[ARVADOS] updated: 1.1.4-251-g2da6fd3
Git user
git at public.curoverse.com
Fri May 11 09:42:22 EDT 2018
Summary of changes:
.../app/controllers/work_units_controller.rb | 7 +-
.../workbench/test/integration/collections_test.rb | 2 +-
build/build.list | 9 +-
build/libcloud-pin.sh | 7 +
build/run-build-packages.sh | 4 +-
build/run-tests.sh | 94 ++++++------
doc/_config.yml | 2 +-
doc/admin/upgrading.html.textile.liquid | 157 ++++++++++++++++++---
doc/install/install-keepstore.html.textile.liquid | 2 +-
doc/install/install-postgresql.html.textile.liquid | 12 +-
sdk/cwl/arvados_cwl/__init__.py | 23 +--
sdk/cwl/arvados_cwl/arvcontainer.py | 7 -
sdk/cwl/arvados_cwl/arvjob.py | 7 -
sdk/cwl/arvados_cwl/arvtool.py | 7 +
sdk/cwl/arvados_cwl/fsaccess.py | 10 +-
sdk/cwl/arvados_cwl/runner.py | 94 +++++++-----
sdk/cwl/setup.py | 8 +-
sdk/cwl/tests/arvados-tests.sh | 3 +
sdk/cwl/tests/arvados-tests.yml | 10 ++
sdk/cwl/tests/secondaryFiles/example1.cwl | 20 +++
sdk/cwl/tests/secondaryFiles/example3.cwl | 12 ++
.../cwl/tests/secondaryFiles/hello.txt | 0
.../cwl/tests/secondaryFiles/hello.txt.idx | 0
sdk/cwl/tests/secondaryFiles/inp3.yml | 3 +
sdk/cwl/tests/test_job.py | 1 -
sdk/cwl/tests/wf/expect_packed.cwl | 6 +-
sdk/go/arvados/client.go | 39 ++++-
sdk/go/arvadosclient/arvadosclient.go | 6 +
sdk/go/arvadostest/run_servers.go | 14 +-
sdk/go/httpserver/id_generator.go | 3 +
sdk/go/httpserver/logger.go | 2 +
sdk/go/keepclient/keepclient.go | 20 ++-
sdk/go/keepclient/keepclient_test.go | 43 +++---
sdk/go/keepclient/support.go | 28 ++--
sdk/python/arvados/collection.py | 14 ++
sdk/python/setup.py | 4 +-
services/api/Gemfile.lock | 28 ++--
.../app/controllers/arvados/v1/users_controller.rb | 56 +++++++-
.../app/controllers/user_sessions_controller.rb | 14 +-
.../api/app/models/api_client_authorization.rb | 2 +-
services/api/app/models/user.rb | 79 +++++++++--
services/api/config/initializers/lograge.rb | 10 ++
services/api/config/routes.rb | 1 +
...501182859_add_redirect_to_user_uuid_to_users.rb | 15 ++
services/api/db/structure.sql | 7 +-
services/api/test/fixtures/collections.yml | 2 +-
.../functional/arvados/v1/users_controller_test.rb | 117 +++++++++++++++
services/api/test/integration/users_test.rb | 35 +++++
services/crunch-dispatch-slurm/squeue.go | 6 +-
services/fuse/setup.py | 5 +-
services/keep-web/cadaver_test.go | 2 +
services/keep-web/handler.go | 32 +++--
services/keep-web/handler_test.go | 52 ++++++-
services/keep-web/main.go | 6 +-
services/keep-web/server.go | 2 +-
services/keepproxy/keepproxy.go | 15 +-
services/keepproxy/proxy_client.go | 6 +-
services/keepstore/azure_blob_volume.go | 77 ++++++----
services/keepstore/azure_blob_volume_test.go | 13 +-
services/keepstore/config.go | 3 +
services/keepstore/keepstore.go | 14 +-
services/keepstore/s3_volume.go | 80 +++++++----
services/keepstore/usage.go | 15 ++
services/keepstore/volume_unix.go | 51 +++++--
services/nodemanager/tests/integration_test.py | 14 +-
.../crunchstat_summary/reader.py | 5 +-
66 files changed, 1097 insertions(+), 347 deletions(-)
create mode 100644 sdk/cwl/tests/secondaryFiles/example1.cwl
create mode 100644 sdk/cwl/tests/secondaryFiles/example3.cwl
copy tools/crunchstat-summary/tests/__init__.py => sdk/cwl/tests/secondaryFiles/hello.txt (100%)
copy tools/crunchstat-summary/tests/__init__.py => sdk/cwl/tests/secondaryFiles/hello.txt.idx (100%)
create mode 100644 sdk/cwl/tests/secondaryFiles/inp3.yml
create mode 100644 services/api/db/migrate/20180501182859_add_redirect_to_user_uuid_to_users.rb
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commit 2da6fd38987ee35cac75420b946d7a3f1738423e
Author: Fuad Muhic <muhic.fuad at gmail.com>
Date: Thu May 10 17:24:49 2018 +0200
Added trash_at and properties parameters to Collections save_new method
in Python SDK.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>
diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py
index 8fb90c9..0bb7ca4 100644
--- a/sdk/python/arvados/collection.py
+++ b/sdk/python/arvados/collection.py
@@ -1484,6 +1484,8 @@ class Collection(RichCollectionBase):
create_collection_record=True,
owner_uuid=None,
ensure_unique_name=False,
+ trash_at=None,
+ properties=None,
num_retries=None):
"""Save collection to a new collection record.
@@ -1508,6 +1510,14 @@ class Collection(RichCollectionBase):
if it conflicts with a collection with the same name and owner. If
False, a name conflict will result in an error.
+ :trash_at:
+ A collection is *expiring* when it has a *trash_at* time in the future.
+ An expiring collection can be accessed as normal,
+ but is scheduled to be trashed automatically at the *trash_at* time.
+
+ :properties:
+ Additional properties of collection.
+
:num_retries:
Retry count on API calls (if None, use the collection default)
@@ -1525,6 +1535,10 @@ class Collection(RichCollectionBase):
"replication_desired": self.replication_desired}
if owner_uuid:
body["owner_uuid"] = owner_uuid
+ if trash_at:
+ body["trash_at"] = trash_at
+ if properties:
+ body["properties"] = properties
self._remember_api_response(self._my_api().collections().create(ensure_unique_name=ensure_unique_name, body=body).execute(num_retries=num_retries))
text = self._api_response["manifest_text"]
commit d5b0290ac26cac5cfd67eaa03446ef9beffcf036
Merge: 2074c17 a20c7c5
Author: Fuad Muhic <muhic.fuad at gmail.com>
Date: Thu May 10 16:32:10 2018 +0200
Merge branch 'master' of git.curoverse.com:arvados into 13330-clean-up-collection-naming-and-properties
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>
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