[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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