[ARVADOS] updated: 2.1.0-2160-ge4f8cfe36
Git user
git at public.arvados.org
Tue Mar 22 04:42:04 UTC 2022
Summary of changes:
.licenseignore | 3 +-
apps/workbench/Gemfile.lock | 98 +++----
.../build-all-build-containers.sh | 2 +-
build/package-build-dockerfiles/centos7/Dockerfile | 10 +-
.../package-build-dockerfiles/debian10/Dockerfile | 10 +-
.../package-build-dockerfiles/debian11/Dockerfile | 10 +-
.../ubuntu1804/Dockerfile | 10 +-
.../ubuntu2004/Dockerfile | 10 +-
build/package-test-dockerfiles/centos7/Dockerfile | 4 +-
build/package-test-dockerfiles/debian10/Dockerfile | 4 +-
build/package-test-dockerfiles/debian11/Dockerfile | 4 +-
.../package-test-dockerfiles/ubuntu1804/Dockerfile | 4 +-
.../package-test-dockerfiles/ubuntu2004/Dockerfile | 4 +-
.../test-package-python3-arvados-python-client.sh | 4 +-
build/run-build-packages-one-target.sh | 12 +-
build/run-build-test-packages-one-target.sh | 21 +-
build/run-library.sh | 6 +-
doc/_config.yml | 3 +-
doc/_includes/_install_ruby_and_bundler.liquid | 16 +-
doc/admin/spot-instances.html.textile.liquid | 19 +-
doc/admin/upgrading.html.textile.liquid | 12 +-
doc/api/index.html.textile.liquid | 4 +
doc/api/methods/collections.html.textile.liquid | 61 +++-
doc/api/methods/groups.html.textile.liquid | 11 +
doc/images/switch-to-wb1.png | Bin 0 -> 35755 bytes
doc/images/switch-to-wb2.png | Bin 0 -> 43350 bytes
doc/images/wb2-example.png | Bin 0 -> 227277 bytes
...nstall-manual-prerequisites.html.textile.liquid | 2 +-
doc/install/install-postgresql.html.textile.liquid | 2 +-
doc/install/salt-multi-host.html.textile.liquid | 3 +-
doc/sdk/python/cookbook.html.textile.liquid | 34 +++
doc/sdk/python/sdk-python.html.textile.liquid | 4 +
doc/user/cwl/cwl-extensions.html.textile.liquid | 11 +
doc/user/cwl/cwl-run-options.html.textile.liquid | 19 ++
doc/user/cwl/cwl-style.html.textile.liquid | 43 ++-
.../getting_started/workbench.html.textile.liquid | 4 +-
.../topics/workbench-migration.html.textile.liquid | 49 ++++
docker/jobs/Dockerfile | 4 +-
go.mod | 4 +-
go.sum | 7 +-
lib/config/config.default.yml | 17 +-
lib/config/export.go | 3 +
lib/controller/handler_test.go | 16 +-
lib/controller/localdb/collection.go | 157 ++++++++++
lib/controller/localdb/collection_test.go | 204 +++++++++++--
lib/controller/router/response.go | 2 +-
lib/crunchrun/crunchrun.go | 29 ++
lib/crunchrun/crunchrun_test.go | 1 +
lib/install/deps.go | 87 +++---
sdk/cli/test/test_arv-collection-create.rb | 69 +++--
sdk/cwl/arvados_cwl/__init__.py | 7 +-
sdk/cwl/arvados_cwl/arv-cwl-schema-v1.0.yml | 49 +++-
sdk/cwl/arvados_cwl/arv-cwl-schema-v1.1.yml | 49 +++-
sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml | 49 +++-
sdk/cwl/arvados_cwl/arvcontainer.py | 21 +-
sdk/cwl/arvados_cwl/context.py | 1 +
sdk/cwl/arvados_cwl/runner.py | 5 +-
sdk/cwl/setup.py | 2 +-
.../DATEST/ChIP-Seq/Raw/fastq/Input_R1.fastq.gz | 0
.../DATEST/ChIP-Seq/Raw/fastq/Input_R2.fastq.gz | 0
.../DATEST/ChIP-Seq/Raw/fastq/Input_R3.fastq.gz | 0
sdk/cwl/tests/chipseq/chip-seq-single.json | 99 +++++++
sdk/cwl/tests/chipseq/cwl-packed.json | 94 ++++++
.../Genomes/Blacklist/lists2/hg38-blacklist.v2.bed | 0
.../dmel_r6.16/Bowtie2Index/genome.fa | 0
.../dmel_r6.16/WholeGenome/genome.fa | 0
.../Homo_sapiens/GRCh38.p2/Bowtie2Index/genome.fa | 0
.../Homo_sapiens/GRCh38.p2/WholeGenome/genome.fa | 0
sdk/cwl/tests/test_container.py | 250 ++++++++++++----
sdk/cwl/tests/test_submit.py | 43 +++
sdk/go/arvados/api.go | 4 +
sdk/go/arvados/config.go | 33 ++-
sdk/go/arvados/fs_backend.go | 14 +
sdk/go/arvados/fs_base.go | 21 +-
sdk/go/arvados/fs_collection.go | 4 +-
sdk/go/arvados/fs_collection_test.go | 24 ++
sdk/go/arvados/fs_filehandle.go | 26 ++
sdk/go/arvados/fs_site_test.go | 60 ++--
sdk/go/arvados/group.go | 1 +
sdk/go/httpserver/error.go | 5 +
sdk/python/arvados/api.py | 1 +
sdk/python/arvados/commands/run.py | 2 +-
sdk/python/arvados/keep.py | 2 +
sdk/python/arvados/util.py | 8 +
sdk/python/arvados/vocabulary.py | 127 ++++++++
sdk/python/setup.py | 2 +-
sdk/python/tests/test_keep_client.py | 6 +
sdk/python/tests/test_vocabulary.py | 319 +++++++++++++++++++++
services/api/Gemfile | 2 -
services/api/Gemfile.lock | 115 ++++----
.../controllers/arvados/v1/schema_controller.rb | 37 ++-
services/api/app/models/arvados_model.rb | 68 +++--
.../frozen_group.rb} | 2 +-
services/api/app/models/group.rb | 160 ++++++++---
services/api/app/models/user.rb | 18 ++
...20220224203102_add_frozen_by_uuid_to_groups.rb} | 4 +-
.../api/db/migrate/20220301155729_frozen_groups.rb | 39 +++
...419_add_frozen_by_uuid_to_group_search_index.rb | 17 ++
services/api/db/structure.sql | 44 ++-
.../20200501150153_permission_table_constants.rb | 20 +-
.../api/lib/tasks/delete_old_container_logs.rake | 2 +-
services/api/lib/tasks/delete_old_job_logs.rake | 16 --
services/api/lib/tasks/symbols.rake | 114 --------
.../arvados/v1/groups_controller_test.rb | 20 ++
.../api/test/tasks/delete_old_job_logs_test.rb | 54 ----
services/api/test/unit/group_test.rb | 215 ++++++++++++++
services/api/test/unit/permission_test.rb | 13 +
tools/arvbash/arvbash.sh | 27 +-
tools/arvbox/lib/arvbox/docker/createusers.sh | 10 +-
tools/arvbox/lib/arvbox/docker/go-setup.sh | 1 +
tools/compute-images/arvados-images-aws.json | 4 +-
tools/compute-images/scripts/base.sh | 92 +++---
tools/crunchstat-summary/setup.py | 7 +-
tools/salt-install/Vagrantfile | 18 +-
.../multi_host/aws/pillars/arvados.sls | 3 +
.../multi_host/aws/pillars/nginx_passenger.sls | 10 +-
.../multi_host/aws/pillars/postgresql.sls | 2 +-
.../multiple_hostnames/pillars/arvados.sls | 2 +-
.../multiple_hostnames/pillars/nginx_passenger.sls | 10 +-
.../single_hostname/pillars/arvados.sls | 23 +-
.../pillars/nginx_api_configuration.sls | 8 +-
.../single_hostname/pillars/nginx_passenger.sls | 10 +-
.../pillars/nginx_workbench2_configuration.sls | 24 +-
.../pillars/nginx_workbench_configuration.sls | 22 +-
.../single_hostname/pillars/postgresql.sls | 21 ++
.../local.params.example.multiple_hosts | 6 +-
...l.params.example.single_host_multiple_hostnames | 6 +-
...ocal.params.example.single_host_single_hostname | 6 +-
tools/salt-install/provision.sh | 95 +++---
129 files changed, 2984 insertions(+), 824 deletions(-)
create mode 100644 doc/images/switch-to-wb1.png
create mode 100644 doc/images/switch-to-wb2.png
create mode 100644 doc/images/wb2-example.png
create mode 100644 doc/user/topics/workbench-migration.html.textile.liquid
copy apps/workbench/app/mailers/.gitkeep => sdk/cwl/tests/chipseq/DATEST/ChIP-Seq/Raw/fastq/Input_R1.fastq.gz (100%)
copy apps/workbench/app/mailers/.gitkeep => sdk/cwl/tests/chipseq/DATEST/ChIP-Seq/Raw/fastq/Input_R2.fastq.gz (100%)
copy apps/workbench/app/mailers/.gitkeep => sdk/cwl/tests/chipseq/DATEST/ChIP-Seq/Raw/fastq/Input_R3.fastq.gz (100%)
create mode 100644 sdk/cwl/tests/chipseq/chip-seq-single.json
create mode 100644 sdk/cwl/tests/chipseq/cwl-packed.json
copy apps/workbench/app/mailers/.gitkeep => sdk/cwl/tests/chipseq/data/Genomes/Blacklist/lists2/hg38-blacklist.v2.bed (100%)
copy apps/workbench/app/mailers/.gitkeep => sdk/cwl/tests/chipseq/data/Genomes/Drosophila_melanogaster/dmel_r6.16/Bowtie2Index/genome.fa (100%)
copy apps/workbench/app/mailers/.gitkeep => sdk/cwl/tests/chipseq/data/Genomes/Drosophila_melanogaster/dmel_r6.16/WholeGenome/genome.fa (100%)
copy apps/workbench/app/mailers/.gitkeep => sdk/cwl/tests/chipseq/data/Genomes/Homo_sapiens/GRCh38.p2/Bowtie2Index/genome.fa (100%)
copy apps/workbench/app/mailers/.gitkeep => sdk/cwl/tests/chipseq/data/Genomes/Homo_sapiens/GRCh38.p2/WholeGenome/genome.fa (100%)
create mode 100644 sdk/python/arvados/vocabulary.py
create mode 100644 sdk/python/tests/test_vocabulary.py
copy services/api/app/{helpers/api_client_authorizations_helper.rb => models/frozen_group.rb} (72%)
copy services/api/db/migrate/{20130107181109_add_uuid_to_collections.rb => 20220224203102_add_frozen_by_uuid_to_groups.rb} (52%)
create mode 100644 services/api/db/migrate/20220301155729_frozen_groups.rb
create mode 100644 services/api/db/migrate/20220303204419_add_frozen_by_uuid_to_group_search_index.rb
delete mode 100644 services/api/lib/tasks/delete_old_job_logs.rake
delete mode 100644 services/api/lib/tasks/symbols.rake
delete mode 100644 services/api/test/tasks/delete_old_job_logs_test.rb
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Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit e4f8cfe369d669444873ded465d6196d3d1ad5a8
Author: Tom Clegg <tom at curii.com>
Date: Tue Mar 22 00:31:19 2022 -0400
18700: Bump workbench2 version.
Use current main, now that yarn3 is merged.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curii.com>
diff --git a/lib/install/deps.go b/lib/install/deps.go
index d4c43aec4..44e46eec4 100644
--- a/lib/install/deps.go
+++ b/lib/install/deps.go
@@ -39,7 +39,7 @@ const (
gradleversion = "5.3.1"
nodejsversion = "v12.22.11"
devtestDatabasePassword = "insecure_arvados_test"
- workbench2version = "cfa81dfc3041cb459c8a0918a2732dfcf3a11d40"
+ workbench2version = "5e020488f67b5bc919796e0dc8b0b9f3b3ff23b0"
)
type installCommand struct {
commit 007b96e9e3acddf01cd9bf441191690c88a22ce8
Author: Tom Clegg <tom at curii.com>
Date: Tue Mar 22 00:21:09 2022 -0400
18700: Omit test/development gems from package.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curii.com>
diff --git a/lib/install/deps.go b/lib/install/deps.go
index b5e4f214d..d4c43aec4 100644
--- a/lib/install/deps.go
+++ b/lib/install/deps.go
@@ -575,7 +575,7 @@ yarn install
{"touch", "log/production.log"},
{"chown", "-R", "--from=root", "www-data:www-data", "/var/www/.gem", "/var/www/.bundle", "/var/www/.passenger", "log", "tmp", ".bundle", "Gemfile.lock", "config.ru", "config/environment.rb"},
{"sudo", "-u", "www-data", "/var/lib/arvados/bin/gem", "install", "--user", "--conservative", "--no-document", "bundler:" + bundlerversion},
- {"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "install", "--deployment", "--jobs", "8", "--path", "/var/www/.gem"},
+ {"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "install", "--deployment", "--jobs", "8", "--path", "/var/www/.gem", "--without", "development test diagnostics performance"},
{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "build-native-support"},
{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "install-standalone-runtime"},
} {
commit 25d749c17c4c0fe654de48dd299d357e3f5808d7
Author: Tom Clegg <tom at curii.com>
Date: Tue Mar 22 00:13:13 2022 -0400
18700: Bump nodejs version.
https://nodejs.org/en/blog/vulnerability/mar-2022-security-releases/
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curii.com>
diff --git a/lib/install/deps.go b/lib/install/deps.go
index 4e5927339..b5e4f214d 100644
--- a/lib/install/deps.go
+++ b/lib/install/deps.go
@@ -37,7 +37,7 @@ const (
pjsversion = "1.9.8"
geckoversion = "0.24.0"
gradleversion = "5.3.1"
- nodejsversion = "v12.22.2"
+ nodejsversion = "v12.22.11"
devtestDatabasePassword = "insecure_arvados_test"
workbench2version = "cfa81dfc3041cb459c8a0918a2732dfcf3a11d40"
)
commit 4453efa68d2f9a7d34b545f0ac7752b16f05a0e4
Author: Tom Clegg <tom at curii.com>
Date: Tue Mar 22 00:12:05 2022 -0400
18700: Const for bundler version.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curii.com>
diff --git a/lib/install/deps.go b/lib/install/deps.go
index ec1eb1957..4e5927339 100644
--- a/lib/install/deps.go
+++ b/lib/install/deps.go
@@ -32,6 +32,7 @@ const goversion = "1.17.7"
const (
rubyversion = "2.7.5"
+ bundlerversion = "2.2.19"
singularityversion = "3.7.4"
pjsversion = "1.9.8"
geckoversion = "0.24.0"
@@ -573,7 +574,7 @@ yarn install
{"mkdir", "-p", "log", "tmp", ".bundle", "/var/www/.gem", "/var/www/.bundle", "/var/www/.passenger"},
{"touch", "log/production.log"},
{"chown", "-R", "--from=root", "www-data:www-data", "/var/www/.gem", "/var/www/.bundle", "/var/www/.passenger", "log", "tmp", ".bundle", "Gemfile.lock", "config.ru", "config/environment.rb"},
- {"sudo", "-u", "www-data", "/var/lib/arvados/bin/gem", "install", "--user", "--conservative", "--no-document", "bundler:2.2.19"},
+ {"sudo", "-u", "www-data", "/var/lib/arvados/bin/gem", "install", "--user", "--conservative", "--no-document", "bundler:" + bundlerversion},
{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "install", "--deployment", "--jobs", "8", "--path", "/var/www/.gem"},
{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "build-native-support"},
{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "install-standalone-runtime"},
commit 7000c1ebd170001e10807b583a29e9e7e9570b23
Merge: 0a40a8007 44c93373e
Author: Tom Clegg <tom at curii.com>
Date: Mon Mar 21 10:38:28 2022 -0400
18700: Merge branch 'main'
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curii.com>
commit 0a40a80076a616f3bd79c863c212bfbb22f775fa
Author: Tom Clegg <tom at curii.com>
Date: Thu Mar 17 01:09:41 2022 -0400
18700: Build faster deps first.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curii.com>
diff --git a/lib/install/deps.go b/lib/install/deps.go
index 70774b313..ec1eb1957 100644
--- a/lib/install/deps.go
+++ b/lib/install/deps.go
@@ -512,12 +512,39 @@ yarn install
}
if prod || pkg {
- // Install workbench2 app to /var/lib/arvados/workbench2/
- if err = inst.runBash(`
-cd /var/lib/arvados/arvados-workbench2
-VERSION="`+inst.PackageVersion+`" BUILD_NUMBER=1 GIT_COMMIT="`+workbench2version+`" yarn build
-rsync -a --delete-after build/ /var/lib/arvados/workbench2/
-`, stdout, stderr); err != nil {
+ // Install Go programs to /var/lib/arvados/bin/
+ for _, srcdir := range []string{
+ "cmd/arvados-client",
+ "cmd/arvados-server",
+ "services/arv-git-httpd",
+ "services/crunch-dispatch-local",
+ "services/crunch-dispatch-slurm",
+ "services/health",
+ "services/keep-balance",
+ "services/keep-web",
+ "services/keepproxy",
+ "services/keepstore",
+ "services/ws",
+ } {
+ fmt.Fprintf(stderr, "building %s...\n", srcdir)
+ cmd := exec.Command("go", "install", "-ldflags", "-X git.arvados.org/arvados.git/lib/cmd.version="+inst.PackageVersion+" -X main.version="+inst.PackageVersion+" -s -w")
+ cmd.Env = append(cmd.Env, os.Environ()...)
+ cmd.Env = append(cmd.Env, "GOBIN=/var/lib/arvados/bin")
+ cmd.Dir = filepath.Join(inst.SourcePath, srcdir)
+ cmd.Stdout = stdout
+ cmd.Stderr = stderr
+ err = cmd.Run()
+ if err != nil {
+ return 1
+ }
+ }
+
+ // Copy assets from source tree to /var/lib/arvados/share
+ cmd := exec.Command("install", "-v", "-t", "/var/lib/arvados/share", filepath.Join(inst.SourcePath, "sdk/python/tests/nginx.conf"))
+ cmd.Stdout = stdout
+ cmd.Stderr = stderr
+ err = cmd.Run()
+ if err != nil {
return 1
}
@@ -575,39 +602,12 @@ rsync -a --delete-after build/ /var/lib/arvados/workbench2/
}
}
- // Install Go programs to /var/lib/arvados/bin/
- for _, srcdir := range []string{
- "cmd/arvados-client",
- "cmd/arvados-server",
- "services/arv-git-httpd",
- "services/crunch-dispatch-local",
- "services/crunch-dispatch-slurm",
- "services/health",
- "services/keep-balance",
- "services/keep-web",
- "services/keepproxy",
- "services/keepstore",
- "services/ws",
- } {
- fmt.Fprintf(stderr, "building %s...\n", srcdir)
- cmd := exec.Command("go", "install", "-ldflags", "-X git.arvados.org/arvados.git/lib/cmd.version="+inst.PackageVersion+" -X main.version="+inst.PackageVersion+" -s -w")
- cmd.Env = append(cmd.Env, os.Environ()...)
- cmd.Env = append(cmd.Env, "GOBIN=/var/lib/arvados/bin")
- cmd.Dir = filepath.Join(inst.SourcePath, srcdir)
- cmd.Stdout = stdout
- cmd.Stderr = stderr
- err = cmd.Run()
- if err != nil {
- return 1
- }
- }
-
- // Copy assets from source tree to /var/lib/arvados/share
- cmd := exec.Command("install", "-v", "-t", "/var/lib/arvados/share", filepath.Join(inst.SourcePath, "sdk/python/tests/nginx.conf"))
- cmd.Stdout = stdout
- cmd.Stderr = stderr
- err = cmd.Run()
- if err != nil {
+ // Install workbench2 app to /var/lib/arvados/workbench2/
+ if err = inst.runBash(`
+cd /var/lib/arvados/arvados-workbench2
+VERSION="`+inst.PackageVersion+`" BUILD_NUMBER=1 GIT_COMMIT="`+workbench2version[:9]+`" yarn build
+rsync -a --delete-after build/ /var/lib/arvados/workbench2/
+`, stdout, stderr); err != nil {
return 1
}
}
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