[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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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 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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