[arvados] updated: 2.7.0-650-g80794f079f
git repository hosting
git at public.arvados.org
Mon Sep 25 18:14:55 UTC 2023
Summary of changes:
AUTHORS | 1 +
.../app/assets/stylesheets/application.css.scss | 11 +
apps/workbench/app/views/layouts/body.html.erb | 26 +-
apps/workbench/test/integration/search_box_test.rb | 2 +-
build/run-build-packages-one-target.sh | 39 +-
build/run-build-test-packages-one-target.sh | 11 +-
build/run-library.sh | 15 +-
build/run-tests.sh | 1 +
doc/_config.yml | 22 +-
.../_multi_host_install_custom_certificates.liquid | 11 +-
doc/_includes/_ssl_config_multi.liquid | 33 +
doc/admin/diagnostics.html.textile.liquid | 16 +
.../logs-table-management.html.textile.liquid | 12 +-
...restricting-upload-download.html.textile.liquid | 4 +-
doc/admin/scoped-tokens.html.textile.liquid | 2 +
doc/admin/upgrading.html.textile.liquid | 31 +-
doc/api/crunch-scripts.html.textile.liquid | 4 +-
.../api_client_authorizations.html.textile.liquid | 11 +-
doc/api/methods/collections.html.textile.liquid | 2 +-
doc/api/methods/humans.html.textile.liquid | 4 +-
doc/api/methods/job_tasks.html.textile.liquid | 4 +-
doc/api/methods/jobs.html.textile.liquid | 4 +-
doc/api/methods/keep_disks.html.textile.liquid | 6 +-
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.../methods/pipeline_templates.html.textile.liquid | 4 +-
doc/api/methods/repositories.html.textile.liquid | 4 +
doc/api/methods/specimens.html.textile.liquid | 4 +-
doc/api/methods/traits.html.textile.liquid | 4 +-
doc/api/tokens.html.textile.liquid | 4 +-
doc/images/switch-to-wb1.png | Bin 35755 -> 0 bytes
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doc/images/wgs-tutorial/image8.png | Bin 0 -> 80845 bytes
doc/install/salt-multi-host.html.textile.liquid | 80 +--
.../topics/workbench-migration.html.textile.liquid | 8 -
...l-keep-collection-lifecycle.html.textile.liquid | 8 +-
.../tutorials/wgs-tutorial.html.textile.liquid | 73 +--
lib/controller/handler.go | 11 +-
lib/diagnostics/cmd.go | 147 ++++-
lib/dispatchcloud/dispatcher_test.go | 18 +-
sdk/cli/arvados-cli.gemspec | 5 +-
sdk/python/arvados/_pycurlhelper.py | 1 +
sdk/python/setup.py | 15 +-
sdk/ruby-google-api-client/README.md | 219 +------
.../arvados-google-api-client.gemspec | 2 +-
sdk/ruby/arvados.gemspec | 5 +-
services/api/app/middlewares/arvados_api_token.rb | 49 +-
.../api/app/models/api_client_authorization.rb | 211 ++++---
services/api/app/models/container_request.rb | 7 +
services/api/app/models/group.rb | 6 +
.../api_client_authorizations_controller_test.rb | 13 +
services/api/test/integration/remote_user_test.rb | 88 ++-
services/api/test/unit/container_request_test.rb | 16 +
services/ws/event_source.go | 39 +-
services/ws/handler.go | 6 +-
services/ws/permission.go | 28 +-
services/ws/permission_test.go | 4 +-
services/ws/service.go | 2 +-
services/ws/session_v0_test.go | 203 +++++--
tools/compute-images/scripts/base.sh | 63 +-
tools/salt-install/common.sh | 9 +
.../multi_host/aws/pillars/arvados.sls | 16 +-
.../multi_host/aws/pillars/postgresql.sls | 3 +-
.../multi_host/aws/pillars/prometheus_server.sls | 9 +-
.../multi_host/aws/states/host_entries.sls | 3 +
.../multiple_hostnames/pillars/arvados.sls | 13 +-
.../single_hostname/pillars/arvados.sls | 13 +-
tools/salt-install/installer.sh | 665 +++++++++++----------
.../local.params.example.multiple_hosts | 18 +-
...l.params.example.single_host_multiple_hostnames | 6 +-
...ocal.params.example.single_host_single_hostname | 6 +-
tools/salt-install/provision.sh | 16 +-
77 files changed, 1405 insertions(+), 999 deletions(-)
delete mode 100644 doc/images/switch-to-wb1.png
delete mode 100644 doc/images/switch-to-wb2.png
create mode 100644 doc/images/wgs-tutorial/image7.png
create mode 100644 doc/images/wgs-tutorial/image8.png
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commit 80794f079f005fd3d927b9d330a46bcc96a1a132
Author: Tom Clegg <tom at curii.com>
Date: Mon Sep 25 14:14:37 2023 -0400
20862: Update docs on google-api-client fork.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curii.com>
diff --git a/sdk/cli/arvados-cli.gemspec b/sdk/cli/arvados-cli.gemspec
index 68a59f76c7..665e8ecf14 100644
--- a/sdk/cli/arvados-cli.gemspec
+++ b/sdk/cli/arvados-cli.gemspec
@@ -40,9 +40,8 @@ Gem::Specification.new do |s|
s.executables << "arv-tag"
s.required_ruby_version = '>= 2.5.0'
s.add_runtime_dependency 'arvados', '~> 2.7.0.rc1'
- # Our google-api-client dependency used to be < 0.9, but that could be
- # satisfied by the buggy 0.9.pre*, cf. https://dev.arvados.org/issues/9213
- # We need at least version 0.8.7.5 for compatibility with faraday >= 1.0.
+ # arvados fork of google-api-client gem with old API and new
+ # compatibility fixes, built from ../ruby-google-api-client/
s.add_runtime_dependency('arvados-google-api-client', '>= 0.8.7.5', '< 0.8.9')
s.add_runtime_dependency 'activesupport', '>= 3.2.13', '< 8.0'
s.add_runtime_dependency 'json', '>= 1.7.7', '<3'
diff --git a/sdk/ruby-google-api-client/README.md b/sdk/ruby-google-api-client/README.md
index 510ae817e9..e0b95adfbe 100644
--- a/sdk/ruby-google-api-client/README.md
+++ b/sdk/ruby-google-api-client/README.md
@@ -1,218 +1,7 @@
-# Google API Client
+# Arvados Google API Client
-<dl>
- <dt>Homepage</dt><dd><a href="http://www.github.com/google/google-api-ruby-client">http://www.github.com/google/google-api-ruby-client</a></dd>
- <dt>Authors</dt><dd>Bob Aman, <a href="mailto:sbazyl at google.com">Steven Bazyl</a></dd>
- <dt>Copyright</dt><dd>Copyright © 2011 Google, Inc.</dd>
- <dt>License</dt><dd>Apache 2.0</dd>
-</dl>
+This is a fork of the google-api-client gem, based on https://github.com/google/google-api-ruby-client version 0.8.6.
-[](http://travis-ci.org/google/google-api-ruby-client)
-[](https://gemnasium.com/google/google-api-ruby-client)
+It adds compatibility fixes for newer versions of dependencies (Ruby, faraday, etc.) while avoiding the breaking API changes that have been made in the upstream project.
-## Description
-
-The Google API Ruby Client makes it trivial to discover and access supported
-APIs.
-
-## Alpha
-
-This library is in Alpha. We will make an effort to support the library, but we reserve the right to make incompatible changes when necessary.
-
-## Install
-
-Be sure `https://rubygems.org/` is in your gem sources.
-
-For normal client usage, this is sufficient:
-
-```bash
-$ gem install google-api-client
-```
-
-## Example Usage
-
-```ruby
-require 'google/api_client'
-require 'google/api_client/client_secrets'
-require 'google/api_client/auth/installed_app'
-
-# Initialize the client.
-client = Google::APIClient.new(
- :application_name => 'Example Ruby application',
- :application_version => '1.0.0'
-)
-
-# Initialize Google+ API. Note this will make a request to the
-# discovery service every time, so be sure to use serialization
-# in your production code. Check the samples for more details.
-plus = client.discovered_api('plus')
-
-# Load client secrets from your client_secrets.json.
-client_secrets = Google::APIClient::ClientSecrets.load
-
-# Run installed application flow. Check the samples for a more
-# complete example that saves the credentials between runs.
-flow = Google::APIClient::InstalledAppFlow.new(
- :client_id => client_secrets.client_id,
- :client_secret => client_secrets.client_secret,
- :scope => ['https://www.googleapis.com/auth/plus.me']
-)
-client.authorization = flow.authorize
-
-# Make an API call.
-result = client.execute(
- :api_method => plus.activities.list,
- :parameters => {'collection' => 'public', 'userId' => 'me'}
-)
-
-puts result.data
-```
-
-## API Features
-
-### API Discovery
-
-To take full advantage of the client, load API definitions prior to use. To load an API:
-
-```ruby
-urlshortener = client.discovered_api('urlshortener')
-```
-
-Specific versions of the API can be loaded as well:
-
-```ruby
-drive = client.discovered_api('drive', 'v2')
-```
-
-Locally cached discovery documents may be used as well. To load an API from a local file:
-
-```ruby
-# Output discovery document to JSON
-File.open('my-api.json', 'w') do |f| f.puts MultiJson.dump(client.discovery_document('myapi', 'v1')) end
-
-# Read discovery document and load API
-doc = File.read('my-api.json')
-client.register_discovery_document('myapi', 'v1', doc)
-my_api = client.discovered_api('myapi', 'v1')
-```
-
-### Authorization
-
-Most interactions with Google APIs require users to authorize applications via OAuth 2.0. The client library uses [Signet](https://github.com/google/signet) to handle most aspects of authorization. For additional details about Google's OAuth support, see [Google Developers](https://developers.google.com/accounts/docs/OAuth2).
-
-Credentials can be managed at the connection level, as shown, or supplied on a per-request basis when calling `execute`.
-
-For server-to-server interactions, like those between a web application and Google Cloud Storage, Prediction, or BigQuery APIs, use service accounts.
-
-As of version 0.8.3, service accounts can be configured using
-[Application Default Credentials][1], which rely on the credentials being
-available in a well-known location. If the credentials are not present
-and it's being used on a Compute Engine VM, it will use the VM's default credentials.
-
-```ruby
-client.authorization = :google_app_default # in a later version, this will become the default
-client.authorization.fetch_access_token!
-client.execute(...)
-```
-
-This is simpler API to use than in previous versions, although that is still available:
-
-```ruby
-key = Google::APIClient::KeyUtils.load_from_pkcs12('client.p12', 'notasecret')
-client.authorization = Signet::OAuth2::Client.new(
- :token_credential_uri => 'https://accounts.google.com/o/oauth2/token',
- :audience => 'https://accounts.google.com/o/oauth2/token',
- :scope => 'https://www.googleapis.com/auth/prediction',
- :issuer => '123456-abcdef at developer.gserviceaccount.com',
- :signing_key => key)
-client.authorization.fetch_access_token!
-client.execute(...)
-```
-
-Service accounts are also used for delegation in Google Apps domains. The target user for impersonation is specified by setting the `:person` parameter to the user's email address
-in the credentials. Detailed instructions on how to enable delegation for your domain can be found at [developers.google.com](https://developers.google.com/drive/delegation).
-
-### Automatic Retries & Backoff
-
-The API client can automatically retry requests for recoverable errors. To enable retries, set the `client.retries` property to
-the number of additional attempts. To avoid flooding servers, retries invovle a 1 second delay that increases on each subsequent retry.
-In the case of authentication token expiry, the API client will attempt to refresh the token and retry the failed operation - this
-is a specific exception to the retry rules.
-
-The default value for retries is 0, but will be enabled by default in future releases.
-
-### Batching Requests
-
-Some Google APIs support batching requests into a single HTTP request. Use `Google::APIClient::BatchRequest`
-to bundle multiple requests together.
-
-Example:
-
-```ruby
-client = Google::APIClient.new
-urlshortener = client.discovered_api('urlshortener')
-
-batch = Google::APIClient::BatchRequest.new do |result|
- puts result.data
-end
-
-batch.add(:api_method => urlshortener.url.insert,
- :body_object => { 'longUrl' => 'http://example.com/foo' })
-batch.add(:api_method => urlshortener.url.insert,
- :body_object => { 'longUrl' => 'http://example.com/bar' })
-client.execute(batch)
-```
-
-Blocks for handling responses can be specified either at the batch level or when adding an individual API call. For example:
-
-```ruby
-batch.add(:api_method=>urlshortener.url.insert, :body_object => { 'longUrl' => 'http://example.com/bar' }) do |result|
- puts result.data
-end
-```
-
-### Media Upload
-
-For APIs that support file uploads, use `Google::APIClient::UploadIO` to load the stream. Both multipart and resumable
-uploads can be used. For example, to upload a file to Google Drive using multipart
-
-```ruby
-drive = client.discovered_api('drive', 'v2')
-
-media = Google::APIClient::UploadIO.new('mymovie.m4v', 'video/mp4')
-metadata = {
- 'title' => 'My movie',
- 'description' => 'The best home movie ever made'
-}
-client.execute(:api_method => drive.files.insert,
- :parameters => { 'uploadType' => 'multipart' },
- :body_object => metadata,
- :media => media )
-```
-
-To use resumable uploads, change the `uploadType` parameter to `resumable`. To check the status of the upload
-and continue if necessary, check `result.resumable_upload`.
-
-```ruby
-client.execute(:api_method => drive.files.insert,
- :parameters => { 'uploadType' => 'resumable' },
- :body_object => metadata,
- :media => media )
-upload = result.resumable_upload
-
-# Resume if needed
-if upload.resumable?
- client.execute(upload)
-end
-```
-
-## Samples
-
-See the full list of [samples on Github](https://github.com/google/google-api-ruby-client-samples).
-
-
-## Support
-
-Please [report bugs at the project on Github](https://github.com/google/google-api-ruby-client/issues). Don't hesitate to [ask questions](http://stackoverflow.com/questions/tagged/google-api-ruby-client) about the client or APIs on [StackOverflow](http://stackoverflow.com).
-
-[1]: https://developers.google.com/accounts/docs/application-default-credentials
+It is entirely focused on the use cases needed by the Arvados Ruby SDK and is not intended or expected to work elsewhere.
diff --git a/sdk/ruby-google-api-client/arvados-google-api-client.gemspec b/sdk/ruby-google-api-client/arvados-google-api-client.gemspec
index f11e60c864..f0117f87ee 100644
--- a/sdk/ruby-google-api-client/arvados-google-api-client.gemspec
+++ b/sdk/ruby-google-api-client/arvados-google-api-client.gemspec
@@ -20,7 +20,7 @@ Gem::Specification.new do |s|
s.files += Dir.glob("vendor/**/*.rb")
s.files += Dir.glob("tasks/**/*")
s.files += Dir.glob("website/**/*")
- s.homepage = "https://github.com/arvados/google-api-ruby-client/"
+ s.homepage = "https://github.com/arvados/arvados/tree/main/sdk/ruby-google-api-client"
s.rdoc_options = ["--main", "README.md"]
s.summary = "Fork of google-api-client used by Ruby-based Arvados components."
diff --git a/sdk/ruby/arvados.gemspec b/sdk/ruby/arvados.gemspec
index 6446cd9269..711b51daaf 100644
--- a/sdk/ruby/arvados.gemspec
+++ b/sdk/ruby/arvados.gemspec
@@ -40,9 +40,8 @@ Gem::Specification.new do |s|
s.required_ruby_version = '>= 2.5.0'
s.add_dependency('activesupport', '>= 3')
s.add_dependency('andand', '~> 1.3', '>= 1.3.3')
- # Our google-api-client dependency used to be < 0.9, but that could be
- # satisfied by the buggy 0.9.pre*, cf. https://dev.arvados.org/issues/9213
- # We need at least version 0.8.7.5 for compatibility with faraday >= 1.0.
+ # arvados fork of google-api-client gem with old API and new
+ # compatibility fixes, built from ../ruby-google-api-client/
s.add_dependency('arvados-google-api-client', '>= 0.8.7.5', '< 0.8.8')
# work around undeclared dependency on i18n in some activesupport 3.x.x:
s.add_dependency('i18n')
commit a29e101e0b0c184206f454932874bc5b23667d75
Author: Tom Clegg <tom at curii.com>
Date: Mon Sep 25 11:56:48 2023 -0400
20862: Emit notice about skipping sdk/ruby-google-api-client tests.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curii.com>
diff --git a/build/run-tests.sh b/build/run-tests.sh
index 49d7243062..481f0c33ab 100755
--- a/build/run-tests.sh
+++ b/build/run-tests.sh
@@ -1028,6 +1028,7 @@ test_sdk/ruby() {
}
test_sdk/ruby-google-api-client() {
+ echo "*** note \`test sdk/ruby-google-api-client\` does not actually run any tests, see https://dev.arvados.org/issues/20993 ***"
true
}
commit aba81749d2477043232b82300c0ce15548b61888
Merge: 905c83db0b 101971b927
Author: Tom Clegg <tom at curii.com>
Date: Mon Sep 25 11:46:36 2023 -0400
20862: Merge branch 'main' into 20862-google-api-client
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curii.com>
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