*.gz.report
*.ico
*.jpg
+*.svg
+*.odg
*.json
*LICENSE*.html
.licenseignore
services/keepproxy/pkg-extras/etc/default/keepproxy
*.tar
tools/crunchstat-summary/tests/crunchstat_error_messages.txt
+tools/crunchstat-summary/crunchstat_summary/synchronizer.js
+build/package-build-dockerfiles/debian9/D39DC0E3.asc
+build/package-test-dockerfiles/debian9/D39DC0E3.asc
+sdk/R/DESCRIPTION
+sdk/R/NAMESPACE
+sdk/R/.Rbuildignore
+sdk/R/ArvadosR.Rproj
+*.Rd
+<!-- Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: AGPL-3.0 -->
+
<div data-mount-mithril="TestComponent"></div>
+<%# Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: AGPL-3.0 %>
+
<%= javascript_tag do %>
function update_visibility() {
if (sessionStorage.getItem('link_account_api_token') &&
| */nodemanager/doc/*.cfg \
| */nodemanager/tests/fake*.cfg.template \
| */nginx.conf \
- | build/build.list)
+ | build/build.list | *.R)
fixer=fixer
cc="#"
;;
wantBYSAmd="[comment]: # (Copyright © The Arvados Authors. All rights reserved.)
[comment]: # ()
[comment]: # (SPDX-License-Identifier: CC-BY-SA-3.0)"
- found=$(head -n20 "$fnm" | egrep -A${grepAfter} -B${grepBefore} 'Copyright.*Arvados' || true)
+ found=$(head -n20 "$fnm" | egrep -A${grepAfter} -B${grepBefore} 'Copyright.*All rights reserved.' || true)
case ${fnm} in
Makefile | build/* | lib/* | tools/* | apps/* | services/* | sdk/cli/bin/crunch-job)
want=${wantGPL}
+/* Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0 */
+
img.full-width {
width: 100%
}
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
#' users.get
#'
#' users.get is a method defined in Arvados class.
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
source("./R/util.R")
#' ArvadosFile
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
source("./R/Subcollection.R")
source("./R/ArvadosFile.R")
source("./R/RESTService.R")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
source("./R/Subcollection.R")
source("./R/ArvadosFile.R")
source("./R/util.R")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
HttpParser <- R6::R6Class(
"HttrParser",
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
source("./R/util.R")
HttpRequest <- R6::R6Class(
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
RESTService <- R6::R6Class(
"RESTService",
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
source("./R/util.R")
#' Subcollection
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
getAPIDocument <- function(){
url <- "https://4xphq.arvadosapi.com/discovery/v1/apis/arvados/v1/rest"
serverResponse <- httr::RETRY("GET", url = url)
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
#' listAll
#'
#' List all resources even if the number of items is greater than maximum API limit.
+[comment]: # (Copyright © The Arvados Authors. All rights reserved.)
+[comment]: # ()
+[comment]: # (SPDX-License-Identifier: CC-BY-SA-3.0)
+
## R SDK for Arvados
This SDK focuses on providing support for accessing Arvados projects, collections, and the files within collections.
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
#Run script with $Rscript createDoc.R input.Rmd output.html
require(knitr) # required for knitting from rmd to md
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
options(repos=structure(c(CRAN="http://cran.wustl.edu/")))
if (!requireNamespace("devtools")) {
install.packages("devtools")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
results <- devtools::test()
any_error <- any(as.data.frame(results)$error)
if (any_error) {
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
library(testthat)
library(ArvadosR)
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
FakeArvados <- R6::R6Class(
"FakeArvados",
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
FakeHttpParser <- R6::R6Class(
"FakeHttrParser",
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
FakeHttpRequest <- R6::R6Class(
"FakeHttpRequest",
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
FakeRESTService <- R6::R6Class(
"FakeRESTService",
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
source("fakes/FakeRESTService.R")
context("ArvadosFile")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
source("fakes/FakeRESTService.R")
context("Collection")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
context("CollectionTree")
test_that("constructor creates file tree from character array properly", {
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
context("Http Parser")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
context("Http Request")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
source("fakes/FakeArvados.R")
source("fakes/FakeHttpRequest.R")
source("fakes/FakeHttpParser.R")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
source("fakes/FakeRESTService.R")
context("Subcollection")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
context("Utility function")
test_that("listAll always returns all resource items from server", {
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: ExpressionTool
requirements:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
dir:
class: Directory
location: samples
\ No newline at end of file
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: CommandLineTool
requirements:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: Workflow
requirements:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
{
"cwlVersion": "v1.0",
"arguments": [
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: CommandLineTool
inputs:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: Workflow
$namespaces:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
i:
class: File
location: keep:f225e6259bdd63bc7240599648dde9f1+97/hg19.fa
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: Workflow
$namespaces:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
class: Workflow
cwlVersion: v1.0
inputs:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
class: CommandLineTool
cwlVersion: v1.0
inputs:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
toplevel_input:
class: File
location: keep:4d8a70b1e63b2aad6984e40e338e2373+69/hello.txt
\ No newline at end of file
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
pw: blorp
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: CommandLineTool
inputs:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: CommandLineTool
inputs:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: CommandLineTool
inputs:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: Workflow
inputs: []
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: Workflow
inputs: []
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: Workflow
inputs: []
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: CommandLineTool
inputs:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: Workflow
inputs:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: CommandLineTool
inputs:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: Workflow
inputs: []
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: Workflow
inputs: []
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: Workflow
inputs: []
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: Workflow
inputs: []
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: Workflow
inputs: []
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: Workflow
inputs: []
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: Workflow
inputs: []
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
import arvados
import sys
import os
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: Workflow
requirements:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: Workflow
$namespaces:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: CommandLineTool
requirements:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: CommandLineTool
requirements:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: CommandLineTool
$namespaces:
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
cwlVersion: v1.0
class: Workflow
$namespaces:
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: Apache-2.0
+
package arvados
import (
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: Apache-2.0
+
package health
import (
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: Apache-2.0
+
package health
import (
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
require 'migrate_yaml_to_json'
class YamlToJson < ActiveRecord::Migration
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
require './db/migrate/20161213172944_full_text_search_indexes'
class JsonCollectionProperties < ActiveRecord::Migration
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
class AddIndexToContainers < ActiveRecord::Migration
def up
ActiveRecord::Base.connection.execute("CREATE INDEX index_containers_on_modified_at_uuid ON containers USING btree (modified_at desc, uuid asc)")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
class FixTrashFlagFollow < ActiveRecord::Migration
def change
ActiveRecord::Base.connection.execute("DROP MATERIALIZED VIEW materialized_permission_view")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
class AddGinIndexToCollectionProperties < ActiveRecord::Migration
def up
ActiveRecord::Base.connection.execute("CREATE INDEX collection_index_on_properties ON collections USING gin (properties);")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
class AddSecretMountsToContainers < ActiveRecord::Migration
def change
add_column :container_requests, :secret_mounts, :jsonb, default: {}
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
class ChangeContainerPriorityBigint < ActiveRecord::Migration
def change
change_column :containers, :priority, :integer, limit: 8
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
class AddRedirectToUserUuidToUsers < ActiveRecord::Migration
def up
add_column :users, :redirect_to_user_uuid, :string
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
class AddContainerAuthUuidIndex < ActiveRecord::Migration
def change
add_index :containers, :auth_uuid
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
package main
import (
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
package main
import (
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
package main
import "golang.org/x/net/webdav"
#!/bin/sh
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
# system one time tasks
PATH=/command:/sbin:/bin:/usr/sbin:/usr/bin
#!/bin/sh
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
PATH=/usr/local/bin:/usr/local/sbin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/X11R6/bin
#!/bin/sh
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
exec 2>&1
PATH=/command:/sbin:/bin:/usr/sbin:/usr/bin
#!/bin/sh
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
exec 2>&1
PATH=/command:/sbin:/bin:/usr/sbin:/usr/bin
+// Copyright (c) 2009 Dan Vanderkam. All rights reserved.
+//
+// SPDX-License-Identifier: MIT
+
/**
* Synchronize zooming and/or selections between a set of dygraphs.
*
* You may also set `range: false` if you wish to only sync the x-axis.
* The `range` option has no effect unless `zoom` is true (the default).
*
- * SPDX-License-Identifier: MIT
* Original source: https://github.com/danvk/dygraphs/blob/master/src/extras/synchronizer.js
* at commit b55a71d768d2f8de62877c32b3aec9e9975ac389
*