[ARVADOS] updated: 2.1.0-2070-gf7bf9d696
Git user
git at public.arvados.org
Fri Mar 11 16:01:52 UTC 2022
Summary of changes:
.licenseignore | 3 +-
apps/workbench/Gemfile.lock | 98 +++----
build/package-build-dockerfiles/centos7/Dockerfile | 4 +-
.../package-build-dockerfiles/debian10/Dockerfile | 4 +-
.../package-build-dockerfiles/debian11/Dockerfile | 4 +-
.../ubuntu1804/Dockerfile | 4 +-
.../ubuntu2004/Dockerfile | 4 +-
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-test-packages-one-target.sh | 21 +-
doc/_includes/_install_ruby_and_bundler.liquid | 16 +-
doc/admin/upgrading.html.textile.liquid | 12 +-
doc/api/index.html.textile.liquid | 4 +
...nstall-manual-prerequisites.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 +
docker/jobs/Dockerfile | 4 +-
go.mod | 4 +-
go.sum | 7 +-
sdk/cwl/arvados_cwl/arv-cwl-schema-v1.0.yml | 34 ++-
sdk/cwl/arvados_cwl/arv-cwl-schema-v1.1.yml | 34 ++-
sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml | 34 ++-
sdk/cwl/arvados_cwl/arvcontainer.py | 4 +-
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 | 153 ++++++----
sdk/python/arvados/api.py | 1 +
sdk/python/arvados/commands/run.py | 2 +-
sdk/python/arvados/util.py | 8 +
sdk/python/arvados/vocabulary.py | 127 ++++++++
sdk/python/setup.py | 2 +-
sdk/python/tests/test_vocabulary.py | 319 +++++++++++++++++++++
services/api/Gemfile.lock | 98 +++----
.../controllers/arvados/v1/schema_controller.rb | 23 +-
tools/crunchstat-summary/setup.py | 7 +-
tools/salt-install/Vagrantfile | 1 +
.../multi_host/aws/pillars/arvados.sls | 3 +
.../multi_host/aws/pillars/nginx_passenger.sls | 2 +-
.../multiple_hostnames/pillars/arvados.sls | 2 +-
.../multiple_hostnames/pillars/nginx_passenger.sls | 2 +-
.../single_hostname/pillars/arvados.sls | 23 +-
.../pillars/nginx_api_configuration.sls | 8 +-
.../single_hostname/pillars/nginx_passenger.sls | 2 +-
.../pillars/nginx_workbench2_configuration.sls | 24 +-
.../pillars/nginx_workbench_configuration.sls | 22 +-
.../single_hostname/pillars/postgresql.sls | 21 ++
...ocal.params.example.single_host_single_hostname | 4 +-
tools/salt-install/provision.sh | 31 +-
62 files changed, 1173 insertions(+), 269 deletions(-)
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
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commit f7bf9d69603db2d500563648460e2a96524de266
Merge: 5cb2775f3 c56098048
Author: Tom Clegg <tom at curii.com>
Date: Fri Mar 11 11:01:30 2022 -0500
18600: Merge branch 'main'
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curii.com>
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