[ARVADOS] updated: 1.3.0-1389-g83ee4d3eb
Git user
git at public.curoverse.com
Mon Jul 22 17:07:37 UTC 2019
Summary of changes:
.../app/controllers/collections_controller.rb | 4 +-
.../controllers/container_requests_controller.rb | 31 ++--
apps/workbench/app/controllers/jobs_controller.rb | 1 -
.../controllers/pipeline_instances_controller.rb | 1 -
apps/workbench/app/helpers/provenance_helper.rb | 136 ++++++++++------
build/package-build-dockerfiles/Makefile | 10 +-
build/package-build-dockerfiles/debian8/Dockerfile | 43 -----
.../ubuntu1404/Dockerfile | 42 -----
build/package-test-dockerfiles/Makefile | 10 +-
build/package-test-dockerfiles/debian8/Dockerfile | 28 ----
.../package-test-dockerfiles/ubuntu1404/Dockerfile | 26 ---
build/run-build-packages-one-target.sh | 7 +-
build/run-build-packages.sh | 4 +-
build/run-library.sh | 2 -
build/run-tests.sh | 42 +++--
cmd/arvados-client/cmd.go | 9 +-
cmd/arvados-server/cmd.go | 7 +-
doc/_config.yml | 10 +-
doc/_includes/_what_is_cwl.liquid | 2 +-
doc/admin/config-migration.html.textile.liquid | 8 +-
doc/admin/troubleshooting.html.textile.liquid | 74 +++++++++
doc/api/methods/collections.html.textile.liquid | 33 ++++
doc/api/methods/groups.html.textile.liquid | 28 ++--
doc/install/install-api-server.html.textile.liquid | 4 +
...nstall-manual-prerequisites.html.textile.liquid | 10 +-
.../install-nodemanager.html.textile.liquid | 2 +-
doc/user/composer/composer.html.textile.liquid | 2 +-
doc/user/cwl/cwl-extensions.html.textile.liquid | 93 ++++++-----
doc/user/cwl/cwl-style.html.textile.liquid | 161 +++++++++---------
doc/user/cwl/cwl-versions.html.textile.liquid | 34 ++++
doc/user/topics/arv-docker.html.textile.liquid | 78 ++-------
.../writing-cwl-workflow.html.textile.liquid | 8 +-
lib/cloud/cloudtest/cmd.go | 4 +-
lib/cmd/cmd.go | 13 +-
lib/config/cmd.go | 75 ++++-----
lib/config/cmd_test.go | 46 +++++-
lib/config/config.default.yml | 26 ++-
lib/config/deprecated.go | 51 +++++-
lib/config/export_test.go | 5 +-
lib/config/generated_config.go | 26 ++-
lib/config/load.go | 158 ++++++++++++++----
lib/config/load_test.go | 179 ++++++++++++++++++---
lib/controller/federation/list.go | 24 +--
lib/controller/federation_test.go | 6 +-
lib/dispatchcloud/container/queue_test.go | 2 +-
lib/service/cmd.go | 16 +-
sdk/go/arvados/config.go | 27 +++-
sdk/python/tests/run_test_server.py | 49 +++---
.../api/app/controllers/application_controller.rb | 12 +-
.../arvados/v1/collections_controller.rb | 112 ++++++++++---
.../controllers/arvados/v1/groups_controller.rb | 3 +
services/api/config/initializers/lograge.rb | 15 ++
.../test/functional/application_controller_test.rb | 19 ++-
.../arvados/v1/schema_controller_test.rb | 2 +-
.../api/test/integration/login_workflow_test.rb | 8 +-
services/fuse/arvados_fuse/__init__.py | 49 +++---
services/fuse/arvados_fuse/command.py | 11 +-
services/fuse/arvados_fuse/crunchstat.py | 12 +-
services/fuse/arvados_fuse/fresh.py | 1 +
services/fuse/arvados_fuse/fusedir.py | 21 ++-
services/fuse/arvados_fuse/fusefile.py | 6 +-
services/fuse/setup.py | 8 +-
services/fuse/tests/fstest.py | 64 ++++----
services/fuse/tests/integration_test.py | 3 +-
services/fuse/tests/mount_test_base.py | 5 +-
.../performance/test_collection_performance.py | 8 +-
services/fuse/tests/prof.py | 6 +-
services/fuse/tests/test_cache.py | 1 +
services/fuse/tests/test_command_args.py | 45 ++++--
services/fuse/tests/test_crunchstat.py | 5 +-
services/fuse/tests/test_exec.py | 12 +-
services/fuse/tests/test_mount.py | 78 ++++-----
services/fuse/tests/test_mount_type.py | 2 +-
services/fuse/tests/test_retry.py | 9 +-
services/fuse/tests/test_tmp_collection.py | 14 +-
services/fuse/tests/test_token_expiry.py | 7 +-
services/fuse/tests/test_unmount.py | 9 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 8 +-
tools/arvbox/lib/arvbox/docker/api-setup.sh | 1 +
.../{service/controller/run => cluster-config.sh} | 15 +-
tools/arvbox/lib/arvbox/docker/common.sh | 5 +
tools/arvbox/lib/arvbox/docker/createusers.sh | 2 +
.../lib/arvbox/docker/service/certificate/run | 29 ++--
.../lib/arvbox/docker/service/controller/run | 82 +---------
tools/arvbox/lib/arvbox/docker/service/nginx/run | 18 ++-
.../lib/arvbox/docker/service/sso/run-service | 2 +-
.../arvbox/lib/arvbox/docker/service/workbench/run | 1 +
87 files changed, 1449 insertions(+), 918 deletions(-)
delete mode 100644 build/package-build-dockerfiles/debian8/Dockerfile
delete mode 100644 build/package-build-dockerfiles/ubuntu1404/Dockerfile
delete mode 100644 build/package-test-dockerfiles/debian8/Dockerfile
delete mode 100644 build/package-test-dockerfiles/ubuntu1404/Dockerfile
create mode 100644 doc/admin/troubleshooting.html.textile.liquid
create mode 100644 doc/user/cwl/cwl-versions.html.textile.liquid
copy tools/arvbox/lib/arvbox/docker/{service/controller/run => cluster-config.sh} (92%)
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commit 83ee4d3ebf739f8aad67cf8faea093fc71d24d01
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date: Mon Jul 22 13:05:35 2019 -0400
14287: Comment multi-dimensional map.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>
diff --git a/lib/controller/federation/list.go b/lib/controller/federation/list.go
index 43ed2cdba..124946de0 100644
--- a/lib/controller/federation/list.go
+++ b/lib/controller/federation/list.go
@@ -140,6 +140,11 @@ func (conn *Conn) splitListRequest(ctx context.Context, opts arvados.ListOptions
}
}
+ // Collate UUIDs in matchAllFilters by remote cluster ID --
+ // e.g., todoByRemote["aaaaa"]["aaaaa-4zz18-000000000000000"]
+ // will be true -- and count the total number of UUIDs we're
+ // filtering on, so we can compare it to our max page size
+ // limit.
nUUIDs := 0
todoByRemote := map[string]map[string]bool{}
for uuid := range matchAllFilters {
commit bd857c2152f66bc17745edcc5a7a88377024ff43
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date: Mon Jul 22 13:05:01 2019 -0400
14287: Fix comment that looked too much like real code.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>
diff --git a/lib/controller/federation/list.go b/lib/controller/federation/list.go
index 4843baa5c..43ed2cdba 100644
--- a/lib/controller/federation/list.go
+++ b/lib/controller/federation/list.go
@@ -130,7 +130,8 @@ func (conn *Conn) splitListRequest(ctx context.Context, opts arvados.ListOptions
if matchAllFilters == nil {
matchAllFilters = matchThisFilter
} else {
- // matchAllFilters = intersect(matchAllFilters, matchThisFilter)
+ // Reduce matchAllFilters to the intersection
+ // of matchAllFilters ∩ matchThisFilter.
for uuid := range matchAllFilters {
if !matchThisFilter[uuid] {
delete(matchAllFilters, uuid)
commit 57c70faf4f31c619984b17331b636f941c84ea05
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date: Mon Jul 22 13:04:07 2019 -0400
14287: Clarify use of separate variables in goroutine.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>
diff --git a/lib/controller/federation/list.go b/lib/controller/federation/list.go
index 5a171c9c3..4843baa5c 100644
--- a/lib/controller/federation/list.go
+++ b/lib/controller/federation/list.go
@@ -181,14 +181,14 @@ func (conn *Conn) splitListRequest(ctx context.Context, opts arvados.ListOptions
defer cancel()
errs := make(chan error, len(todoByRemote))
for clusterID, todo := range todoByRemote {
- clusterID, todo := clusterID, todo
- batch := make([]string, 0, len(todo))
- for uuid := range todo {
- batch = append(batch, uuid)
- }
- go func() {
+ go func(clusterID string, todo map[string]bool) {
// This goroutine sends exactly one value to
// errs.
+ batch := make([]string, 0, len(todo))
+ for uuid := range todo {
+ batch = append(batch, uuid)
+ }
+
var backend arvados.API
if clusterID == conn.cluster.ClusterID {
backend = conn.local
@@ -225,13 +225,13 @@ func (conn *Conn) splitListRequest(ctx context.Context, opts arvados.ListOptions
}
}
errs <- nil
- }()
+ }(clusterID, todo)
}
// Wait for all goroutines to return, then return the first
// non-nil error, if any.
var firstErr error
- for i := 0; i < len(todoByRemote); i++ {
+ for range todoByRemote {
if err := <-errs; err != nil && firstErr == nil {
firstErr = err
// Signal to any remaining fn() calls that
commit 91cd750b78b39195b0e8f3328a3e7f34484172a3
Merge: b3a016e9a c1cf71ba7
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date: Mon Jul 22 11:25:03 2019 -0400
14287: Merge branch 'master'
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>
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