[ARVADOS] updated: 1.3.0-1271-g94972ae20
Git user
git at public.curoverse.com
Tue Jul 9 14:00:30 UTC 2019
Summary of changes:
.../app/controllers/actions_controller.rb | 2 +-
.../app/controllers/application_controller.rb | 18 +-
.../app/controllers/collections_controller.rb | 35 ++--
.../controllers/container_requests_controller.rb | 2 +-
.../app/controllers/containers_controller.rb | 2 +-
.../app/controllers/healthcheck_controller.rb | 2 +-
apps/workbench/app/controllers/jobs_controller.rb | 4 +-
.../controllers/pipeline_instances_controller.rb | 2 +-
.../controllers/pipeline_templates_controller.rb | 2 +-
.../app/controllers/projects_controller.rb | 6 +-
apps/workbench/app/controllers/users_controller.rb | 2 +-
.../app/controllers/virtual_machines_controller.rb | 13 +-
.../app/controllers/work_units_controller.rb | 2 +-
.../app/controllers/workflows_controller.rb | 2 +-
apps/workbench/app/helpers/application_helper.rb | 4 +-
apps/workbench/app/helpers/collections_helper.rb | 2 +-
apps/workbench/app/mailers/issue_reporter.rb | 4 +-
.../app/mailers/request_shell_access_reporter.rb | 4 +-
apps/workbench/app/models/arvados_api_client.rb | 36 ++--
apps/workbench/app/models/repository.rb | 6 +-
.../api_client_authorizations/_show_help.html.erb | 2 +-
.../app/views/application/_breadcrumbs.html.erb | 2 +-
.../app/views/application/_report_error.html.erb | 2 +-
.../views/application/_report_issue_popup.html.erb | 4 +-
.../app/views/application/_show_sharing.html.erb | 2 +-
.../app/views/collections/show_file_links.html.erb | 2 +-
.../_getting_started_popup.html.erb | 2 +-
apps/workbench/app/views/jobs/_show_log.html.erb | 4 +-
.../app/views/layouts/application.html.erb | 10 +-
apps/workbench/app/views/layouts/body.html.erb | 38 ++--
.../_collections_notification.html.erb | 6 +-
.../notifications/_jobs_notification.html.erb | 7 +-
.../notifications/_pipelines_notification.html.erb | 6 +-
.../app/views/projects/_show_dashboard.html.erb | 6 +-
.../app/views/repositories/_show_help.html.erb | 6 +-
.../app/views/user_agreements/index.html.erb | 2 +-
.../app/views/users/_add_ssh_key_popup.html.erb | 2 +-
.../app/views/users/_current_token.html.erb | 4 +-
.../app/views/users/_setup_popup.html.erb | 2 +-
apps/workbench/app/views/users/_ssh_keys.html.erb | 2 +-
apps/workbench/app/views/users/_tables.html.erb | 4 +-
.../app/views/users/_virtual_machines.html.erb | 6 +-
apps/workbench/app/views/users/profile.html.erb | 31 +--
apps/workbench/app/views/users/welcome.html.erb | 8 +-
.../app/views/virtual_machines/_show_help.html.erb | 2 +-
.../app/views/virtual_machines/webshell.html.erb | 2 +-
.../app/views/work_units/_show_log.html.erb | 2 +-
apps/workbench/config/application.default.yml | 208 +--------------------
apps/workbench/config/application.rb | 5 +-
apps/workbench/config/arvados_config.rb | 194 +++++++++++++++++++
apps/workbench/config/load_config.rb | 71 -------
.../api => apps/workbench}/lib/config_loader.rb | 141 +++++++-------
apps/workbench/lib/config_validators.rb | 36 ++--
.../api => apps/workbench}/lib/tasks/config.rake | 0
apps/workbench/lib/tasks/config_check.rake | 23 ---
apps/workbench/lib/tasks/config_dump.rake | 10 -
.../test/controllers/actions_controller_test.rb | 4 +-
.../controllers/application_controller_test.rb | 16 +-
.../controllers/collections_controller_test.rb | 30 +--
.../test/controllers/disabled_api_test.rb | 2 +-
.../test/controllers/projects_controller_test.rb | 26 +--
.../test/controllers/users_controller_test.rb | 4 +-
.../test/integration/anonymous_access_test.rb | 8 +-
.../test/integration/application_layout_test.rb | 27 +--
apps/workbench/test/integration/download_test.rb | 4 +-
apps/workbench/test/integration/errors_test.rb | 6 +-
apps/workbench/test/integration/jobs_test.rb | 2 +-
.../test/integration/link_account_test.rb | 22 +--
apps/workbench/test/integration/projects_test.rb | 10 +-
.../test/integration/report_issue_test.rb | 4 +-
.../test/integration/user_profile_test.rb | 26 +--
.../test/integration/user_settings_menu_test.rb | 4 +-
apps/workbench/test/integration/websockets_test.rb | 4 +-
apps/workbench/test/integration/work_units_test.rb | 2 +-
apps/workbench/test/integration_helper.rb | 4 +-
.../collection_unit_test.rb | 2 +-
apps/workbench/test/test_helper.rb | 13 +-
apps/workbench/test/unit/user_test.rb | 2 +-
apps/workbench/test/unit/work_unit_test.rb | 2 +-
build/run-library.sh | 14 --
build/run-tests.sh | 14 +-
cmd/arvados-server/cmd.go | 11 +-
doc/admin/config-migration.html.textile.liquid | 27 ++-
doc/admin/upgrading.html.textile.liquid | 4 +
doc/install/index.html.textile.liquid | 2 +-
doc/install/install-api-server.html.textile.liquid | 150 +++++++++------
.../install-dispatch-cloud.html.textile.liquid | 2 +-
.../install-workbench-app.html.textile.liquid | 60 ++++--
lib/config/cmd.go | 19 ++
lib/config/config.default.yml | 172 +++++++++++++++--
lib/config/export.go | 187 +++++++++++-------
lib/config/generated_config.go | 172 +++++++++++++++--
sdk/go/arvados/config.go | 11 +-
services/api/config/arvados_config.rb | 48 +++--
services/api/config/config.default.yml | 1 -
services/login-sync/Gemfile.lock | 6 +-
96 files changed, 1236 insertions(+), 892 deletions(-)
create mode 100644 apps/workbench/config/arvados_config.rb
delete mode 100644 apps/workbench/config/load_config.rb
copy {services/api => apps/workbench}/lib/config_loader.rb (61%)
copy {services/api => apps/workbench}/lib/tasks/config.rake (100%)
delete mode 100644 apps/workbench/lib/tasks/config_check.rake
delete mode 100644 apps/workbench/lib/tasks/config_dump.rake
delete mode 120000 services/api/config/config.default.yml
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commit 94972ae20fa5d9dde7dc814695a970e9d5bad4a7
Merge: f73b7d2ff cc3ea291a
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Tue Jul 9 10:00:13 2019 -0400
Merge branch '14812-wb1-new-config' refs #14812
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
commit cc3ea291af0cf8e1a1cc5f357a393bd0e08e53b4
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Tue Jul 9 09:59:02 2019 -0400
14812: Documentation fixes
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/doc/admin/config-migration.html.textile.liquid b/doc/admin/config-migration.html.textile.liquid
index fd4942527..4862bfe33 100644
--- a/doc/admin/config-migration.html.textile.liquid
+++ b/doc/admin/config-migration.html.textile.liquid
@@ -23,7 +23,7 @@ $ bundle exec rake config:migrate > config.yml
$ cp config.yml /etc/arvados/config.yml
</pre>
-This will print the contents of @config.yml@ after merging with legacy @application.yml at . It may then be redirected to a file and copied to @/etc/arvados/config.yml at .
+This will print the contents of @config.yml@ after merging the legacy @application.yml@ and @database.yml@ into the existing systemwide @config.yml at . It may be redirected to a file and copied to @/etc/arvados/config.yml@ (it is safe to copy over, all configuration items from the existing @/etc/arvados/config.yml@ will be included in the migrated output).
If you wish to update @config.yml@ configuration by hand, or check that everything has been migrated, use @config:diff@ to print configuration items that differ between @application.yml@ and the system @config.yml at .
@@ -35,7 +35,7 @@ This command will also report if no migrations are required.
h2. Workbench
-The legacy workbench configuration is stored in @config/application.yml@ and @config/database.yml at . After migration to @/etc/arvados/config.yml@, both of these files should be moved out of the way and/or deleted.
+The legacy workbench configuration is stored in @config/application.yml at . After migration to @/etc/arvados/config.yml@, this file should be moved out of the way and/or deleted.
Change to the workbench server directory and use the following commands:
@@ -44,7 +44,7 @@ $ bundle exec rake config:migrate > config.yml
$ cp config.yml /etc/arvados/config.yml
</pre>
-This will print the contents of @config.yml@ after merging with legacy @application.yml at . It may then be redirected to a file and copied to @/etc/arvados/config.yml at .
+This will print the contents of @config.yml@ after merging the legacy @application.yml@ into the existing systemwide @config.yml at . It may be redirected to a file and copied to @/etc/arvados/config.yml@ (it is safe to copy over, all configuration items from the existing @/etc/arvados/config.yml@ will be included in the migrated output).
If you wish to update @config.yml@ configuration by hand, or check that everything has been migrated, use @config:diff@ to print configuration items that differ between @application.yml@ and the system @config.yml at .
diff --git a/doc/install/install-api-server.html.textile.liquid b/doc/install/install-api-server.html.textile.liquid
index f9fecea4a..424fc3cf2 100644
--- a/doc/install/install-api-server.html.textile.liquid
+++ b/doc/install/install-api-server.html.textile.liquid
@@ -35,21 +35,13 @@ On a Red Hat-based system, install the following packages:
{% include 'install_git' %}
-h2(#configure). Set up the database
-
-Configure the API server to connect to your database by updating @/etc/arvados/api/database.yml at . Replace the @xxxxxxxx@ database password placeholder with the "password you generated during database setup":install-postgresql.html#api. Be sure to update the @production@ section.
-
-<notextile>
-<pre><code>~$ <span class="userinput">editor /etc/arvados/api/database.yml</span>
-</code></pre></notextile>
-
h2(#configure_application). Configure the API server
-Edit @/etc/arvados/config.yml@ to set the keys below. Only the most important configuration options are listed here. The full set of configuration options are listed in "config.yml":{{site.baseurl}}/admin/config.html
+Edit @/etc/arvados/config.yml@ to set the keys below. Only the most important configuration options are listed here. The example configuration fragments given below should be merged into a single configuration structure. Correct indentation is important. The full set of configuration options are listed in "config.yml":{{site.baseurl}}/admin/config.html
h3(#uuid_prefix). ClusterID
-The @ClusterID@ is used for all database identifiers to identify the record as originating from this site. It is the first key under @Clusters@ in @config.yml at . It must be exactly 5 lowercase ASCII letters and digits.
+The @ClusterID@ is used for all database identifiers to identify the record as originating from this site. It is the first key under @Clusters@ in @config.yml at . It must be exactly 5 lowercase ASCII letters and digits. All configuration items go under the cluster id key (replace @zzzzz@ with your cluster id in the examples below).
<notextile>
<pre><code>Clusters:
@@ -57,6 +49,22 @@ The @ClusterID@ is used for all database identifiers to identify the record as o
...</code></pre>
</notextile>
+h3(#configure). PostgreSQL.Connection
+
+Replace the @xxxxxxxx@ database password placeholder with the "password you generated during database setup":install-postgresql.html#api.
+
+<notextile>
+<pre><code>Clusters:
+ zzzzz:
+ PostgreSQL:
+ Connection:
+ host: <span class="userinput">localhost</span>
+ user: <span class="userinput">arvados</span>
+ password: <span class="userinput">xxxxxxxx</span>
+ dbname: <span class="userinput">arvados_production</span>
+ </code></pre>
+</notextile>
+
h3. API.RailsSessionSecretToken
The @API.RailsSessionSecretToken@ is used for for signing cookies. IMPORTANT: This is a site secret. It should be at least 50 characters. Generate a random value and set it in @config.yml@:
@@ -77,7 +85,7 @@ Example @config.yml@:
h3(#blob_signing_key). Collections.BlobSigningKey
-The @Collections.BlobSigningKey@ is used to enforce access control to Keep blocks. This same key must be provided to the Keepstore daemons when "installing Keepstore servers.":install-keepstore.html IMPORTANT: This is a site secret. It should be at least 50 characters. Generate a random value and set it in @application.yml@:
+The @Collections.BlobSigningKey@ is used to enforce access control to Keep blocks. This same key must be provided to the Keepstore daemons when "installing Keepstore servers.":install-keepstore.html IMPORTANT: This is a site secret. It should be at least 50 characters. Generate a random value and set it in @config.yml@:
<notextile>
<pre><code>~$ <span class="userinput">ruby -e 'puts rand(2**400).to_s(36)'</span>
@@ -90,7 +98,7 @@ Example @config.yml@:
<pre><code>Clusters:
zzzzz:
Collections:
- BlobSigningKey: <span class="userinput">yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy</span></code></pre>
+ BlobSigningKey: <span class="userinput">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span></code></pre>
</notextile>
h3(#omniauth). Login.ProviderAppID, Login.ProviderAppSecret, Services.SSO.ExternalURL
@@ -165,7 +173,7 @@ h3(#enable_legacy_jobs_api). Containers.JobsAPI.Enable
Enable the legacy "Jobs API":install-crunch-dispatch.html . Note: new installations should use the "Containers API":crunch2-slurm/install-prerequisites.html
-Disabling the jobs API means methods involving @jobs@, @job_tasks@, @pipeline_templates@ and @pipeline_instances@ are disabled. This functionality is superceded by the containers API which consists of @container_requests@, @containers@ and @workflows at . Arvados clients (such as @arvados-cwl-runner@) detect which APIs are available and adjust behavior accordingly.
+Disabling the jobs API means methods involving @jobs@, @job_tasks@, @pipeline_templates@ and @pipeline_instances@ are disabled. This functionality is superceded by the containers API which consists of @container_requests@, @containers@ and @workflows at . Arvados clients (such as @arvados-cwl-runner@) detect which APIs are available and adjust behavior accordingly. Note the configuration value must be a quoted string.
* 'auto' -- (default) enable the Jobs API only if it has been used before (i.e., there are job records in the database), otherwise disable jobs API .
* 'true' -- enable the Jobs API even if there are no existing job records.
diff --git a/doc/install/install-workbench-app.html.textile.liquid b/doc/install/install-workbench-app.html.textile.liquid
index f67ba8d6d..72a80fd83 100644
--- a/doc/install/install-workbench-app.html.textile.liquid
+++ b/doc/install/install-workbench-app.html.textile.liquid
@@ -100,9 +100,9 @@ For testing only. Allows use of self-signed certificates. If true, workbench w
</code></pre>
</notextile>
-h2. Configure Piwik
+h2. Configure Piwik (optional)
-Piwik is optional, and can be to gather usage analytics. In @/var/www/arvados-workbench/current/config@, copy @piwik.yml.example@ to @piwik.yml@ and edit to suit.
+Piwik can be used to gather usage analytics. In @/var/www/arvados-workbench/current/config@, copy @piwik.yml.example@ to @piwik.yml@ and edit to suit.
h2. Set up Web server
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