[ARVADOS] updated: 1.2.0-9-g37e385b7a
Git user
git at public.curoverse.com
Thu Aug 16 13:52:17 EDT 2018
Summary of changes:
apps/workbench/app/helpers/application_helper.rb | 2 +-
.../test/controllers/projects_controller_test.rb | 14 +++-
build/build.list | 7 +-
build/package-testing/deb-common-test-packages.sh | 8 +-
build/run-library.sh | 9 ++-
doc/admin/metrics.html.textile.liquid | 30 +++++++-
sdk/cwl/arvados_cwl/arvcontainer.py | 2 +-
sdk/cwl/arvados_cwl/fsaccess.py | 13 +++-
sdk/cwl/arvados_cwl/runner.py | 11 ++-
sdk/cwl/setup.py | 6 +-
sdk/cwl/tests/13931-size-job.yml | 3 +
sdk/cwl/tests/13931-size.cwl | 10 +++
sdk/cwl/tests/13976-keepref-wf.cwl | 17 +++++
sdk/cwl/tests/arvados-tests.sh | 4 +
sdk/cwl/tests/arvados-tests.yml | 17 +++++
sdk/cwl/tests/test_container.py | 3 +-
sdk/cwl/tests/test_job.py | 4 +-
sdk/cwl/tests/test_submit.py | 10 ++-
sdk/cwl/tests/wf/expect_packed.cwl | 3 +-
sdk/dev-jobs.dockerfile | 2 +-
.../api/app/controllers/application_controller.rb | 4 +-
.../controllers/arvados/v1/groups_controller.rb | 7 +-
.../migrate/20180806133039_index_all_filenames.rb | 6 --
services/api/lib/load_param.rb | 14 ++--
.../arvados/v1/groups_controller_test.rb | 74 ++++++++++--------
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 6 --
.../crunch-dispatch-slurm_test.go | 2 +-
services/crunch-dispatch-slurm/squeue.go | 72 ++++++++++--------
services/keep-web/cache.go | 33 --------
services/keep-web/cache_test.go | 87 ++++++++++++++--------
services/keep-web/handler.go | 9 +--
services/keep-web/status_test.go | 1 -
32 files changed, 315 insertions(+), 175 deletions(-)
create mode 100644 sdk/cwl/tests/13931-size-job.yml
create mode 100644 sdk/cwl/tests/13931-size.cwl
create mode 100644 sdk/cwl/tests/13976-keepref-wf.cwl
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commit 37e385b7aaf52ac391c6964557e30f662cb1de36
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date: Thu Aug 16 13:52:07 2018 -0400
13752: Don't rewrite entire file_names column during the migration.
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 ff7f1804c..55f39f7d8 100644
--- a/doc/admin/upgrading.html.textile.liquid
+++ b/doc/admin/upgrading.html.textile.liquid
@@ -30,10 +30,6 @@ 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. 2018-08-09: "21bf21abe":https://dev.arvados.org/projects/arvados/repository/revisions/21bf21abe includes a slow migration
-* The migration removes the size constraint on the file_names column in the collections table, and reparses all manifests to fix any truncated values.
-* Migration time depends on the size and number of collections in the database. Our test clusters processed about 20K collections per minute.
-
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.
diff --git a/services/api/db/migrate/20180806133039_index_all_filenames.rb b/services/api/db/migrate/20180806133039_index_all_filenames.rb
index 79259f91d..36b155cc2 100644
--- a/services/api/db/migrate/20180806133039_index_all_filenames.rb
+++ b/services/api/db/migrate/20180806133039_index_all_filenames.rb
@@ -5,12 +5,6 @@
class IndexAllFilenames < ActiveRecord::Migration
def up
ActiveRecord::Base.connection.execute 'ALTER TABLE collections ALTER COLUMN file_names TYPE text'
- Collection.find_each(batch_size: 20) do |c|
- ActiveRecord::Base.connection.execute "UPDATE collections
- SET file_names = #{ActiveRecord::Base.connection.quote(c.manifest_files)}
- WHERE uuid = #{ActiveRecord::Base.connection.quote(c.uuid)}
- AND portable_data_hash = #{ActiveRecord::Base.connection.quote(c.portable_data_hash)}"
- end
end
def down
ActiveRecord::Base.connection.execute 'ALTER TABLE collections ALTER COLUMN file_names TYPE varchar(8192)'
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