[arvados] updated: 2.7.0-45-ge082e93a42
git repository hosting
git at public.arvados.org
Tue Dec 12 21:00:00 UTC 2023
Summary of changes:
build/package-build-dockerfiles/centos7/Dockerfile | 4 +-
.../package-build-dockerfiles/debian10/Dockerfile | 4 +-
.../package-build-dockerfiles/debian11/Dockerfile | 4 +-
build/package-build-dockerfiles/rocky8/Dockerfile | 6 +-
.../ubuntu1804/Dockerfile | 4 +-
.../ubuntu2004/Dockerfile | 4 +-
build/package-test-dockerfiles/rocky8/Dockerfile | 2 +-
build/run-build-packages-one-target.sh | 2 +-
build/run-tests.sh | 27 +-
cmd/arvados-client/cmd_test.go | 5 +-
cmd/arvados-server/arvados-controller.service | 1 +
cmd/arvados-server/arvados-dispatch-cloud.service | 1 +
cmd/arvados-server/arvados-dispatch-lsf.service | 1 +
cmd/arvados-server/arvados-git-httpd.service | 1 +
cmd/arvados-server/arvados-health.service | 1 +
cmd/arvados-server/arvados-ws.service | 1 +
cmd/arvados-server/crunch-dispatch-slurm.service | 1 +
cmd/arvados-server/keep-balance.service | 3 +-
cmd/arvados-server/keep-web.service | 1 +
cmd/arvados-server/keepproxy.service | 1 +
cmd/arvados-server/keepstore.service | 1 +
doc/Gemfile.lock | 2 +-
doc/README.textile | 2 +-
doc/Rakefile | 4 +-
doc/_config.yml | 1 +
doc/admin/keep-balance.html.textile.liquid | 6 +-
doc/admin/keep-faster-gc-s3.html.textile.liquid | 41 +
doc/admin/upgrading.html.textile.liquid | 20 +
.../install-keep-balance.html.textile.liquid | 2 +-
doc/pysdk_pdoc.py | 51 +
doc/user/topics/arv-copy.html.textile.liquid | 32 +-
go.mod | 31 +-
go.sum | 96 +-
lib/boot/supervisor.go | 23 +-
lib/cli/get.go | 4 +-
lib/cloud/ec2/ec2.go | 60 +-
lib/cloud/ec2/ec2_test.go | 48 +-
lib/cloud/interfaces.go | 14 +
lib/cmd/cmd.go | 6 +-
lib/cmd/parseflags.go | 4 +-
lib/config/cmd_test.go | 2 +-
lib/config/config.default.yml | 37 +-
lib/config/export.go | 4 +
lib/controller/federation/conn.go | 136 +-
lib/controller/federation/login_test.go | 39 -
lib/controller/federation/logout_test.go | 246 +++
lib/controller/federation/user_test.go | 4 +-
lib/controller/localdb/container_test.go | 1 +
lib/controller/localdb/login_oidc.go | 46 +-
lib/controller/localdb/login_oidc_test.go | 70 +
lib/controller/rpc/conn.go | 33 +-
lib/crunchrun/crunchrun.go | 23 +-
lib/crunchrun/crunchrun_test.go | 10 +-
lib/crunchrun/executor_test.go | 4 +
lib/dispatchcloud/container/queue.go | 23 +-
lib/dispatchcloud/container/queue_test.go | 11 +-
lib/dispatchcloud/dispatcher.go | 2 +-
lib/dispatchcloud/dispatcher_test.go | 15 +-
lib/dispatchcloud/node_size.go | 65 +-
lib/dispatchcloud/node_size_test.go | 68 +-
lib/dispatchcloud/scheduler/interfaces.go | 1 +
lib/dispatchcloud/scheduler/run_queue.go | 125 +-
lib/dispatchcloud/scheduler/run_queue_test.go | 119 +-
lib/dispatchcloud/test/queue.go | 10 +-
lib/dispatchcloud/test/stub_driver.go | 16 +-
lib/dispatchcloud/worker/pool.go | 42 +-
lib/install/deps.go | 19 +-
lib/service/cmd.go | 23 +-
lib/service/cmd_test.go | 71 +-
sdk/cwl/arvados_cwl/__init__.py | 14 +-
sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml | 19 +
sdk/cwl/arvados_cwl/arvcontainer.py | 12 +-
sdk/cwl/arvados_cwl/arvtool.py | 9 +-
sdk/cwl/arvados_cwl/arvworkflow.py | 104 +-
sdk/cwl/arvados_cwl/context.py | 3 +
sdk/cwl/arvados_cwl/executor.py | 24 +-
sdk/cwl/arvados_cwl/pathmapper.py | 3 +-
sdk/cwl/arvados_cwl/runner.py | 48 +-
sdk/cwl/setup.py | 6 +-
sdk/cwl/tests/arvados-tests.yml | 6 +
sdk/cwl/tests/test_container.py | 6 +-
sdk/cwl/tests/test_submit.py | 54 +-
.../tool/{submit_tool.cwl => submit_tool_map.cwl} | 4 +-
...d_wrapper.cwl => expect_upload_wrapper_map.cwl} | 6 +-
.../tests/wf/{runin-wf.cwl => runseparate-wf.cwl} | 6 +-
.../tests/wf/{submit_wf.cwl => submit_wf_map.cwl} | 12 +-
sdk/go/arvados/api.go | 2 +
sdk/go/arvados/client.go | 68 +-
sdk/go/arvados/client_test.go | 14 +
sdk/go/arvados/config.go | 17 +-
sdk/go/arvados/keep_service.go | 3 +-
sdk/go/arvados/tls_certs.go | 23 +
sdk/go/arvados/tls_certs_test.go | 32 +
sdk/go/arvados/tls_certs_test_showenv.go | 22 +
sdk/go/arvadosclient/arvadosclient.go | 36 +-
sdk/go/arvadostest/api.go | 4 +
sdk/go/arvadostest/oidc_provider.go | 21 +-
sdk/go/auth/auth.go | 12 +-
sdk/go/auth/handlers_test.go | 36 +-
sdk/go/keepclient/keepclient.go | 21 +
sdk/python/arvados-v1-discovery.json | 2 +-
sdk/python/arvados/__init__.py | 38 +-
sdk/python/arvados/api.py | 286 +--
sdk/python/arvados/collection.py | 2213 +++++++++++---------
sdk/python/arvados/commands/arv_copy.py | 241 ++-
sdk/python/arvados/commands/keepdocker.py | 5 +-
sdk/python/arvados/http_to_keep.py | 62 +-
sdk/python/arvados/retry.py | 102 +-
sdk/python/arvados/safeapi.py | 45 +-
sdk/python/arvados/util.py | 511 +++--
sdk/python/discovery2pydoc.py | 109 +-
sdk/python/tests/run_test_server.py | 10 +-
sdk/python/tests/test_http.py | 35 +-
.../controllers/arvados/v1/schema_controller.rb | 2 +-
.../app/controllers/arvados/v1/users_controller.rb | 40 +-
.../api/app/models/api_client_authorization.rb | 62 +-
services/api/app/models/arvados_model.rb | 45 +-
services/api/app/models/group.rb | 85 +-
services/api/app/models/link.rb | 11 +-
services/api/app/models/user.rb | 120 +-
...d_btree_name_index_to_collections_and_groups.rb | 24 +
.../20231013000000_compute_permission_index.rb | 27 +
services/api/db/structure.sql | 83 +-
services/api/lib/update_permissions.rb | 126 +-
services/api/test/fixtures/links.yml | 14 +
.../arvados/v1/collections_controller_test.rb | 4 +-
.../arvados/v1/groups_controller_test.rb | 4 +-
.../functional/arvados/v1/users_controller_test.rb | 19 +-
services/api/test/integration/users_test.rb | 6 +-
services/api/test/unit/container_request_test.rb | 6 +-
services/api/test/unit/user_test.rb | 10 +-
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 8 +-
services/fuse/arvados_fuse/command.py | 31 +-
services/fuse/tests/test_command_args.py | 45 +
services/keep-balance/balance.go | 65 +-
services/keep-balance/balance_run_test.go | 53 +-
services/keep-balance/balance_test.go | 78 +-
services/keep-balance/change_set.go | 25 +-
services/keep-balance/integration_test.go | 3 -
services/keep-balance/main.go | 15 +-
services/keep-balance/server.go | 10 +-
services/keep-web/cache.go | 2 +-
services/keep-web/handler.go | 38 +-
services/keep-web/handler_test.go | 80 +-
services/keepproxy/keepproxy.go | 50 +-
services/keepstore/azure_blob_volume.go | 7 +-
services/keepstore/command.go | 8 +-
services/keepstore/handlers.go | 6 +-
services/keepstore/keepstore.go | 4 +-
services/keepstore/proxy_remote.go | 4 +-
services/keepstore/pull_worker.go | 4 +-
services/keepstore/s3aws_volume.go | 6 +-
services/keepstore/trash_worker.go | 6 +-
services/keepstore/unix_volume.go | 7 +-
services/keepstore/volume.go | 10 +-
services/ws/session_v0.go | 1 +
tools/arvbox/bin/arvbox | 2 +
tools/arvbox/lib/arvbox/docker/go-setup.sh | 1 +
.../crunchstat_summary/summarizer.py | 7 +-
.../multi_host/aws/pillars/arvados.sls | 8 +-
.../multi_host/aws/pillars/nginx_passenger.sls | 2 +-
161 files changed, 5067 insertions(+), 2300 deletions(-)
create mode 100644 doc/admin/keep-faster-gc-s3.html.textile.liquid
create mode 100755 doc/pysdk_pdoc.py
create mode 100644 lib/controller/federation/logout_test.go
copy sdk/cwl/tests/tool/{submit_tool.cwl => submit_tool_map.cwl} (92%)
copy sdk/cwl/tests/wf/{expect_upload_wrapper.cwl => expect_upload_wrapper_map.cwl} (93%)
copy sdk/cwl/tests/wf/{runin-wf.cwl => runseparate-wf.cwl} (90%)
copy sdk/cwl/tests/wf/{submit_wf.cwl => submit_wf_map.cwl} (78%)
create mode 100644 sdk/go/arvados/tls_certs.go
create mode 100644 sdk/go/arvados/tls_certs_test.go
create mode 100644 sdk/go/arvados/tls_certs_test_showenv.go
create mode 100644 services/api/db/migrate/20230922000000_add_btree_name_index_to_collections_and_groups.rb
create mode 100644 services/api/db/migrate/20231013000000_compute_permission_index.rb
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