[ARVADOS] updated: 2.1.0-2037-gec3d70f72
Git user
git at public.arvados.org
Mon Mar 7 20:11:37 UTC 2022
Summary of changes:
.licenseignore | 3 +-
.../app/views/users/link_account.html.erb | 11 +-
build/run-library.sh | 6 +-
..._multi_host_install_custom_certificates.liquid} | 6 +-
doc/admin/link-accounts.html.textile.liquid | 2 +
doc/api/index.html.textile.liquid | 4 +
doc/install/salt-multi-host.html.textile.liquid | 4 +-
doc/install/salt-single-host.html.textile.liquid | 181 ++++++------
doc/install/salt.html.textile.liquid | 2 -
doc/sdk/python/cookbook.html.textile.liquid | 34 +++
doc/user/topics/link-accounts.html.textile.liquid | 2 +
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 | 136 +++++----
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/tests/test_vocabulary.py | 319 +++++++++++++++++++++
.../controllers/arvados/v1/schema_controller.rb | 23 +-
tools/salt-install/Vagrantfile | 13 +-
.../single_host/multiple_hostnames/states/dns.sls | 8 +-
.../single_hostname/pillars/arvados.sls | 34 ++-
.../single_hostname}/pillars/aws_credentials.sls | 0
.../single_host/single_hostname/pillars/docker.sls | 1 +
.../single_hostname}/pillars/letsencrypt.sls | 8 +-
.../pillars/nginx_api_configuration.sls | 12 +-
.../pillars/nginx_controller_configuration.sls | 14 +-
.../pillars/nginx_keepproxy_configuration.sls | 22 +-
.../pillars/nginx_keepweb_configuration.sls | 10 +-
.../single_hostname/pillars/nginx_passenger.sls | 14 +-
.../pillars/nginx_webshell_configuration.sls | 10 +-
.../pillars/nginx_websocket_configuration.sls | 10 +-
.../pillars/nginx_workbench2_configuration.sls | 32 ++-
.../pillars/nginx_workbench_configuration.sls | 34 ++-
.../single_hostname/pillars/postgresql.sls | 21 ++
.../single_hostname}/states/custom_certs.sls | 0
.../single_host/single_hostname/states/dns.sls | 8 +-
.../single_hostname/states/host_entries.sls | 11 +-
.../single_hostname/states/snakeoil_certs.sls | 101 +++----
.../local.params.example.multiple_hosts | 20 +-
...l.params.example.single_host_multiple_hostnames | 47 +--
...ocal.params.example.single_host_single_hostname | 70 +++--
tools/salt-install/provision.sh | 146 ++++++----
tools/salt-install/tests/run-test.sh | 4 -
58 files changed, 1393 insertions(+), 429 deletions(-)
rename doc/_includes/{_install_custom_certificates.liquid => _multi_host_install_custom_certificates.liquid} (57%)
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 build/package-testing/test-package-python3-cwltest.sh => tools/salt-install/config_examples/single_host/multiple_hostnames/states/dns.sls (65%)
mode change 100755 => 100644
copy tools/salt-install/config_examples/{multi_host/aws => single_host/single_hostname}/pillars/aws_credentials.sls (100%)
copy tools/salt-install/config_examples/{multi_host/aws => single_host/single_hostname}/pillars/letsencrypt.sls (78%)
copy tools/salt-install/config_examples/{multi_host/aws => single_host/single_hostname}/states/custom_certs.sls (100%)
copy build/package-testing/test-package-python3-cwltest.sh => tools/salt-install/config_examples/single_host/single_hostname/states/dns.sls (65%)
mode change 100755 => 100644
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commit ec3d70f727cf622db949b72d85cdb36504b07f13
Merge: 0d0161c65 0e2f3e506
Author: Ward Vandewege <ward at curii.com>
Date: Mon Mar 7 15:11:12 2022 -0500
18838: Merge branch 'main' into 18838-bump-nokogiri
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward at curii.com>
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