[ARVADOS] updated: 1.3.0-1148-gf5764a05d
Git user
git at public.curoverse.com
Mon Jun 24 13:23:29 UTC 2019
Summary of changes:
.licenseignore | 1 +
.../app/views/projects/_container_summary.html.erb | 42 ++++
.../app/views/projects/_show_dashboard.html.erb | 10 +
build/run-tests.sh | 43 +++--
doc/_config.yml | 2 +
doc/_includes/_federated_cwl.liquid | 2 +-
doc/_includes/_install_postgres_database.liquid | 31 ++-
doc/_includes/_navbar_top.liquid | 11 +-
doc/admin/upgrading.html.textile.liquid | 6 +-
.../crunch2-slurm/install-test.html.textile.liquid | 2 +-
doc/install/install-controller.html.textile.liquid | 16 ++
doc/install/install-postgresql.html.textile.liquid | 6 +-
doc/sdk/cli/subcommands.html.textile.liquid | 14 +-
doc/sdk/python/sdk-python.html.textile.liquid | 8 +-
.../cwl/federated-workflows.html.textile.liquid | 2 +-
doc/user/cwl/federated/FileOnCluster.yml | 5 +
doc/user/cwl/federated/cat.cwl | 14 --
doc/user/cwl/federated/colors_to_select.txt | 2 +
doc/user/cwl/federated/extract.cwl | 22 +++
doc/user/cwl/federated/extract.py | 31 +++
.../cwl/federated/{federated.cwl => feddemo.cwl} | 68 ++++---
doc/user/cwl/federated/file-on-clsr1.dat | 1 -
doc/user/cwl/federated/file-on-clsr2.dat | 1 -
doc/user/cwl/federated/file-on-clsr3.dat | 1 -
doc/user/cwl/federated/items1.csv | 29 +++
doc/user/cwl/federated/items2.csv | 33 ++++
doc/user/cwl/federated/items3.csv | 41 ++++
doc/user/cwl/federated/md5sum.cwl | 21 --
doc/user/cwl/federated/merge.cwl | 23 +++
doc/user/cwl/federated/merge.py | 15 ++
doc/user/cwl/federated/shards.yml | 21 +-
doc/user/index.html.textile.liquid | 2 +-
doc/user/topics/keep.html.textile.liquid | 12 +-
...rial-gatk-variantfiltration.html.textile.liquid | 2 +-
doc/user/topics/tutorial-job1.html.textile.liquid | 8 +-
.../topics/tutorial-parallel.html.textile.liquid | 2 +-
.../tutorials/tutorial-keep.html.textile.liquid | 16 +-
lib/config/cmd.go | 48 ++++-
lib/config/cmd_test.go | 23 ++-
lib/config/config.default.yml | 105 +++++++---
lib/config/export.go | 155 +++++++++++++++
lib/config/export_test.go | 37 ++++
lib/config/generated_config.go | 105 +++++++---
lib/config/load.go | 8 +
lib/config/load_test.go | 18 ++
lib/controller/federation_test.go | 8 +-
lib/controller/handler.go | 15 ++
lib/controller/handler_test.go | 21 +-
lib/controller/server_test.go | 2 +-
lib/dispatchcloud/dispatcher.go | 4 +-
lib/dispatchcloud/dispatcher_test.go | 14 ++
lib/dispatchcloud/driver.go | 70 ++++++-
lib/dispatchcloud/worker/pool.go | 14 ++
sdk/cwl/arvados_cwl/executor.py | 15 +-
sdk/cwl/arvados_cwl/pathmapper.py | 20 +-
sdk/cwl/arvados_cwl/runner.py | 5 +-
...13976-keepref-wf.cwl => 15295-bad-keep-ref.cwl} | 7 +-
sdk/cwl/tests/arvados-tests.yml | 6 +
sdk/cwl/tests/badkeep.yml | 3 +
sdk/go/arvados/config.go | 212 ++++++++++++++++-----
sdk/go/arvados/duration.go | 4 +-
sdk/go/arvados/duration_test.go | 17 ++
sdk/python/arvados_version.py | 2 +-
.../arvados/v1/containers_controller.rb | 3 +-
services/api/app/models/arvados_model.rb | 12 ++
services/api/app/models/container.rb | 61 +++---
...0523180148_add_trigram_index_for_text_search.rb | 44 +++++
services/api/db/structure.sql | 67 ++++++-
services/api/lib/config_loader.rb | 33 +++-
services/api/lib/record_filters.rb | 8 +
services/api/test/fixtures/containers.yml | 1 +
.../arvados/v1/containers_controller_test.rb | 2 +-
services/api/test/unit/arvados_model_test.rb | 24 +++
tools/arvbox/bin/arvbox | 6 +
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 2 +-
tools/arvbox/lib/arvbox/docker/api-setup.sh | 2 +-
76 files changed, 1447 insertions(+), 322 deletions(-)
create mode 100644 apps/workbench/app/views/projects/_container_summary.html.erb
create mode 100644 doc/user/cwl/federated/FileOnCluster.yml
delete mode 100644 doc/user/cwl/federated/cat.cwl
create mode 100644 doc/user/cwl/federated/colors_to_select.txt
create mode 100644 doc/user/cwl/federated/extract.cwl
create mode 100644 doc/user/cwl/federated/extract.py
rename doc/user/cwl/federated/{federated.cwl => feddemo.cwl} (51%)
delete mode 100644 doc/user/cwl/federated/file-on-clsr1.dat
delete mode 100644 doc/user/cwl/federated/file-on-clsr2.dat
delete mode 100644 doc/user/cwl/federated/file-on-clsr3.dat
create mode 100644 doc/user/cwl/federated/items1.csv
create mode 100644 doc/user/cwl/federated/items2.csv
create mode 100644 doc/user/cwl/federated/items3.csv
delete mode 100644 doc/user/cwl/federated/md5sum.cwl
create mode 100644 doc/user/cwl/federated/merge.cwl
create mode 100644 doc/user/cwl/federated/merge.py
create mode 100644 lib/config/export.go
create mode 100644 lib/config/export_test.go
copy sdk/cwl/tests/{13976-keepref-wf.cwl => 15295-bad-keep-ref.cwl} (54%)
create mode 100644 sdk/cwl/tests/badkeep.yml
create mode 100644 services/api/db/migrate/20190523180148_add_trigram_index_for_text_search.rb
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commit f5764a05d616e8d3c55b94503d5a1f789ac66ea7
Merge: 067bb74eb 2f4429e62
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date: Mon Jun 24 10:22:52 2019 -0300
Merge branch 'master' into 14874-protected-collection-properties
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>
diff --cc lib/config/config.default.yml
index 1c4542e45,dc128e56b..aaf88a0d7
--- a/lib/config/config.default.yml
+++ b/lib/config/config.default.yml
@@@ -269,24 -274,11 +274,24 @@@ Clusters
# the current collection.
CollectionVersioning: false
- # 0 = auto-create a new version on every update.
- # -1 = never auto-create new versions.
- # > 0 = auto-create a new version when older than the specified number of seconds.
- PreserveVersionIfIdle: -1
+ # 0s = auto-create a new version on every update.
+ # -1s = never auto-create new versions.
+ # > 0s = auto-create a new version when older than the specified number of seconds.
+ PreserveVersionIfIdle: -1s
+ # Managed collection properties. At creation time, if the client didn't
+ # provide the listed keys, they will be automatically populated following
+ # one of the following behaviors:
+ #
+ # * UUID of the user who owns the containing project.
+ # responsible_person_uuid: {function: original_owner, protected: true}
+ #
+ # * Default concrete value.
+ # foo_bar: {value: baz, protected: false}
+ #
+ # If protected is true, only an admin user can modify its value.
+ ManagedProperties: {}
+
Login:
# These settings are provided by your OAuth2 provider (e.g.,
# sso-provider).
diff --cc lib/config/generated_config.go
index ede9f4953,98cd343bd..15004ca98
--- a/lib/config/generated_config.go
+++ b/lib/config/generated_config.go
@@@ -275,24 -280,11 +280,24 @@@ Clusters
# the current collection.
CollectionVersioning: false
- # 0 = auto-create a new version on every update.
- # -1 = never auto-create new versions.
- # > 0 = auto-create a new version when older than the specified number of seconds.
- PreserveVersionIfIdle: -1
+ # 0s = auto-create a new version on every update.
+ # -1s = never auto-create new versions.
+ # > 0s = auto-create a new version when older than the specified number of seconds.
+ PreserveVersionIfIdle: -1s
+ # Managed collection properties. At creation time, if the client didn't
+ # provide the listed keys, they will be automatically populated following
+ # one of the following behaviors:
+ #
+ # * UUID of the user who owns the containing project.
+ # responsible_person_uuid: {function: original_owner, protected: true}
+ #
+ # * Default concrete value.
+ # foo_bar: {value: baz, protected: false}
+ #
+ # If protected is true, only an admin user can modify its value.
+ ManagedProperties: {}
+
Login:
# These settings are provided by your OAuth2 provider (e.g.,
# sso-provider).
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