +
sdk/cwl/tests/secondary/wf-job.yml | 3 +
sdk/cwl/tests/secondary/wf.cwl | 23 ++
sdk/go/arvados/collection_fs.go | 4 +
sdk/go/arvados/collection_fs_test.go | 24 ++
sdk/go/arvadostest/fixtures.go | 1 +
.../app/controllers/arvados/v1/users_controller.rb | 17 +-
services/api/app/models/user.rb | 26 ++
services/api/config/routes.rb | 1 +
.../test/fixtures/api_client_authorizations.yml | 8 +-
services/api/test/fixtures/containers.yml | 3 +-
.../functional/arvados/v1/users_controller_test.rb | 21 ++
services/api/test/unit/container_test.rb | 2 +-
services/api/test/unit/user_test.rb | 79 +++++
services/arv-git-httpd/arvados-git-httpd.service | 9 +-
.../crunch-dispatch-slurm.service | 9 +-
services/crunch-run/crunchrun.go | 19 +-
services/crunch-run/crunchrun_test.go | 2 +-
services/crunch-run/logging.go | 6 +-
.../dockercleaner/arvados-docker-cleaner.service | 9 +-
services/fuse/arvados_fuse/__init__.py | 5 +-
services/fuse/tests/test_inodes.py | 2 +-
services/health/arvados-health.service | 27 ++
services/keep-balance/keep-balance.service | 9 +-
services/keep-web/cadaver_test.go | 11 +
services/keep-web/keep-web.service | 9 +-
services/keepproxy/keepproxy.service | 9 +-
services/keepstore/keepstore.service | 9 +-
services/ws/arvados-ws.service | 9 +-
vendor/vendor.json | 384 ++++++++++++++++++++-
68 files changed, 1884 insertions(+), 419 deletions(-)
create mode 100644 cmd/arvados-client/.gitignore
create mode 100644 cmd/arvados-client/cmd.go
create mode 100644 cmd/arvados-client/cmd_test.go
create mode 100644 lib/cli/external.go
create mode 100644 lib/cli/flags.go
create mode 100644 lib/cli/get.go
create mode 100644 lib/cli/get_test.go
create mode 100644 lib/cmd/cmd.go
create mode 100644 lib/cmd/cmd_test.go
create mode 100644 lib/cmdtest/leakcheck.go
create mode 100644 sdk/R/tests/testthat.R
create mode 100644 sdk/R/tests/testthat/HttpRequestStub.R
create mode 100644 sdk/R/tests/testthat/test-Arvados.R
copy tools/crunchstat-summary/tests/__init__.py => sdk/cwl/tests/secondary/dir/hg19.fa (100%)
copy tools/crunchstat-summary/tests/__init__.py => sdk/cwl/tests/secondary/dir/hg19.fa.amb (100%)
copy tools/crunchstat-summary/tests/__init__.py => sdk/cwl/tests/secondary/dir/hg19.fa.ann (100%)
copy tools/crunchstat-summary/tests/__init__.py => sdk/cwl/tests/secondary/dir/hg19.fa.fai (100%)
create mode 100644 sdk/cwl/tests/secondary/ls.cwl
create mode 100644 sdk/cwl/tests/secondary/sub.cwl
create mode 100644 sdk/cwl/tests/secondary/wf-job.yml
create mode 100644 sdk/cwl/tests/secondary/wf.cwl
create mode 100644 services/health/arvados-health.service
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commit 2d3726dd11046146731f7f7391659a5eaf44702b
Merge: 7b76c49 3cca12f
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date: Tue Jan 9 17:21:49 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 7b76c49887aecdb2bf0be7eecf8f5b271d5f0c38
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date: Tue Jan 9 17:21:18 2018 +0100
Added support for unit testing.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>
diff --git a/sdk/R/DESCRIPTION b/sdk/R/DESCRIPTION
index 0e586e9..ce96f05 100644
--- a/sdk/R/DESCRIPTION
+++ b/sdk/R/DESCRIPTION
@@ -17,3 +17,4 @@ Imports:
jsonlite,
curl,
XML
+Suggests: testthat
diff --git a/sdk/R/R/Arvados.R b/sdk/R/R/Arvados.R
index e08ce61..b58b287 100644
--- a/sdk/R/R/Arvados.R
+++ b/sdk/R/R/Arvados.R
@@ -30,9 +30,6 @@ Arvados <- R6::R6Class(
stop("Please provide host name and authentification token or set
ARVADOS_API_HOST and ARVADOS_API_TOKEN environmental variables.")
- discoveryDocumentURL <- paste0("https://", host,
- "/discovery/v1/apis/arvados/v1/rest")
-
version <- "v1"
host <- paste0("https://", host, "/arvados/", version, "/")
@@ -40,22 +37,31 @@ Arvados <- R6::R6Class(
private$httpParser <- HttpParser$new()
private$token <- token
private$host <- host
-
- headers <- list(Authorization = paste("OAuth2", private$token))
-
- serverResponse <- private$http$GET(discoveryDocumentURL, headers)
-
- discoveryDocument <- private$httpParser$parseJSONResponse(serverResponse)
- private$webDavHostName <- discoveryDocument$keepWebServiceUrl
-
- if(is.null(private$webDavHostName))
- stop("Unable to find WebDAV server.")
},
getToken = function() private$token,
getHostName = function() private$host,
- getWebDavHostName = function() private$webDavHostName,
+ getWebDavHostName = function()
+ {
+ if(is.null(private$webDavHostName))
+ {
+ discoveryDocumentURL <- paste0("https://", host,
+ "/discovery/v1/apis/arvados/v1/rest")
+
+ headers <- list(Authorization = paste("OAuth2", private$token))
+
+ serverResponse <- private$http$GET(discoveryDocumentURL, headers)
+
+ discoveryDocument <- private$httpParser$parseJSONResponse(serverResponse)
+ private$webDavHostName <- discoveryDocument$keepWebServiceUrl
+
+ if(is.null(private$webDavHostName))
+ stop("Unable to find WebDAV server.")
+ }
+
+ private$webDavHostName
+ },
getCollection = function(uuid)
{
diff --git a/sdk/R/tests/testthat.R b/sdk/R/tests/testthat.R
new file mode 100644
index 0000000..18ef411
--- /dev/null
+++ b/sdk/R/tests/testthat.R
@@ -0,0 +1,4 @@
+library(testthat)
+library(ArvadosR)
+
+test_check("ArvadosR")
diff --git a/sdk/R/tests/testthat/HttpRequestStub.R b/sdk/R/tests/testthat/HttpRequestStub.R
new file mode 100644
index 0000000..31f8759
--- /dev/null
+++ b/sdk/R/tests/testthat/HttpRequestStub.R
@@ -0,0 +1,52 @@
+HttpRequest <- R6::R6Class(
+
+ "HttrRequestStub",
+
+ public = list(
+
+ validContentTypes = NULL,
+
+ content = NULL,
+
+ initialize = function(returnContent)
+ {
+ self$validContentTypes <- c("text", "raw")
+ self$content <- returnContent
+ },
+
+ GET = function(url, headers = NULL, queryFilters = NULL, limit = NULL, offset = NULL)
+ {
+ return self$content
+ },
+
+ PUT = function(url, headers = NULL, body = NULL,
+ queryFilters = NULL, limit = NULL, offset = NULL)
+ {
+ return self$content
+ },
+
+ POST = function(url, headers = NULL, body = NULL,
+ queryFilters = NULL, limit = NULL, offset = NULL)
+ {
+ return self$content
+ },
+
+ DELETE = function(url, headers = NULL, body = NULL,
+ queryFilters = NULL, limit = NULL, offset = NULL)
+ {
+ return self$content
+ },
+
+ PROPFIND = function(url, headers = NULL)
+ {
+ return self$content
+ },
+
+ MOVE = function(url, headers = NULL)
+ {
+ return self$content
+ }
+ ),
+
+ cloneable = FALSE
+)
diff --git a/sdk/R/tests/testthat/test-Arvados.R b/sdk/R/tests/testthat/test-Arvados.R
new file mode 100644
index 0000000..35b4152
--- /dev/null
+++ b/sdk/R/tests/testthat/test-Arvados.R
@@ -0,0 +1,35 @@
+context("Arvados API")
+
+test_that("Arvados constructor will use environment variables if no parameters are passed to it", {
+
+ Sys.setenv(ARVADOS_API_HOST = "environment_api_host")
+ Sys.setenv(ARVADOS_API_TOKEN = "environment_api_token")
+
+ arv <- Arvados$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("Arvados 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$getToken()))
+})
commit 8daddfe53514b71ef229e9c2985e116fa6614858
Merge: d246f53 b37da0c
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date: Tue Jan 9 15:31:19 2018 +0100
Merge branch '11876-r-sdk' of git.curoverse.com:arvados into 11876-r-sdk
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>
commit d246f53c1d991f1572d6701569aa8c7eac4d722d
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date: Tue Jan 9 15:28:42 2018 +0100
Collection classes no longer use each others private state.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>
diff --git a/sdk/R/R/ArvadosFile.R b/sdk/R/R/ArvadosFile.R
index 3be24c4..8c2e9e2 100644
--- a/sdk/R/R/ArvadosFile.R
+++ b/sdk/R/R/ArvadosFile.R
@@ -37,17 +37,21 @@ ArvadosFile <- R6::R6Class(
as.numeric(sizes)
},
- removeFromCollection = function()
+ get = function(fileLikeObjectName)
{
- if(is.null(private$collection))
- stop("ArvadosFile doesn't belong to any collection.")
-
- private$collection$.__enclos_env__$private$deleteFromREST(self$getRelativePath())
+ return(NULL)
+ },
- private$addToCollection(NULL)
- private$detachFromParent()
+ getFirst = function()
+ {
+ return(NULL)
+ },
- "Content removed successfully."
+ getCollection = function() private$collection,
+
+ setCollection = function(collection)
+ {
+ private$collection <- collection
},
getRelativePath = function()
@@ -67,6 +71,8 @@ ArvadosFile <- R6::R6Class(
getParent = function() private$parent,
+ setParent = function(newParent) private$parent <- newParent,
+
read = function(contentType = "raw", offset = 0, length = 0)
{
if(is.null(private$collection))
@@ -128,17 +134,21 @@ ArvadosFile <- R6::R6Class(
move = function(newLocation)
{
+ #todo test if file can be moved
+
if(is.null(private$collection))
stop("ArvadosFile doesn't belong to any collection.")
if(endsWith(newLocation, paste0(private$name, "/")))
{
newLocation <- substr(newLocation, 0,
- nchar(newLocation) - nchar(paste0(private$name, "/")))
+ nchar(newLocation)
+ - nchar(paste0(private$name, "/")))
}
else if(endsWith(newLocation, private$name))
{
- newLocation <- substr(newLocation, 0, nchar(newLocation) - nchar(private$name))
+ newLocation <- substr(newLocation, 0,
+ nchar(newLocation) - nchar(private$name))
}
else
{
@@ -152,10 +162,25 @@ ArvadosFile <- R6::R6Class(
stop("Unable to get destination subcollection.")
}
- status <- private$collection$.__enclos_env__$private$moveOnREST(self$getRelativePath(),
- paste0(newParent$getRelativePath(), "/", self$getName()))
+ childWithSameName <- newParent$get(private$name)
+
+ if(!is.null(childWithSameName))
+ stop("Destination already contains file with same name.")
- private$attachToParent(newParent)
+ status <- private$collection$moveOnREST(self$getRelativePath(),
+ paste0(newParent$getRelativePath(),
+ "/", self$getName()))
+
+ #Note: We temporary set parents collection to NULL. This will ensure that
+ # add method doesn't post file on REST server.
+ parentsCollection <- newParent$getCollection()
+ newParent$setCollection(NULL, setRecursively = FALSE)
+
+ newParent$add(self)
+
+ newParent$setCollection(parentsCollection, setRecursively = FALSE)
+
+ private$parent <- newParent
"Content moved successfully."
}
@@ -168,37 +193,7 @@ ArvadosFile <- R6::R6Class(
parent = NULL,
collection = NULL,
http = NULL,
- httpParser = NULL,
-
- getChild = function(name)
- {
- return(NULL)
- },
-
- getFirstChild = function()
- {
- return(NULL)
- },
-
- addToCollection = function(collection)
- {
- private$collection <- collection
- },
-
- detachFromParent = function()
- {
- if(!is.null(private$parent))
- {
- private$parent$.__enclos_env__$private$removeChild(private$name)
- private$parent <- NULL
- }
- },
-
- attachToParent = function(parent)
- {
- parent$.__enclos_env__$private$children <- c(parent$.__enclos_env__$private$children, self)
- private$parent <- parent
- }
+ httpParser = NULL
),
cloneable = FALSE
diff --git a/sdk/R/R/Collection.R b/sdk/R/R/Collection.R
index 8e6895e..8bd4655 100644
--- a/sdk/R/R/Collection.R
+++ b/sdk/R/R/Collection.R
@@ -37,7 +37,7 @@ Collection <- R6::R6Class(
relativePath == "." ||
relativePath == "./")
{
- subcollection <- private$tree$.__enclos_env__$private$tree
+ subcollection <- private$tree$getTree()
}
else
{
@@ -71,7 +71,7 @@ Collection <- R6::R6Class(
relativePath == "." ||
relativePath == "./")
{
- subcollection <- private$tree$.__enclos_env__$private$tree
+ subcollection <- private$tree$getTree()
}
else
{
@@ -89,6 +89,10 @@ Collection <- R6::R6Class(
arvadosFiles <- NULL
sapply(fileNames, function(fileName)
{
+ childWithSameName <- subcollection$get(fileName)
+ if(!is.null(childWithSameName))
+ stop("Destination already contains file with same name.")
+
newFile <- ArvadosFile$new(fileName)
subcollection$add(newFile)
@@ -122,14 +126,15 @@ Collection <- R6::R6Class(
if(is.null(file))
stop(paste("File", filePath, "doesn't exist."))
- file$removeFromCollection()
+ parent <- file$getParent()
+ parent$remove(filePath)
})
}
else if("ArvadosFile" %in% class(content) ||
"Subcollection" %in% class(content))
{
- if(is.null(content$.__enclos_env__$private$collection) ||
- content$.__enclos_env__$private$collection$uuid != self$uuid)
+ if(is.null(content$getCollection()) ||
+ content$getCollection()$uuid != self$uuid)
stop("Subcollection doesn't belong to this collection.")
content$removeFromCollection()
@@ -154,44 +159,14 @@ Collection <- R6::R6Class(
get = function(relativePath)
{
private$tree$getElement(relativePath)
- }
- ),
-
- private = list(
-
- http = NULL,
- httpParser = NULL,
- tree = NULL,
-
- fileContent = NULL,
-
- getCollectionContent = function()
- {
- collectionURL <- URLencode(paste0(self$api$getWebDavHostName(), "c=", self$uuid))
-
- headers = list("Authorization" = paste("OAuth2", self$api$getToken()))
-
- response <- private$http$PROPFIND(collectionURL, headers)
-
- parsedResponse <- private$httpParser$parseWebDAVResponse(response, collectionURL)
- parsedResponse[-1]
},
-
+
+ #Todo: Move these methods to another class.
createFilesOnREST = function(files)
{
sapply(files, function(filePath)
{
- private$createNewFile(filePath, NULL, "text/html")
- })
- },
-
- generateTree = function(content)
- {
- treeBranches <- sapply(collectionContent, function(filePath)
- {
- splitPath <- unlist(strsplit(filePath$name, "/", fixed = TRUE))
-
- branch = private$createBranch(splitPath, filePath$fileSize)
+ self$createNewFile(filePath, NULL, "text/html")
})
},
@@ -209,7 +184,7 @@ Collection <- R6::R6Class(
print(paste("File created:", relativePath))
},
-
+
deleteFromREST = function(relativePath)
{
fileURL <- paste0(self$api$getWebDavHostName(), "c=", self$uuid, "/", relativePath);
@@ -241,5 +216,36 @@ Collection <- R6::R6Class(
}
),
+ private = list(
+
+ http = NULL,
+ httpParser = NULL,
+ tree = NULL,
+
+ fileContent = NULL,
+
+ getCollectionContent = function()
+ {
+ collectionURL <- URLencode(paste0(self$api$getWebDavHostName(), "c=", self$uuid))
+
+ headers = list("Authorization" = paste("OAuth2", self$api$getToken()))
+
+ response <- private$http$PROPFIND(collectionURL, headers)
+
+ parsedResponse <- private$httpParser$parseWebDAVResponse(response, collectionURL)
+ parsedResponse[-1]
+ },
+
+ generateTree = function(content)
+ {
+ treeBranches <- sapply(collectionContent, function(filePath)
+ {
+ splitPath <- unlist(strsplit(filePath$name, "/", fixed = TRUE))
+
+ branch = private$createBranch(splitPath, filePath$fileSize)
+ })
+ }
+ ),
+
cloneable = FALSE
)
diff --git a/sdk/R/R/CollectionTree.R b/sdk/R/R/CollectionTree.R
index 3bf89e5..e024f5e 100644
--- a/sdk/R/R/CollectionTree.R
+++ b/sdk/R/R/CollectionTree.R
@@ -21,7 +21,7 @@ CollectionTree <- R6::R6Class(
treeBranches <- sapply(fileContent, function(filePath)
{
splitPath <- unlist(strsplit(filePath, "/", fixed = TRUE))
- branch = private$createBranch(splitPath)
+ branch <- private$createBranch(splitPath)
})
root <- Subcollection$new("")
@@ -31,7 +31,7 @@ CollectionTree <- R6::R6Class(
private$addBranch(root, branch)
})
- root$.__enclos_env__$private$addToCollection(collection)
+ root$setCollection(collection)
private$tree <- root
},
@@ -41,18 +41,20 @@ CollectionTree <- R6::R6Class(
relativePath <- substr(relativePath, 0, nchar(relativePath) - 1)
splitPath <- unlist(strsplit(relativePath, "/", fixed = TRUE))
- returnElement = private$tree
+ returnElement <- private$tree
for(pathFragment in splitPath)
{
- returnElement = returnElement$.__enclos_env__$private$getChild(pathFragment)
+ returnElement <- returnElement$get(pathFragment)
if(is.null(returnElement))
return(NULL)
}
returnElement
- }
+ },
+
+ getTree = function() private$tree
),
private = list(
@@ -68,13 +70,13 @@ CollectionTree <- R6::R6Class(
{
if(elementIndex == lastElementIndex)
{
- branch = ArvadosFile$new(splitPath[[elementIndex]])
+ branch <- ArvadosFile$new(splitPath[[elementIndex]])
}
else
{
- newFolder = Subcollection$new(splitPath[[elementIndex]])
+ newFolder <- Subcollection$new(splitPath[[elementIndex]])
newFolder$add(branch)
- branch = newFolder
+ branch <- newFolder
}
}
@@ -83,7 +85,7 @@ CollectionTree <- R6::R6Class(
addBranch = function(container, node)
{
- child = container$.__enclos_env__$private$getChild(node$getName())
+ child <- container$get(node$getName())
if(is.null(child))
{
@@ -96,18 +98,18 @@ CollectionTree <- R6::R6Class(
child = private$replaceFileWithSubcollection(child)
}
- private$addBranch(child, node$.__enclos_env__$private$getFirstChild())
+ private$addBranch(child, node$getFirst())
}
},
replaceFileWithSubcollection = function(arvadosFile)
{
subcollection <- Subcollection$new(arvadosFile$getName())
- fileParent <- arvadosFile$.__enclos_env__$private$parent
- fileParent$.__enclos_env__$private$removeChild(arvadosFile$getName())
+ fileParent <- arvadosFile$getParent()
+ fileParent$remove(arvadosFile$getName())
fileParent$add(subcollection)
- arvadosFile$.__enclos_env__$private$parent <- NULL
+ arvadosFile$setParent(NULL)
subcollection
}
diff --git a/sdk/R/R/HttpRequest.R b/sdk/R/R/HttpRequest.R
index a1e1f61..ad153a0 100644
--- a/sdk/R/R/HttpRequest.R
+++ b/sdk/R/R/HttpRequest.R
@@ -21,17 +21,18 @@ HttpRequest <- R6::R6Class(
},
PUT = function(url, headers = NULL, body = NULL,
- queryFilters = NULL, limit = 100, offset = 0)
+ queryFilters = NULL, limit = NULL, offset = NULL)
{
headers <- httr::add_headers(unlist(headers))
query <- private$createQuery(queryFilters, limit, offset)
url <- paste0(url, query)
+ print(url)
serverResponse <- httr::PUT(url = url, config = headers, body = body)
},
POST = 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 <- private$createQuery(queryFilters, limit, offset)
@@ -141,7 +142,8 @@ HttpRequest <- R6::R6Class(
finalQuery <- paste0(finalQuery, collapse = "&")
}
- finalQuery <- paste0("/?", finalQuery)
+ if(!is.null(finalQuery))
+ finalQuery <- paste0("/?", finalQuery)
finalQuery
}
diff --git a/sdk/R/R/Subcollection.R b/sdk/R/R/Subcollection.R
index 296cb92..06df7c4 100644
--- a/sdk/R/R/Subcollection.R
+++ b/sdk/R/R/Subcollection.R
@@ -15,31 +15,48 @@ Subcollection <- R6::R6Class(
private$http <- HttpRequest$new()
private$httpParser <- HttpParser$new()
},
+
+ getName = function() private$name,
+ getRelativePath = function()
+ {
+ relativePath <- c(private$name)
+ parent <- private$parent
+
+ while(!is.null(parent))
+ {
+ relativePath <- c(parent$getName(), relativePath)
+ parent <- parent$getParent()
+ }
+
+ relativePath <- relativePath[relativePath != ""]
+ paste0(relativePath, collapse = "/")
+ },
+
add = function(content)
{
if("ArvadosFile" %in% class(content) ||
"Subcollection" %in% class(content))
{
- if(!is.null(content$.__enclos_env__$private$collection))
- stop("ArvadosFile/Subcollection already belongs to a collection.")
-
- childWithSameName <- private$getChild(content$getName())
+ childWithSameName <- self$get(content$getName())
if(!is.null(childWithSameName))
stop("Subcollection already contains ArvadosFile
or Subcollection with same name.")
if(!is.null(private$collection))
{
- contentPath <- paste0(self$getRelativePath(),
- "/", content$getFileListing())
-
- private$collection$.__enclos_env__$private$createFilesOnREST(contentPath)
- content$.__enclos_env__$private$addToCollection(private$collection)
+ if(self$getRelativePath() != "")
+ contentPath <- paste0(self$getRelativePath(),
+ "/", content$getFileListing())
+ else
+ contentPath <- content$getFileListing()
+
+ private$collection$createFilesOnREST(contentPath)
+ content$setCollection(private$collection)
}
private$children <- c(private$children, content)
- content$.__enclos_env__$private$parent = self
+ content$setParent(self)
"Content added successfully."
}
@@ -50,25 +67,31 @@ Subcollection <- R6::R6Class(
}
},
- removeFromCollection = function()
+ remove = function(name)
{
- if(is.null(private$collection))
- stop("Subcollection doesn't belong to any collection.")
+ if(is.character(name))
+ {
+ child <- self$get(name)
- if(private$name == "")
- stop("Unable to delete root folder.")
+ if(is.null(child))
+ stop("Subcollection doesn't contains ArvadosFile
+ or Subcollection with same name.")
- collectionList <- paste0(self$getRelativePath(),
- "/", self$getFileListing(fullpath = FALSE))
- sapply(collectionList, function(file)
- {
- private$collection$.__enclos_env__$private$deleteFromREST(file)
- })
+ if(!is.null(private$collection))
+ {
+ private$collection$deleteFromREST(child$getRelativePath())
+ child$setCollection(NULL)
+ }
- private$addToCollection(NULL)
- private$dettachFromParent()
+ private$removeChild(name)
+ child$setParent(NULL)
- "Content removed successfully."
+ "Content removed"
+ }
+ else
+ {
+ stop(paste("Expected character, got", class(content), "."))
+ }
},
getFileListing = function(fullpath = TRUE)
@@ -108,23 +131,6 @@ Subcollection <- R6::R6Class(
sum(sizes)
},
- getName = function() private$name,
-
- getRelativePath = function()
- {
- relativePath <- c(private$name)
- parent <- private$parent
-
- while(!is.null(parent))
- {
- relativePath <- c(parent$getName(), relativePath)
- parent <- parent$getParent()
- }
-
- relativePath <- relativePath[relativePath != ""]
- paste0(relativePath, collapse = "/")
- },
-
move = function(newLocation)
{
if(is.null(private$collection))
@@ -152,27 +158,25 @@ Subcollection <- R6::R6Class(
stop("Unable to get destination subcollection.")
}
- status <- private$collection$.__enclos_env__$private$moveOnREST(self$getRelativePath(),
- paste0(newParent$getRelativePath(), "/", self$getName()))
+ status <- private$collection$moveOnREST(self$getRelativePath(),
+ paste0(newParent$getRelativePath(),
+ "/", self$getName()))
- private$attachToParent(newParent)
+ #Note: We temporary set parents collection to NULL. This will ensure that
+ # add method doesn't post file on REST server.
+ parentsCollection <- newParent$getCollection()
+ newParent$setCollection(NULL, setRecursively = FALSE)
- "Content moved successfully."
- },
+ newParent$add(self)
- getParent = function() private$parent
- ),
+ newParent$setCollection(parentsCollection, setRecursively = FALSE)
- private = list(
+ private$parent <- newParent
- name = NULL,
- children = NULL,
- parent = NULL,
- collection = NULL,
- http = NULL,
- httpParser = NULL,
+ "Content moved successfully."
+ },
- getChild = function(name)
+ get = function(name)
{
for(child in private$children)
{
@@ -183,7 +187,7 @@ Subcollection <- R6::R6Class(
return(NULL)
},
- getFirstChild = function()
+ getFirst = function()
{
if(length(private$children) == 0)
return(NULL)
@@ -191,6 +195,33 @@ Subcollection <- R6::R6Class(
private$children[[1]]
},
+ setCollection = function(collection, setRecursively = TRUE)
+ {
+ private$collection = collection
+
+ if(setRecursively)
+ {
+ for(child in private$children)
+ child$setCollection(collection)
+ }
+ },
+
+ getCollection = function() private$collection,
+
+ getParent = function() private$parent,
+
+ setParent = function(newParent) private$parent <- newParent
+ ),
+
+ private = list(
+
+ name = NULL,
+ children = NULL,
+ parent = NULL,
+ collection = NULL,
+ http = NULL,
+ httpParser = NULL,
+
removeChild = function(name)
{
numberOfChildren = length(private$children)
@@ -205,34 +236,6 @@ Subcollection <- R6::R6Class(
}
}
}
- },
-
- addToCollection = function(collection)
- {
- for(child in private$children)
- child$.__enclos_env__$private$addToCollection(collection)
-
- private$collection = collection
- },
-
- dettachFromParent = function()
- {
- if(!is.null(private$parent))
- {
- private$parent$.__enclos_env__$private$removeChild(private$name)
- private$parent <- NULL
- }
- else
- stop("Parent doesn't exists.")
- },
-
- attachToParent = function(parent)
- {
- if(private$name != "")
- {
- parent$.__enclos_env__$private$children <- c(parent$.__enclos_env__$private$children, self)
- private$parent <- parent
- }
}
),
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