## Development
[![Build Status](https://ci.curoverse.com/buildStatus/icon?job=run-tests)](https://ci.curoverse.com/job/run-tests/)
-[![Go Report Card](https://goreportcard.com/badge/github.com/curoverse/arvados)](https://goreportcard.com/report/github.com/curoverse/arvados)
+[![Go Report Card](https://goreportcard.com/badge/github.com/arvados/arvados)](https://goreportcard.com/report/github.com/arvados/arvados)
The Arvados public bug tracker is located at https://dev.arvados.org/projects/arvados/issues
source 'https://rubygems.org'
gem 'rails', '~> 5.0.0'
-gem 'arvados', git: 'https://github.com/curoverse/arvados.git', glob: 'sdk/ruby/arvados.gemspec'
+gem 'arvados', git: 'https://github.com/arvados/arvados.git', glob: 'sdk/ruby/arvados.gemspec'
-gem 'activerecord-nulldb-adapter', git: 'https://github.com/curoverse/nulldb'
+gem 'activerecord-nulldb-adapter', git: 'https://github.com/arvados/nulldb'
gem 'multi_json'
gem 'oj'
gem 'sass'
# Wiselinks hasn't been updated for many years and it's using deprecated methods
# Use our own Wiselinks fork until this PR is accepted:
# https://github.com/igor-alexandrov/wiselinks/pull/116
-# gem 'wiselinks', git: 'https://github.com/curoverse/wiselinks.git', branch: 'rails-5.1-compatibility'
+# gem 'wiselinks', git: 'https://github.com/arvados/wiselinks.git', branch: 'rails-5.1-compatibility'
gem 'sshkey'
gem 'httpclient', '~> 2.5'
# This fork has Rails 4 compatible routes
-gem 'themes_for_rails', git: 'https://github.com/curoverse/themes_for_rails'
+gem 'themes_for_rails', git: 'https://github.com/arvados/themes_for_rails'
gem "deep_merge", :require => 'deep_merge/rails_compat'
GIT
- remote: https://github.com/curoverse/arvados.git
+ remote: https://github.com/arvados/arvados.git
revision: dd9f2403f43bcb93da5908ddde57d8c0491bb4c2
glob: sdk/ruby/arvados.gemspec
specs:
jwt (>= 0.1.5, < 2)
GIT
- remote: https://github.com/curoverse/nulldb
+ remote: https://github.com/arvados/nulldb
revision: d8e0073b665acdd2537c5eb15178a60f02f4b413
specs:
activerecord-nulldb-adapter (0.3.9)
activerecord (>= 2.0.0)
GIT
- remote: https://github.com/curoverse/themes_for_rails
+ remote: https://github.com/arvados/themes_for_rails
revision: ddf6e592b3b6493ea0c2de7b5d3faa120ed35be0
specs:
themes_for_rails (0.5.1)
using_fork=true
if [[ $using_fork = true ]]; then
- LIBCLOUD_PIN_SRC="https://github.com/curoverse/libcloud/archive/apache-libcloud-$LIBCLOUD_PIN.zip"
+ LIBCLOUD_PIN_SRC="https://github.com/arvados/libcloud/archive/apache-libcloud-$LIBCLOUD_PIN.zip"
else
LIBCLOUD_PIN_SRC=""
fi
|repository|string|Git repository name or URL.|Source of the repository where the given script_version is to be found. This can be given as the name of a locally hosted repository, or as a publicly accessible URL starting with @git://@, @http://@, or @https://@.
Examples:
@yourusername/yourrepo@
-@https://github.com/curoverse/arvados.git@|
+@https://github.com/arvados/arvados.git@|
|script_version|string|Git commit|During a **create** transaction, this is the Git branch, tag, or hash supplied by the client. Before the job starts, Arvados updates it to the full 40-character SHA-1 hash of the commit used by the job.
See "Specifying Git versions":#script_version below for more detail about acceptable ways to specify a commit.|
|cancelled_by_client_uuid|string|API client ID|Is null if job has not been cancelled|
<p>Curii Corporation provides managed Arvados installations as well as commercial support for Arvados. Please contact <a href="mailto:info@curii.com">info@curii.com</a> for more information.</p>
<p><strong>Contributing</strong></p>
- <p>Please visit the <a href="https://dev.arvados.org/projects/arvados/wiki/Wiki#Contributing-and-hacking">developer site</a>. Arvados is 100% free and open source software, check out the code on <a href="https://github.com/curoverse/arvados">github</a>.
+ <p>Please visit the <a href="https://dev.arvados.org/projects/arvados/wiki/Wiki#Contributing-and-hacking">developer site</a>. Arvados is 100% free and open source software, check out the code on <a href="https://github.com/arvados/arvados">github</a>.
<p>Arvados is under active development, see the <a href="https://dev.arvados.org/projects/arvados/activity">recent developer activity</a>.
</p>
<p><strong>License</strong></p>
- <p>Most of Arvados is licensed under the <a href="{{ site.baseurl }}/user/copying/agpl-3.0.html">GNU AGPL v3</a>. The SDKs are licensed under the <a href="{{ site.baseurl }}/user/copying/LICENSE-2.0.html">Apache License 2.0</a> so that they can be incorporated into proprietary code. See the <a href="https://github.com/curoverse/arvados/blob/master/COPYING">COPYING file</a> for more information.
+ <p>Most of Arvados is licensed under the <a href="{{ site.baseurl }}/user/copying/agpl-3.0.html">GNU AGPL v3</a>. The SDKs are licensed under the <a href="{{ site.baseurl }}/user/copying/LICENSE-2.0.html">Apache License 2.0</a> so that they can be incorporated into proprietary code. See the <a href="https://github.com/arvados/arvados/blob/master/COPYING">COPYING file</a> for more information.
</p>
</div>
Clone the repository and nagivate to the @arvados-kubernetes/charts/arvados@ directory:
<pre>
-$ git clone https://github.com/curoverse/arvados-kubernetes.git
+$ git clone https://github.com/arvados/arvados-kubernetes.git
$ cd arvados-kubernetes/charts/arvados
</pre>
h2. Quick start
<pre>
-$ git clone https://github.com/curoverse/arvados.git
+$ git clone https://github.com/arvados/arvados.git
$ cd arvados/tools/arvbox/bin
$ ./arvbox start localdemo
</pre>
<notextile>
<pre><code>~$ <span class="userinput">cd /tmp</span>
-/tmp$ <span class="userinput">git clone --bare https://github.com/curoverse/arvados.git</span>
+/tmp$ <span class="userinput">git clone --bare https://github.com/arvados/arvados.git</span>
/tmp <span class="userinput">git --git-dir arvados.git push https://git.<b>uuid_prefix.your.domain</b>/arvados.git '*:*'</span>
</code></pre>
</notextile>
<notextile>
<pre><code>gitserver:~$ <span class="userinput">sudo -u git -i bash</span>
-git@gitserver:~$ <span class="userinput">git clone --bare https://github.com/curoverse/arvados.git /tmp/arvados.git</span>
+git@gitserver:~$ <span class="userinput">git clone --bare https://github.com/arvados/arvados.git /tmp/arvados.git</span>
git@gitserver:~$ <span class="userinput">cd /tmp/arvados.git</span>
git@gitserver:/tmp/arvados.git$ <span class="userinput">gitolite push /var/lib/arvados/git/repositories/<b>your_arvados_repo_uuid</b>.git '*:*'</span>
</code></pre>
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-The Keep-web server provides read/write HTTP (WebDAV) access to files stored in Keep. It serves public data to unauthenticated clients, and serves private data to clients that supply Arvados API tokens. It can be installed anywhere with access to Keep services, typically behind a web proxy that provides TLS support. See the "godoc page":http://godoc.org/github.com/curoverse/arvados/services/keep-web for more detail.
+The Keep-web server provides read/write HTTP (WebDAV) access to files stored in Keep. It serves public data to unauthenticated clients, and serves private data to clients that supply Arvados API tokens. It can be installed anywhere with access to Keep services, typically behind a web proxy that provides TLS support. See the "godoc page":http://godoc.org/github.com/arvados/arvados/services/keep-web for more detail.
By convention, we use the following hostnames for the Keep-web service:
</pre></notextile>
{% include 'notebox_begin' %}
-If you restrict access to your Arvados services based on network topology -- for example, your proxy server is not reachable from the public internet -- additional proxy configuration might be needed to thwart cross-site scripting attacks that would circumvent your restrictions. Read the "'Intranet mode' section of the Keep-web documentation":https://godoc.org/github.com/curoverse/arvados/services/keep-web#hdr-Intranet_mode now.
+If you restrict access to your Arvados services based on network topology -- for example, your proxy server is not reachable from the public internet -- additional proxy configuration might be needed to thwart cross-site scripting attacks that would circumvent your restrictions. Read the "'Intranet mode' section of the Keep-web documentation":https://godoc.org/github.com/arvados/arvados/services/keep-web#hdr-Intranet_mode now.
{% include 'notebox_end' %}
h3(#dns). Configure DNS
If neither of the above wildcard options is feasible, you have two choices:
# Serve web content at @collections.uuid_prefix.your.domain@, but only for unauthenticated requests (public data and collection sharing links). Authenticated requests will always result in file downloads, using the @download@ name. For example, the Workbench "preview" button and the "view entire log file" link will invoke file downloads instead of displaying content in the browser window.
-# In the special case where you know you are immune to XSS exploits, you can enable the "trust all content" mode in Keep-web and Workbench (setting @Collections.TrustAllContent: true@ on the config file). With this enabled, inline web content can be served from a single @collections@ host name; no wildcard DNS or certificate is needed. Do not do this without understanding the security implications described in the "Keep-web documentation":http://godoc.org/github.com/curoverse/arvados/services/keep-web.
+# In the special case where you know you are immune to XSS exploits, you can enable the "trust all content" mode in Keep-web and Workbench (setting @Collections.TrustAllContent: true@ on the config file). With this enabled, inline web content can be served from a single @collections@ host name; no wildcard DNS or certificate is needed. Do not do this without understanding the security implications described in the "Keep-web documentation":http://godoc.org/github.com/arvados/arvados/services/keep-web.
h2. Configure Keep-web
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-The arvados-ws server provides event notifications to websocket clients. It can be installed anywhere with access to Postgres database and the Arvados API server, typically behind a web proxy that provides SSL support. See the "godoc page":http://godoc.org/github.com/curoverse/arvados/services/ws for additional information.
+The arvados-ws server provides event notifications to websocket clients. It can be installed anywhere with access to Postgres database and the Arvados API server, typically behind a web proxy that provides SSL support. See the "godoc page":http://godoc.org/github.com/arvados/arvados/services/ws for additional information.
By convention, we use the following hostname for the websocket service.
<notextile>
<pre>
-~$ <code class="userinput">git clone https://github.com/curoverse/arvados.git</code>
+~$ <code class="userinput">git clone https://github.com/arvados/arvados.git</code>
~$ <code class="userinput">cd arvados/sdk/cli</code>
~/arvados/sdk/cli$ <code class="userinput">gem build arvados-cli.gemspec</code>
~/arvados/sdk/cli$ <code class="userinput">sudo -i gem install arvados-cli-*.gem</code>
<notextile>
<pre>
-$ <code class="userinput">git clone https://github.com/curoverse/arvados.git</code>
+$ <code class="userinput">git clone https://github.com/arvados/arvados.git</code>
$ <code class="userinput">cd arvados/sdk/java-v2</code>
$ <code class="userinput">gradle test</code>
$ <code class="userinput">gradle jar</code>
Then run the following:
<notextile>
-<pre><code>~$ <span class="userinput">git clone https://github.com/curoverse/arvados.git</span>
+<pre><code>~$ <span class="userinput">git clone https://github.com/arvados/arvados.git</span>
~$ <span class="userinput">cd arvados/sdk/perl</span>
~$ <span class="userinput">perl Makefile.PL</span>
~$ <span class="userinput">sudo make install</span>
Install the @python-setuptools@ package from your distribution. Then run the following:
<notextile>
-<pre><code>~$ <span class="userinput">git clone https://github.com/curoverse/arvados.git</span>
+<pre><code>~$ <span class="userinput">git clone https://github.com/arvados/arvados.git</span>
~$ <span class="userinput">cd arvados/services/fuse</span>
~/arvados/services/fuse$ <span class="userinput">python setup.py install</span>
</code></pre>
<notextile>
<pre>
-$ <code class="userinput">git clone https://github.com/curoverse/arvados.git</code>
+$ <code class="userinput">git clone https://github.com/arvados/arvados.git</code>
$ <code class="userinput">cd arvados/sdk/ruby</code>
$ <code class="userinput">gem build arvados.gemspec</code>
$ <code class="userinput">sudo -i gem install arvados-*.gem</code>
rsc.io/getopt v0.0.0-20170811000552-20be20937449
)
-replace github.com/AdRoll/goamz => github.com/curoverse/goamz v0.0.0-20190905141525-1bba09f407ef
+replace github.com/AdRoll/goamz => github.com/arvados/goamz v0.0.0-20190905141525-1bba09f407ef
github.com/alecthomas/units v0.0.0-20190717042225-c3de453c63f4/go.mod h1:ybxpYRFXyAe+OPACYpWeL0wqObRcbAqCMya13uyzqw0=
github.com/anmitsu/go-shlex v0.0.0-20161002113705-648efa622239 h1:kFOfPq6dUM1hTo4JG6LR5AXSUEsOjtdm0kw0FtQtMJA=
github.com/anmitsu/go-shlex v0.0.0-20161002113705-648efa622239/go.mod h1:2FmKhYUyUczH0OGQWaF5ceTx0UBShxjsH6f8oGKYe2c=
+github.com/arvados/goamz v0.0.0-20190905141525-1bba09f407ef h1:cl7DIRbiAYNqaVxg3CZY8qfZoBOKrj06H/x9SPGaxas=
+github.com/arvados/goamz v0.0.0-20190905141525-1bba09f407ef/go.mod h1:rCtgyMmBGEbjTm37fCuBYbNL0IhztiALzo3OB9HyiOM=
github.com/aws/aws-sdk-go v1.25.30 h1:I9qj6zW3mMfsg91e+GMSN/INcaX9tTFvr/l/BAHKaIY=
github.com/aws/aws-sdk-go v1.25.30/go.mod h1:KmX6BPdI08NWTb3/sm4ZGu5ShLoqVDhKgpiN924inxo=
github.com/beorn7/perks v0.0.0-20180321164747-3a771d992973/go.mod h1:Dwedo/Wpr24TaqPxmxbtue+5NUziq4I4S80YR8gNf3Q=
author='Arvados',
author_email='info@arvados.org',
url="https://arvados.org",
- download_url="https://github.com/curoverse/arvados.git",
+ download_url="https://github.com/arvados/arvados.git",
license='Apache 2.0',
packages=find_packages(),
package_data={'arvados_cwl': ['arv-cwl-schema-v1.0.yml', 'arv-cwl-schema-v1.1.yml']},
mkdir -p $ARVBOX_DATA
if ! test -d $ARVBOX_DATA/arvados ; then
cd $ARVBOX_DATA
- git clone https://github.com/curoverse/arvados.git
+ git clone https://github.com/arvados/arvados.git
fi
cd $ARVBOX_DATA/arvados
gitver=`git rev-parse HEAD`
##### About
Arvados Java Client allows to access Arvados servers and uses two APIs:
* lower level [Keep Server API](https://doc.arvados.org/api/index.html)
-* higher level [Keep-Web API](https://godoc.org/github.com/curoverse/arvados/services/keep-web) (when needed)
+* higher level [Keep-Web API](https://godoc.org/github.com/arvados/arvados/services/keep-web) (when needed)
##### Required Java version
This SDK requires Java 8+
packaging 'jar'
groupId 'org.arvados'
description 'Arvados Java SDK'
- url 'https://github.com/curoverse/arvados'
+ url 'https://github.com/arvados/arvados'
scm {
- url 'scm:git@https://github.com/curoverse/arvados.git'
- connection 'scm:git@https://github.com/curoverse/arvados.git'
- developerConnection 'scm:git@https://github.com/curoverse/arvados.git'
+ url 'scm:git@https://github.com/arvados/arvados.git'
+ connection 'scm:git@https://github.com/arvados/arvados.git'
+ developerConnection 'scm:git@https://github.com/arvados/arvados.git'
}
licenses {
author='Arvados',
author_email='info@arvados.org',
url='https://arvados.org',
- download_url='https://github.com/curoverse/arvados.git',
+ download_url='https://github.com/arvados/arvados.git',
license='Apache 2.0',
packages=[
'arvados_pam',
author='Arvados',
author_email='info@arvados.org',
url="https://arvados.org",
- download_url="https://github.com/curoverse/arvados.git",
+ download_url="https://github.com/arvados/arvados.git",
license='Apache 2.0',
packages=find_packages(),
scripts=[
gem 'optimist'
gem 'faye-websocket'
-gem 'themes_for_rails', git: 'https://github.com/curoverse/themes_for_rails'
+gem 'themes_for_rails', git: 'https://github.com/arvados/themes_for_rails'
# We need arvados-cli because of crunchv1. Note: bundler can't handle
# two gems with the same "git" url but different "glob" values, hence
# the use of a wildcard here instead of literal paths
# (sdk/cli/arvados-cli.gem and sdk/ruby/arvados.gem).
-gem 'arvados-cli', git: 'https://github.com/curoverse/arvados.git', glob: 'sdk/*/*.gemspec'
-gem 'arvados', git: 'https://github.com/curoverse/arvados.git', glob: 'sdk/*/*.gemspec'
+gem 'arvados-cli', git: 'https://github.com/arvados/arvados.git', glob: 'sdk/*/*.gemspec'
+gem 'arvados', git: 'https://github.com/arvados/arvados.git', glob: 'sdk/*/*.gemspec'
gem 'httpclient'
gem 'sshkey'
GIT
- remote: https://github.com/curoverse/arvados.git
+ remote: https://github.com/arvados/arvados.git
revision: dd9f2403f43bcb93da5908ddde57d8c0491bb4c2
glob: sdk/*/*.gemspec
specs:
optimist (~> 3.0)
GIT
- remote: https://github.com/curoverse/themes_for_rails
+ remote: https://github.com/arvados/themes_for_rails
revision: ddf6e592b3b6493ea0c2de7b5d3faa120ed35be0
specs:
themes_for_rails (0.5.1)
end
[
- 'https://github.com/curoverse/arvados.git',
- 'http://github.com/curoverse/arvados.git',
- 'git://github.com/curoverse/arvados.git',
+ 'https://github.com/arvados/arvados.git',
+ 'http://github.com/arvados/arvados.git',
+ 'git://github.com/arvados/arvados.git',
].each do |url|
test "find_commit_range uses fetch_remote_repository to get #{url}" do
fake_gitdir = repositories(:foo).server_path
'/not/allowed/.git',
'file:///not/allowed.git',
'git.arvados.org/arvados.git',
- 'github.com/curoverse/arvados.git',
+ 'github.com/arvados/arvados.git',
].each do |url|
test "find_commit_range skips fetch_remote_repository for #{url}" do
CommitsHelper::expects(:fetch_remote_repository).never
author="Arvados",
author_email="info@arvados.org",
url="https://arvados.org",
- download_url="https://github.com/curoverse/arvados.git",
+ download_url="https://github.com/arvados/arvados.git",
license="GNU Affero General Public License version 3.0",
packages=find_packages(),
entry_points={
author='Arvados',
author_email='info@arvados.org',
url="https://arvados.org",
- download_url="https://github.com/curoverse/arvados.git",
+ download_url="https://github.com/arvados/arvados.git",
license='GNU Affero General Public License, version 3.0',
packages=['arvados_fuse'],
scripts=[
mkdir -p "$PG_DATA" "$VAR_DATA" "$PASSENGER" "$GEMS" "$PIPCACHE" "$NPMCACHE" "$GOSTUFF" "$RLIBS"
if ! test -d "$ARVADOS_ROOT" ; then
- git clone https://github.com/curoverse/arvados.git "$ARVADOS_ROOT"
+ git clone https://github.com/arvados/arvados.git "$ARVADOS_ROOT"
fi
if ! test -d "$SSO_ROOT" ; then
- git clone https://github.com/curoverse/sso-devise-omniauth-provider.git "$SSO_ROOT"
+ git clone https://github.com/arvados/sso-devise-omniauth-provider.git "$SSO_ROOT"
fi
if ! test -d "$COMPOSER_ROOT" ; then
- git clone https://github.com/curoverse/composer.git "$COMPOSER_ROOT"
+ git clone https://github.com/arvados/composer.git "$COMPOSER_ROOT"
git -C "$COMPOSER_ROOT" checkout arvados-fork
git -C "$COMPOSER_ROOT" pull
fi
if ! test -d "$WORKBENCH2_ROOT" ; then
- git clone https://github.com/curoverse/arvados-workbench2.git "$WORKBENCH2_ROOT"
+ git clone https://github.com/arvados/arvados-workbench2.git "$WORKBENCH2_ROOT"
fi
if [[ "$CONFIG" = test ]] ; then
ARG workbench2_version=master
RUN cd /usr/src && \
- git clone --no-checkout https://github.com/curoverse/arvados.git && \
+ git clone --no-checkout https://github.com/arvados/arvados.git && \
git -C arvados checkout ${arvados_version} && \
git -C arvados pull && \
- git clone --no-checkout https://github.com/curoverse/sso-devise-omniauth-provider.git sso && \
+ git clone --no-checkout https://github.com/arvados/sso-devise-omniauth-provider.git sso && \
git -C sso checkout ${sso_version} && \
git -C sso pull && \
- git clone --no-checkout https://github.com/curoverse/composer.git && \
+ git clone --no-checkout https://github.com/arvados/composer.git && \
git -C composer checkout ${composer_version} && \
git -C composer pull && \
- git clone --no-checkout https://github.com/curoverse/arvados-workbench2.git workbench2 && \
+ git clone --no-checkout https://github.com/arvados/arvados-workbench2.git workbench2 && \
git -C workbench2 checkout ${workbench2_version} && \
git -C workbench2 pull
author='Arvados',
author_email='info@arvados.org',
url="https://arvados.org",
- download_url="https://github.com/curoverse/arvados.git",
+ download_url="https://github.com/arvados/arvados.git",
license='GNU Affero General Public License, version 3.0',
packages=['crunchstat_summary'],
include_package_data=True,