[ARVADOS] updated: 1.3.0-1045-g333b241e8
Git user
git at public.curoverse.com
Mon Jun 10 14:09:31 UTC 2019
Summary of changes:
build/build-dev-docker-jobs-image.sh | 8 +-
build/run-build-packages-one-target.sh | 5 +-
build/run-build-packages-sso.sh | 4 +-
build/run-build-test-packages-one-target.sh | 6 +-
build/run-tests.sh | 3 +
doc/admin/upgrading.html.textile.liquid | 49 +++-
doc/install/install-controller.html.textile.liquid | 11 +-
.../install-dispatch-cloud.html.textile.liquid | 87 ++++---
lib/cloud/azure/azure.go | 51 ++--
lib/cloud/azure/azure_test.go | 27 ++-
lib/cloud/ec2/ec2.go | 66 ++----
lib/cloud/ec2/ec2_test.go | 12 +-
lib/cloud/interfaces.go | 35 ++-
lib/config/cmd_test.go | 19 ++
lib/config/config.default.yml | 171 ++++++++++++-
lib/config/deprecated.go | 24 +-
lib/config/generated_config.go | 171 ++++++++++++-
lib/config/load.go | 23 +-
lib/config/load_test.go | 58 +++++
lib/controller/cmd.go | 4 +-
lib/controller/federation_test.go | 62 +----
lib/controller/handler.go | 42 ++--
lib/controller/handler_test.go | 14 +-
lib/controller/server_test.go | 15 +-
lib/dispatchcloud/cmd.go | 4 +-
lib/dispatchcloud/dispatcher.go | 12 +-
lib/dispatchcloud/dispatcher_test.go | 47 ++--
lib/dispatchcloud/driver.go | 67 +++++-
lib/dispatchcloud/test/stub_driver.go | 2 +-
lib/dispatchcloud/worker/pool.go | 47 ++--
lib/dispatchcloud/worker/pool_test.go | 27 ++-
lib/dispatchcloud/worker/verify.go | 6 +-
lib/dispatchcloud/worker/worker.go | 4 +-
lib/dispatchcloud/worker/worker_test.go | 2 +-
lib/service/cmd.go | 38 +--
lib/service/cmd_test.go | 2 +-
lib/service/error.go | 2 +-
sdk/cli/bin/crunch-job | 4 +-
sdk/cli/test/test_crunch-job.rb | 2 +
sdk/cwl/arvados_cwl/__init__.py | 21 +-
...{arv-cwl-schema.yml => arv-cwl-schema-v1.0.yml} | 0
...{arv-cwl-schema.yml => arv-cwl-schema-v1.1.yml} | 56 -----
sdk/cwl/arvados_cwl/arvcontainer.py | 12 +-
sdk/cwl/arvados_cwl/arvjob.py | 7 +-
sdk/cwl/arvados_cwl/arvtool.py | 26 +-
sdk/cwl/arvados_cwl/arvworkflow.py | 13 +-
sdk/cwl/arvados_cwl/done.py | 2 +-
sdk/cwl/arvados_cwl/executor.py | 72 ++++--
sdk/cwl/arvados_cwl/runner.py | 180 ++++++++++++--
sdk/cwl/setup.py | 6 +-
sdk/cwl/test_with_arvbox.sh | 35 ++-
sdk/cwl/tests/test_container.py | 264 ++++++++++++++++++++-
sdk/cwl/tests/test_job.py | 49 ++--
sdk/cwl/tests/test_submit.py | 31 ++-
sdk/cwl/tests/wf/scatter2_subwf.cwl | 12 +-
sdk/dev-jobs.dockerfile | 17 +-
sdk/go/arvados/config.go | 183 +++++---------
sdk/go/arvados/duration.go | 11 +-
sdk/go/arvados/duration_test.go | 45 ++++
sdk/go/arvados/fs_collection_test.go | 3 +-
sdk/go/arvados/fs_project_test.go | 7 +-
sdk/go/arvados/fs_site_test.go | 36 ++-
sdk/go/arvadostest/fixtures.go | 1 -
sdk/go/arvadostest/stub.go | 22 ++
sdk/go/health/aggregator.go | 71 +++---
sdk/go/health/aggregator_test.go | 144 ++++++-----
sdk/pam/arvados_pam/__init__.py | 2 +-
sdk/python/tests/run_test_server.py | 40 ++--
.../api/app/controllers/application_controller.rb | 17 +-
.../arvados/v1/collections_controller.rb | 12 +
.../arvados/v1/container_requests_controller.rb | 18 ++
.../controllers/arvados/v1/groups_controller.rb | 9 +
services/api/app/models/arvados_model.rb | 53 -----
services/api/app/models/user.rb | 2 +-
services/api/config/arvados_config.rb | 7 +
.../20190322174136_add_file_info_to_collection.rb | 52 +---
services/api/lib/record_filters.rb | 8 +
services/api/lib/tasks/symbols.rake | 109 +++++++++
.../populate-file-info-columns-in-collections.rb | 97 ++++++++
services/api/test/fixtures/links.yml | 9 +
.../arvados/v1/collections_controller_test.rb | 22 +-
.../arvados/v1/groups_controller_test.rb | 17 ++
.../api/test/integration/collections_api_test.rb | 98 ++++++++
...eep_munge_test.rb => container_request_test.rb} | 28 +--
services/api/test/unit/arvados_model_test.rb | 11 -
services/crunch-run/copier_test.go | 6 +-
services/health/main.go | 69 +-----
services/keep-web/cache_test.go | 12 +-
services/keep-web/cadaver_test.go | 4 +-
services/keep-web/handler_test.go | 6 +-
services/keep-web/server_test.go | 6 +-
.../lib/arvbox/docker/service/certificate/run | 3 +-
92 files changed, 2212 insertions(+), 1064 deletions(-)
copy sdk/cwl/arvados_cwl/{arv-cwl-schema.yml => arv-cwl-schema-v1.0.yml} (100%)
rename sdk/cwl/arvados_cwl/{arv-cwl-schema.yml => arv-cwl-schema-v1.1.yml} (80%)
create mode 100644 sdk/go/arvados/duration_test.go
mode change 100755 => 100644 services/api/db/migrate/20190322174136_add_file_info_to_collection.rb
create mode 100644 services/api/lib/tasks/symbols.rake
create mode 100755 services/api/script/populate-file-info-columns-in-collections.rb
copy services/api/test/integration/{noop_deep_munge_test.rb => container_request_test.rb} (62%)
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commit 333b241e8ef7b1aca7aea85952424586c1f25299
Author: Eric Biagiotti <ebiagiotti at veritasgenetics.com>
Date: Mon Jun 10 10:09:27 2019 -0400
15106: Adds trigram search to the api
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti at veritasgenetics.com>
diff --git a/services/api/lib/record_filters.rb b/services/api/lib/record_filters.rb
index 831e357b4..7b0d48b05 100644
--- a/services/api/lib/record_filters.rb
+++ b/services/api/lib/record_filters.rb
@@ -44,6 +44,14 @@ module RecordFilters
cond_out = []
+ if attrs_in == 'any' && operator.casecmp('ilike') && operand.match('^[%].*[%]$')
+ # Trigram index search
+ cond_out << model_class.full_text_trgm + " ilike ?"
+ param_out << operand
+ # Skip the generic per-column operator loop below
+ attrs = []
+ end
+
if operator == '@@'
# Full-text search
if attrs_in != 'any'
commit 442a871e7f3476938d0ebb3adbe3b9a7742f03ad
Merge: 9d4c7ff60 a061ac178
Author: Eric Biagiotti <ebiagiotti at veritasgenetics.com>
Date: Mon Jun 10 10:07:59 2019 -0400
Merge branch 'master' into 15106-trgm-text-search
refs #15106
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti at veritasgenetics.com>
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