[ARVADOS] updated: 1.1.4-725-gc8a4dee5e
Git user
git at public.curoverse.com
Tue Jul 31 11:38:43 EDT 2018
Summary of changes:
README.md | 4 +-
apps/workbench/Gemfile.lock | 4 +-
.../app/assets/javascripts/models/session_db.js | 11 +-
build/run-library.sh | 3 +-
doc/_config.yml | 34 +-
doc/_includes/_install_compute_docker.liquid | 27 +
doc/_includes/_skip_sso_server_install.liquid | 12 -
doc/admin/health-checks.html.textile.liquid | 70 +
doc/admin/management-token.html.textile.liquid | 56 +
doc/admin/metrics.html.textile.liquid | 163 ++
doc/admin/upgrading.html.textile.liquid | 46 +-
doc/api/execution.html.textile.liquid | 28 +
doc/css/images.css | 8 +
doc/install/cheat_sheet.html.textile.liquid | 2 +-
...opy_pipeline_from_curoverse.html.textile.liquid | 20 +-
.../create-standard-objects.html.textile.liquid | 84 -
.../install-dispatch.html.textile.liquid | 31 +-
.../install-slurm.html.textile.liquid | 2 -
doc/install/index.html.textile.liquid | 16 +-
doc/install/install-api-server.html.textile.liquid | 32 +-
.../install-arv-git-httpd.html.textile.liquid | 45 +
doc/install/install-components.html.textile.liquid | 28 +
doc/install/install-composer.html.textile.liquid | 59 +
doc/install/install-controller.html.textile.liquid | 180 ++
.../install-keep-balance.html.textile.liquid | 7 +-
doc/install/install-keepproxy.html.textile.liquid | 23 +-
doc/install/install-keepstore.html.textile.liquid | 39 +-
...nstall-manual-prerequisites.html.textile.liquid | 8 +-
.../install-nodemanager.html.textile.liquid | 29 +-
.../firstpipeline.html.textile.liquid | 2 +-
doc/user/composer/c1.png | Bin 0 -> 17420 bytes
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doc/user/composer/composer.html.textile.liquid | 119 +
doc/user/cwl/cwl-runner.html.textile.liquid | 10 +-
doc/user/cwl/cwl-style.html.textile.liquid | 2 +
doc/user/topics/arv-copy.html.textile.liquid | 4 +-
doc/user/topics/arv-docker.html.textile.liquid | 10 +-
.../running-external-program.html.textile.liquid | 4 +-
...tutorial-workflow-workbench.html.textile.liquid | 4 +
.../writing-cwl-workflow.html.textile.liquid | 6 +-
lib/controller/federation.go | 117 +
lib/controller/federation_test.go | 301 +++
lib/controller/handler.go | 146 +-
lib/controller/handler_test.go | 14 +-
lib/controller/proxy.go | 83 +
lib/controller/server_test.go | 68 +
lib/crunchstat/crunchstat.go | 64 +-
sdk/R/R/Arvados.R | 2796 ++++++++++----------
sdk/R/R/ArvadosFile.R | 20 +-
sdk/R/R/Collection.R | 22 +-
sdk/R/R/CollectionTree.R | 10 +-
sdk/R/R/HttpParser.R | 6 +-
sdk/R/R/HttpRequest.R | 15 +-
sdk/R/R/RESTService.R | 15 +-
sdk/R/R/Subcollection.R | 14 +-
sdk/R/R/autoGenAPI.R | 16 +-
sdk/R/tests/testthat/fakes/FakeHttpParser.R | 6 +-
sdk/R/tests/testthat/fakes/FakeHttpRequest.R | 29 +-
sdk/R/tests/testthat/fakes/FakeRESTService.R | 4 +-
sdk/R/tests/testthat/test-ArvadosFile.R | 46 +-
sdk/R/tests/testthat/test-Collection.R | 6 +-
sdk/R/tests/testthat/test-CollectionTree.R | 20 +-
sdk/R/tests/testthat/test-HttpParser.R | 10 +-
sdk/R/tests/testthat/test-HttpRequest.R | 85 +-
sdk/R/tests/testthat/test-RESTService.R | 99 +-
sdk/R/tests/testthat/test-Subcollection.R | 62 +-
sdk/R/tests/testthat/test-util.R | 20 +-
sdk/cli/arvados-cli.gemspec | 4 +-
sdk/cli/bin/crunch-job | 10 +
sdk/go/arvados/api_client_authorization.go | 4 +
sdk/go/arvados/config.go | 26 +-
sdk/go/arvados/postgresql.go | 20 +
sdk/go/arvadostest/fixtures.go | 2 +
sdk/go/auth/auth.go | 24 +-
sdk/go/auth/salt.go | 48 +
sdk/go/dispatch/dispatch.go | 12 +-
sdk/go/httpserver/metrics.go | 129 +
sdk/python/tests/run_test_server.py | 17 +-
sdk/ruby/lib/arvados/google_api_client.rb | 5 +
services/api/Gemfile | 5 +-
services/api/Gemfile.lock | 14 +-
services/api/app/controllers/static_controller.rb | 2 +-
services/api/config/initializers/oj_mimic_json.rb | 11 +
services/api/config/initializers/time_format.rb | 2 +
services/api/db/structure.sql | 3 +-
services/api/lib/crunch_dispatch.rb | 5 +
services/api/lib/safe_json.rb | 6 +
services/api/test/integration/cross_origin_test.rb | 4 +-
services/api/test/test_helper.rb | 2 +-
.../crunch-dispatch-slurm_test.go | 14 +-
services/crunch-dispatch-slurm/squeue.go | 24 +-
services/crunch-dispatch-slurm/squeue_test.go | 44 +
services/crunch-run/crunchrun.go | 1 +
services/crunchstat/crunchstat.go | 4 +-
services/keep-web/doc.go | 6 +
services/keep-web/handler.go | 4 +
services/keep-web/handler_test.go | 5 +-
services/keep-web/server.go | 7 +-
services/keep-web/server_test.go | 72 +
services/keepproxy/keepproxy_test.go | 2 +-
services/keepstore/config.go | 64 -
services/keepstore/handlers.go | 12 +-
services/login-sync/arvados-login-sync.gemspec | 2 +-
.../arvnodeman/computenode/dispatch/__init__.py | 24 +-
.../arvnodeman/computenode/driver/__init__.py | 8 +-
.../arvnodeman/computenode/driver/azure.py | 4 +-
.../arvnodeman/computenode/driver/dummy.py | 2 +-
.../arvnodeman/computenode/driver/ec2.py | 4 +-
.../arvnodeman/computenode/driver/gce.py | 5 +-
services/nodemanager/arvnodeman/config.py | 3 +-
services/nodemanager/arvnodeman/daemon.py | 69 +-
services/nodemanager/arvnodeman/jobqueue.py | 5 +-
services/nodemanager/arvnodeman/launcher.py | 3 +-
services/nodemanager/doc/azure.example.cfg | 10 +
services/nodemanager/doc/ec2.example.cfg | 9 +
services/nodemanager/doc/gce.example.cfg | 9 +
services/nodemanager/tests/fake_azure.cfg.template | 6 +-
services/nodemanager/tests/integration_test.py | 5 +-
.../nodemanager/tests/test_computenode_dispatch.py | 14 +-
services/nodemanager/tests/test_daemon.py | 16 +
services/ws/config.go | 4 +-
services/ws/event_source.go | 16 -
services/ws/event_source_test.go | 30 +-
services/ws/server.go | 2 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 2 +-
tools/arvbox/lib/arvbox/docker/api-setup.sh | 8 +-
tools/arvbox/lib/arvbox/docker/common.sh | 4 +-
tools/arvbox/lib/arvbox/docker/crunch-setup.sh | 2 +-
tools/arvbox/lib/arvbox/docker/keep-setup.sh | 23 +-
.../lib/arvbox/docker/service/api/run-service | 4 +-
.../docker/service/arv-git-httpd/run-service | 2 +-
.../lib/arvbox/docker/service/composer/run-service | 2 +-
.../service/{api => controller}/log/main/.gitstub | 0
.../docker/service/{api => controller}/log/run | 0
.../lib/arvbox/docker/service/controller/run | 50 +
.../service/crunch-dispatch-local/run-service | 2 +-
tools/arvbox/lib/arvbox/docker/service/doc/run | 10 +-
.../lib/arvbox/docker/service/doc/run-service | 31 +-
.../lib/arvbox/docker/service/gitolite/run-service | 4 +-
.../lib/arvbox/docker/service/keep-web/run-service | 2 +-
.../arvbox/docker/service/keepproxy/run-service | 2 +-
.../service/{api => nginx}/log/main/.gitstub | 0
.../arvbox/docker/service/{api => nginx}/log/run | 0
.../lib/arvbox/docker/service/{api => nginx}/run | 0
.../lib/arvbox/docker/service/nginx/run-service | 54 +
tools/arvbox/lib/arvbox/docker/service/ready/run | 10 +-
.../lib/arvbox/docker/service/ready/run-service | 4 +-
.../lib/arvbox/docker/service/sso/run-service | 2 +-
tools/arvbox/lib/arvbox/docker/service/vm/run | 2 +-
.../lib/arvbox/docker/service/vm/run-service | 2 +-
.../arvbox/docker/service/websockets/run-service | 2 +-
.../arvbox/docker/service/workbench/run-service | 6 +-
...application_yml_override.py => yml_override.py} | 9 +-
vendor/vendor.json | 26 +-
178 files changed, 4254 insertions(+), 2201 deletions(-)
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create mode 100644 lib/controller/federation_test.go
create mode 100644 lib/controller/proxy.go
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create mode 100644 sdk/go/arvados/postgresql.go
create mode 100644 sdk/go/auth/salt.go
create mode 100644 sdk/go/httpserver/metrics.go
create mode 100644 services/api/config/initializers/oj_mimic_json.rb
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commit c8a4dee5e52feed137ca3cb4c4a4e224efbb694f
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date: Tue Jul 31 11:31:55 2018 -0400
13497: Link issues and commit hashes to redmine.
"#1234" and "commit:foo" markup doesn't work here like it did on the
redmine wiki where the content came from.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>
diff --git a/doc/admin/upgrading.html.textile.liquid b/doc/admin/upgrading.html.textile.liquid
index 359142dd7..55f39f7d8 100644
--- a/doc/admin/upgrading.html.textile.liquid
+++ b/doc/admin/upgrading.html.textile.liquid
@@ -30,7 +30,7 @@ Note to developers: Add new items at the top. Include the date, issue number, co
TODO: extract this information based on git commit messages and generate changelogs / release notes automatically.
{% endcomment %}
-h3. 2018-07-31: #13497 commit:db5107dca adds a new system service, arvados-controller
+h3. 2018-07-31: "#13497":https://dev.arvados.org/issues/13497 "db5107dca":https://dev.arvados.org/projects/arvados/repository/revisions/db5107dca adds a new system service, arvados-controller
* "Install the controller":../install/install-controller.html after upgrading your system.
* Verify your setup by confirming that API calls appear in the controller's logs (_e.g._, @journalctl -fu arvados-controller@) while loading a workbench page.
@@ -155,7 +155,7 @@ baseCommand: echo
This bug will be fixed in an upcoming release of Arvados.
-h3. 2017-12-08: #11908 commit:8f987a9271 now requires minimum of Postgres 9.4 (previously 9.3)
+h3. 2017-12-08: "#11908":https://dev.arvados.org/issues/11908 "8f987a9271":https://dev.arvados.org/projects/arvados/repository/revisions/8f987a9271 now requires minimum of Postgres 9.4 (previously 9.3)
* Debian 8 (pg 9.4) and Debian 9 (pg 9.6) do not require an upgrade
* Ubuntu 16.04 (pg 9.5) does not require an upgrade
* Ubuntu 14.04 (pg 9.3) requires upgrade to Postgres 9.4: https://www.postgresql.org/download/linux/ubuntu/
@@ -164,7 +164,7 @@ h3. 2017-12-08: #11908 commit:8f987a9271 now requires minimum of Postgres 9.4 (p
*# Install the @rh-postgresql94@ backport package from either Software Collections: http://doc.arvados.org/install/install-postgresql.html or the Postgres developers: https://www.postgresql.org/download/linux/redhat/
*# Restore from the backup using @psql@
-h3. 2017-09-25: #12032 commit:68bdf4cbb now requires minimum of Postgres 9.3 (previously 9.1)
+h3. 2017-09-25: "#12032":https://dev.arvados.org/issues/12032 "68bdf4cbb":https://dev.arvados.org/projects/arvados/repository/revisions/68bdf4cbb now requires minimum of Postgres 9.3 (previously 9.1)
* Debian 8 (pg 9.4) and Debian 9 (pg 9.6) do not require an upgrade
* Ubuntu 16.04 (pg 9.5) does not require an upgrade
* Ubuntu 14.04 (pg 9.3) is compatible, however upgrading to Postgres 9.4 is recommended: https://www.postgresql.org/download/linux/ubuntu/
@@ -173,21 +173,21 @@ h3. 2017-09-25: #12032 commit:68bdf4cbb now requires minimum of Postgres 9.3 (pr
*# Install the @rh-postgresql94@ backport package from either Software Collections: http://doc.arvados.org/install/install-postgresql.html or the Postgres developers: https://www.postgresql.org/download/linux/redhat/
*# Restore from the backup using @psql@
-h3. 2017-06-30: #11807 commit:55aafbb converts old "jobs" database records from YAML to JSON, making the upgrade process slower than usual.
-* The migration can take some time if your database contains a substantial number of YAML-serialized rows (i.e., you installed Arvados before March 3, 2017 commit:660a614 and used the jobs/pipelines APIs). Otherwise, the upgrade will be no slower than usual.
+h3. 2017-06-30: "#11807":https://dev.arvados.org/issues/11807 "55aafbb":https://dev.arvados.org/projects/arvados/repository/revisions/55aafbb converts old "jobs" database records from YAML to JSON, making the upgrade process slower than usual.
+* The migration can take some time if your database contains a substantial number of YAML-serialized rows (i.e., you installed Arvados before March 3, 2017 "660a614":https://dev.arvados.org/projects/arvados/repository/revisions/660a614 and used the jobs/pipelines APIs). Otherwise, the upgrade will be no slower than usual.
* The conversion runs as a database migration, i.e., during the deb/rpm package upgrade process, while your API server is unavailable.
* Expect it to take about 1 minute per 20K jobs that have ever been created/run.
-h3. 2017-06-05: #9005 commit:cb230b0 reduces service discovery overhead in keep-web requests.
+h3. 2017-06-05: "#9005":https://dev.arvados.org/issues/9005 "cb230b0":https://dev.arvados.org/projects/arvados/repository/revisions/cb230b0 reduces service discovery overhead in keep-web requests.
* When upgrading keep-web _or keepproxy_ to/past this version, make sure to update API server as well. Otherwise, a bad token in a request can cause keep-web to fail future requests until either keep-web restarts or API server gets upgraded.
-h3. 2017-04-12: #11349 commit:2c094e2 adds a "management" http server to nodemanager.
+h3. 2017-04-12: "#11349":https://dev.arvados.org/issues/11349 "2c094e2":https://dev.arvados.org/projects/arvados/repository/revisions/2c094e2 adds a "management" http server to nodemanager.
* To enable it, add to your configuration file: <pre>[Manage]
address = 127.0.0.1
port = 8989</pre> (see example configuration files in source:services/nodemanager/doc or https://doc.arvados.org/install/install-nodemanager.html for more info)
* The server responds to @http://{address}:{port}/status.json@ with a summary of how many nodes are in each state (booting, busy, shutdown, etc.)
-h3. 2017-03-23: #10766 commit:e8cc0d7 replaces puma with arvados-ws as the recommended websocket server.
+h3. 2017-03-23: "#10766":https://dev.arvados.org/issues/10766 "e8cc0d7":https://dev.arvados.org/projects/arvados/repository/revisions/e8cc0d7 replaces puma with arvados-ws as the recommended websocket server.
* See http://doc.arvados.org/install/install-ws.html for install/upgrade instructions.
* Remove the old puma server after the upgrade is complete. Example, with runit: <pre>
$ sudo sv down /etc/sv/puma
@@ -197,17 +197,17 @@ $ systemctl disable puma
$ systemctl stop puma
</pre>
-h3. 2017-03-06: #11168 commit:660a614 uses JSON instead of YAML to encode hashes and arrays in the database.
+h3. 2017-03-06: "#11168":https://dev.arvados.org/issues/11168 "660a614":https://dev.arvados.org/projects/arvados/repository/revisions/660a614 uses JSON instead of YAML to encode hashes and arrays in the database.
* Aside from a slight performance improvement, this should have no externally visible effect.
* Downgrading past this version is not supported, and is likely to cause errors. If this happens, the solution is to upgrade past this version.
* After upgrading, make sure to restart puma and crunch-dispatch-* processes.
-h3. 2017-02-03: #10969 commit:74a9dec introduces a Docker image format compatibility check: the @arv keep docker@ command prevents users from inadvertently saving docker images that compute nodes won't be able to run.
+h3. 2017-02-03: "#10969":https://dev.arvados.org/issues/10969 "74a9dec":https://dev.arvados.org/projects/arvados/repository/revisions/74a9dec introduces a Docker image format compatibility check: the @arv keep docker@ command prevents users from inadvertently saving docker images that compute nodes won't be able to run.
* If your compute nodes run a version of *docker older than 1.10* you must override the default by adding to your API server configuration (@/etc/arvados/api/application.yml@): <pre><code class="yaml">docker_image_formats: ["v1"]</code></pre>
-* Refer to the comments above @docker_image_formats@ in @/var/www/arvados-api/current/config/application.default.yml@ or source:services/api/config/application.default.yml or issue #10969 for more detail.
+* Refer to the comments above @docker_image_formats@ in @/var/www/arvados-api/current/config/application.default.yml@ or source:services/api/config/application.default.yml or issue "#10969":https://dev.arvados.org/issues/10969 for more detail.
* *NOTE:* This does *not* include any support for migrating existing Docker images from v1 to v2 format. This will come later: for now, sites running Docker 1.9 or earlier should still *avoid upgrading Docker further than 1.9.*
-h3. 2016-09-27: several Debian and RPM packages -- keep-balance (commit:d9eec0b), keep-web (commit:3399e63), keepproxy (commit:6de67b6), and arvados-git-httpd (commit:9e27ddf) -- now enable their respective components using systemd. These components prefer YAML configuration files over command line flags (commit:3bbe1cd).
+h3. 2016-09-27: several Debian and RPM packages -- keep-balance ("d9eec0b":https://dev.arvados.org/projects/arvados/repository/revisions/d9eec0b), keep-web ("3399e63":https://dev.arvados.org/projects/arvados/repository/revisions/3399e63), keepproxy ("6de67b6":https://dev.arvados.org/projects/arvados/repository/revisions/6de67b6), and arvados-git-httpd ("9e27ddf":https://dev.arvados.org/projects/arvados/repository/revisions/9e27ddf) -- now enable their respective components using systemd. These components prefer YAML configuration files over command line flags ("3bbe1cd":https://dev.arvados.org/projects/arvados/repository/revisions/3bbe1cd).
* On Debian-based systems using systemd, services are enabled automatically when packages are installed.
* On RedHat-based systems using systemd, unit files are installed but services must be enabled explicitly: e.g., <code>"sudo systemctl enable keep-web; sudo systemctl start keep-web"</code>.
* The new systemd-supervised services will not start up successfully until configuration files are installed in /etc/arvados/: e.g., <code>"Sep 26 18:23:55 62751f5bb946 keep-web[74]: 2016/09/26 18:23:55 open /etc/arvados/keep-web/keep-web.yml: no such file or directory"</code>
@@ -222,33 +222,33 @@ h3. 2016-09-27: several Debian and RPM packages -- keep-balance (commit:d9eec0b)
** keepproxy - /etc/arvados/keepproxy/keepproxy.yml
** arvados-git-httpd - /etc/arvados/arv-git-httpd/arv-git-httpd.yml
-h3. 2016-05-31: commit:ae72b172c8 and commit:3aae316c25 install Python modules and scripts to different locations on the filesystem.
-* Previous packages installed these files to the distribution's preferred path under @/usr/local@ (or the equivalent location in a Software Collection). Now they get installed to a path under @/usr at . This improves compatibility with other Python packages provided by the distribution. See #9242 for more background.
+h3. 2016-05-31: "ae72b172c8":https://dev.arvados.org/projects/arvados/repository/revisions/ae72b172c8 and "3aae316c25":https://dev.arvados.org/projects/arvados/repository/revisions/3aae316c25 install Python modules and scripts to different locations on the filesystem.
+* Previous packages installed these files to the distribution's preferred path under @/usr/local@ (or the equivalent location in a Software Collection). Now they get installed to a path under @/usr at . This improves compatibility with other Python packages provided by the distribution. See "#9242":https://dev.arvados.org/issues/9242 for more background.
* If you simply import Python modules from scripts, or call Python tools relying on $PATH, you don't need to make any changes. If you have hardcoded full paths to some of these files (e.g., in symbolic links or configuration files), you will need to update those paths after this upgrade.
-h3. 2016-04-25: commit:eebcb5e requires the crunchrunner package to be installed on compute nodes and shell nodes in order to run CWL workflows.
+h3. 2016-04-25: "eebcb5e":https://dev.arvados.org/projects/arvados/repository/revisions/eebcb5e requires the crunchrunner package to be installed on compute nodes and shell nodes in order to run CWL workflows.
* On each Debian-based compute node and shell node, run: @sudo apt-get install crunchrunner@
* On each Red Hat-based compute node and shell node, run: @sudo yum install crunchrunner@
-h3. 2016-04-21: commit:3c88abd changes the Keep permission signature algorithm.
+h3. 2016-04-21: "3c88abd":https://dev.arvados.org/projects/arvados/repository/revisions/3c88abd changes the Keep permission signature algorithm.
* All software components that generate signatures must be upgraded together. These are: keepstore, API server, keep-block-check, and keep-rsync. For example, if keepstore < 0.1.20160421183420 but API server >= 0.1.20160421183420, clients will not be able to read or write data in Keep.
* Jobs and client operations that are in progress during the upgrade (including arv-put's "resume cache") will fail.
-h3. 2015-01-05: commit:e1276d6e disables Workbench's "Getting Started" popup by default.
+h3. 2015-01-05: "e1276d6e":https://dev.arvados.org/projects/arvados/repository/revisions/e1276d6e disables Workbench's "Getting Started" popup by default.
* If you want new users to continue seeing this popup, set @enable_getting_started_popup: true@ in Workbench's @application.yml@ configuration.
-h3. 2015-12-03: commit:5590c9ac makes a Keep-backed writable scratch directory available in crunch jobs (see #7751)
-* All compute nodes must be upgraded to arvados-fuse >= 0.1.2015112518060 because crunch-job uses some new arv-mount flags (--mount-tmp, --mount-by-pdh) introduced in merge commit:346a558
+h3. 2015-12-03: "5590c9ac":https://dev.arvados.org/projects/arvados/repository/revisions/5590c9ac makes a Keep-backed writable scratch directory available in crunch jobs (see "#7751":https://dev.arvados.org/issues/7751)
+* All compute nodes must be upgraded to arvados-fuse >= 0.1.2015112518060 because crunch-job uses some new arv-mount flags (--mount-tmp, --mount-by-pdh) introduced in merge "346a558":https://dev.arvados.org/projects/arvados/repository/revisions/346a558
* Jobs will fail if the API server (in particular crunch-job from the arvados-cli gem) is upgraded without upgrading arvados-fuse on compute nodes.
-h3. 2015-11-11: commit:1e2ace5 changes recommended config for keep-web (see #5824)
+h3. 2015-11-11: "1e2ace5":https://dev.arvados.org/projects/arvados/repository/revisions/1e2ace5 changes recommended config for keep-web (see "#5824":https://dev.arvados.org/issues/5824)
* proxy/dns/ssl config should be updated to route "https://download.uuid_prefix.arvadosapi.com/" requests to keep-web (alongside the existing "collections" routing)
* keep-web command line adds @-attachment-only-host download.uuid_prefix.arvadosapi.com@
* Workbench config adds @keep_web_download_url@
* More info on the (still beta/non-TOC-linked) "keep-web doc page":http://doc.arvados.org/install/install-keep-web.html
-h3. 2015-11-04: commit:1d1c6de removes stopped containers (see #7444)
+h3. 2015-11-04: "1d1c6de":https://dev.arvados.org/projects/arvados/repository/revisions/1d1c6de removes stopped containers (see "#7444":https://dev.arvados.org/issues/7444)
* arvados-docker-cleaner removes _all_ docker containers as soon as they exit, effectively making @docker run@ default to @--rm at . If you run arvados-docker-cleaner on a host that does anything other than run crunch-jobs, and you still want to be able to use @docker start@, read the "new doc page":http://doc.arvados.org/install/install-compute-node.html to learn how to turn this off before upgrading.
-h3. 2015-11-04: commit:21006cf adds a keep-web service (see #5824)
+h3. 2015-11-04: "21006cf":https://dev.arvados.org/projects/arvados/repository/revisions/21006cf adds a keep-web service (see "#5824":https://dev.arvados.org/issues/5824)
* Nothing relies on it yet, but early adopters can install it now by following http://doc.arvados.org/install/install-keep-web.html (it is not yet linked in the TOC).
commit d80674f09b714ee2ced537f18d73d325672db3c2
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date: Tue Jul 31 11:26:36 2018 -0400
13497: Add controller to upgrade notes.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>
diff --git a/doc/admin/upgrading.html.textile.liquid b/doc/admin/upgrading.html.textile.liquid
index 7a330a963..359142dd7 100644
--- a/doc/admin/upgrading.html.textile.liquid
+++ b/doc/admin/upgrading.html.textile.liquid
@@ -30,6 +30,10 @@ Note to developers: Add new items at the top. Include the date, issue number, co
TODO: extract this information based on git commit messages and generate changelogs / release notes automatically.
{% endcomment %}
+h3. 2018-07-31: #13497 commit:db5107dca adds a new system service, arvados-controller
+* "Install the controller":../install/install-controller.html after upgrading your system.
+* Verify your setup by confirming that API calls appear in the controller's logs (_e.g._, @journalctl -fu arvados-controller@) while loading a workbench page.
+
h3. 2018-04-05: v1.1.4 regression in arvados-cwl-runner for workflows that rely on implicit discovery of secondaryFiles
h4. Secondary files missing from toplevel workflow inputs
commit db33fa2b2d1f09a186bc07a2956cb0edae380d2c
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date: Mon Jul 30 15:53:45 2018 -0400
13497: Add controller to install docs.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>
diff --git a/doc/_config.yml b/doc/_config.yml
index 03fc5af0c..c2c97a9ff 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -177,6 +177,7 @@ navbar:
- Core:
- install/install-postgresql.html.textile.liquid
- install/install-api-server.html.textile.liquid
+ - install/install-controller.html.textile.liquid
- Keep:
- install/install-keepstore.html.textile.liquid
- install/configure-fs-storage.html.textile.liquid
diff --git a/doc/install/install-api-server.html.textile.liquid b/doc/install/install-api-server.html.textile.liquid
index 7201460dd..1d071a46d 100644
--- a/doc/install/install-api-server.html.textile.liquid
+++ b/doc/install/install-api-server.html.textile.liquid
@@ -164,10 +164,11 @@ The Nginx server will serve API requests using Passenger. It will also be used t
First, "Install Nginx and Phusion Passenger":https://www.phusionpassenger.com/library/walkthroughs/deploy/ruby/ownserver/nginx/oss/install_passenger_main.html.
-Edit the http section of your Nginx configuration to run the Passenger server, and serve SSL requests. Add a block like the following, adding SSL and logging parameters to taste:
+Edit the http section of your Nginx configuration to run the Passenger server. Add a block like the following, adding SSL and logging parameters to taste:
<notextile>
-<pre><code>server {
+<pre><code>
+server {
listen 127.0.0.1:8000;
server_name localhost-api;
@@ -202,33 +203,6 @@ geo $external_client {
default 1;
<span class="userinput">10.20.30.0/24</span> 0;
}
-
-server {
- listen <span class="userinput">[your public IP address]</span>:443 ssl;
- server_name <span class="userinput">uuid_prefix.your.domain</span>;
-
- ssl on;
- ssl_certificate <span class="userinput">/YOUR/PATH/TO/cert.pem</span>;
- ssl_certificate_key <span class="userinput">/YOUR/PATH/TO/cert.key</span>;
-
- index index.html index.htm index.php;
-
- # Refer to the comment about this setting in the server section above.
- client_max_body_size 128m;
-
- location / {
- proxy_pass http://api;
- proxy_redirect off;
- proxy_connect_timeout 90s;
- proxy_read_timeout 300s;
-
- proxy_set_header X-Forwarded-Proto https;
- proxy_set_header Host $http_host;
- proxy_set_header X-External-Client $external_client;
- proxy_set_header X-Real-IP $remote_addr;
- proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
- }
-}
</code></pre>
</notextile>
diff --git a/doc/install/install-controller.html.textile.liquid b/doc/install/install-controller.html.textile.liquid
new file mode 100644
index 000000000..ccb8d980a
--- /dev/null
+++ b/doc/install/install-controller.html.textile.liquid
@@ -0,0 +1,180 @@
+---
+layout: default
+navsection: installguide
+title: Install the controller
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+The arvados-controller service must be installed on your API server node.
+
+On Debian-based systems:
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo apt-get install arvados-controller</span>
+</code></pre>
+</notextile>
+
+On Red Hat-based systems:
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo yum install arvados-controller</span>
+</code></pre>
+</notextile>
+
+Verify the @arvados-controller@ program is functional:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arvados-controller -h</span>
+Usage:
+ -config file
+[...]
+</code></pre>
+</notextile>
+
+h3. Configure Nginx to route requests to the controller
+
+Add @upstream@ and @server@ definitions inside the @http@ section of your Nginx configuration using the following template.
+
+{% include 'notebox_begin' %}
+
+If you are adding arvados-controller to an existing system as part of the upgrade procedure, do not add a new "server" part here. Instead, add only the "upstream" part as shown here, and update your existing "server" section by changing its @proxy_pass@ directive from @http://api@ to @http://controller@.
+
+{% include 'notebox_end' %}
+
+<notextile>
+<pre><code>upstream controller {
+ server 127.0.0.1:9004 fail_timeout=10s;
+}
+
+server {
+ listen <span class="userinput">[your public IP address]</span>:443 ssl;
+ server_name <span class="userinput">uuid_prefix.your.domain</span>;
+
+ ssl on;
+ ssl_certificate <span class="userinput">/YOUR/PATH/TO/cert.pem</span>;
+ ssl_certificate_key <span class="userinput">/YOUR/PATH/TO/cert.key</span>;
+
+ # Refer to the comment about this setting in the passenger (arvados
+ # api server) section of your Nginx configuration.
+ client_max_body_size 128m;
+
+ location / {
+ proxy_pass http://controller;
+ proxy_redirect off;
+ proxy_connect_timeout 90s;
+ proxy_read_timeout 300s;
+
+ proxy_set_header X-Forwarded-Proto https;
+ proxy_set_header Host $http_host;
+ proxy_set_header X-External-Client $external_client;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ }
+}
+</code></pre>
+</notextile>
+
+Restart Nginx to apply the new configuration.
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo nginx -s reload</span>
+</code></pre>
+</notextile>
+
+h3. Configure arvados-controller
+
+Create the cluster configuration file @/etc/arvados/config.yml@ using the following template.
+
+<notextile>
+<pre><code>Clusters:
+ <span class="userinput">uuid_prefix</span>:
+ NodeProfiles:
+ apiserver:
+ arvados-controller:
+ Listen: ":<span class="userinput">9004</span>" # must match the "upstream controller" section of your Nginx config
+ arvados-api-server:
+ Listen: ":<span class="userinput">8000</span>" # must match the "upstream api" section of your Nginx config
+ PostgreSQL:
+ ConnectionPool: 128
+ Connection:
+ host: localhost
+ dbname: arvados_production
+ user: arvados
+ password: <span class="userinput">xxxxxxxx</span>
+ sslmode: require
+</code></pre>
+</notextile>
+
+Create the host configuration file @/etc/arvados/environment at .
+
+<notextile>
+<pre><code>ARVADOS_NODE_PROFILE=apiserver
+</code></pre>
+</notextile>
+
+h3. Start the service (option 1: systemd)
+
+If your system does not use systemd, skip this section and follow the "runit instructions":#runit instead.
+
+If your system uses systemd, the arvados-controller service should already be set up. Restart it to load the new configuration file, and check its status:
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo systemctl restart arvados-controller</span>
+~$ <span class="userinput">sudo systemctl status arvados-controller</span>
+● arvados-controller.service - Arvados controller
+ Loaded: loaded (/lib/systemd/system/arvados-controller.service; enabled; vendor preset: enabled)
+ Active: active (running) since Tue 2018-07-31 13:17:44 UTC; 3s ago
+ Docs: https://doc.arvados.org/
+ Main PID: 25066 (arvados-control)
+ CGroup: /system.slice/arvados-controller.service
+ └─25066 /usr/bin/arvados-controller
+
+Jul 31 13:17:44 zzzzz systemd[1]: Starting Arvados controller...
+Jul 31 13:17:44 zzzzz arvados-controller[25191]: {"Listen":"[::]:9004","Service":"arvados-controller","level":"info","msg":"listening","time":"2018-07-31T13:17:44.521694195Z"}
+Jul 31 13:17:44 zzzzz systemd[1]: Started Arvados controller.
+</code></pre>
+</notextile>
+
+Skip ahead to "confirm the service is working":#confirm.
+
+h3(#runit). Start the service (option 2: runit)
+
+Install runit to supervise the arvados-controller daemon. {% include 'install_runit' %}
+
+Create a supervised service.
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo mkdir /etc/service/arvados-controller</span>
+~$ <span class="userinput">cd /etc/service/arvados-controller</span>
+~$ <span class="userinput">sudo mkdir log log/main</span>
+~$ <span class="userinput">printf '#!/bin/sh\nset -a\n. /etc/arvados/environment\nexec arvados-controller 2>&1\n' | sudo tee run</span>
+~$ <span class="userinput">printf '#!/bin/sh\nexec svlogd main\n' | sudo tee log/run</span>
+~$ <span class="userinput">sudo chmod +x run log/run</span>
+~$ <span class="userinput">sudo sv exit .</span>
+~$ <span class="userinput">cd -</span>
+</code></pre>
+</notextile>
+
+Use @sv stat@ and check the log file to verify the service is running.
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo sv stat /etc/service/arvados-controller</span>
+run: /etc/service/arvados-controller: (pid 12520) 2s; run: log: (pid 12519) 2s
+~$ <span class="userinput">tail /etc/service/arvados-controller/log/main/current</span>
+{"Listen":"[::]:9004","Service":"arvados-controller","level":"info","msg":"listening","time":"2018-07-31T13:17:44.521694195Z"}
+</code></pre>
+</notextile>
+
+h3(#confirm). Confirm the service is working
+
+Confirm the service is listening on its assigned port and responding to requests.
+
+<notextile>
+<pre><code>~$ <span class="userinput">curl -X OPTIONS http://0.0.0.0:<b>9004</b>/login</span>
+{"errors":["Forbidden"],"error_token":"1533044555+684b532c"}
+</code></pre>
+</notextile>
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