[ARVADOS] updated: 1.3.0-1480-g35658af99
Git user
git at public.curoverse.com
Mon Aug 12 14:36:53 UTC 2019
Summary of changes:
.../pipeline_instances_controller_test.rb | 103 -
.../test/controllers/projects_controller_test.rb | 26 -
.../test/helpers/repository_stub_helper.rb | 1 -
apps/workbench/test/integration/jobs_test.rb | 94 -
.../test/integration/pipeline_instances_test.rb | 369 ---
.../test/integration/pipeline_templates_test.rb | 29 -
apps/workbench/test/integration/projects_test.rb | 1 -
.../test/integration/repositories_browse_test.rb | 23 -
apps/workbench/test/integration/websockets_test.rb | 61 -
apps/workbench/test/integration/work_units_test.rb | 30 -
apps/workbench/test/unit/disabled_api_test.rb | 8 +-
build/run-build-packages.sh | 2 -
cmd/arvados-client/cmd.go | 16 +-
crunch_scripts/GATK2-VariantFiltration | 64 -
crunch_scripts/GATK2-bqsr | 103 -
crunch_scripts/GATK2-merge-call | 242 --
crunch_scripts/GATK2-realign | 163 --
crunch_scripts/arvados-bcbio-nextgen.py | 145 --
crunch_scripts/arvados_bwa.py | 115 -
crunch_scripts/arvados_gatk2.py | 52 -
crunch_scripts/arvados_ipc.py | 51 -
crunch_scripts/arvados_picard.py | 42 -
crunch_scripts/arvados_samtools.py | 110 -
crunch_scripts/bwa-aln | 127 -
crunch_scripts/bwa-index | 41 -
crunch_scripts/collection-merge | 49 -
crunch_scripts/crunchrunner | 10 -
crunch_scripts/crunchutil/__init__.py | 0
crunch_scripts/crunchutil/robust_put.py | 56 -
crunch_scripts/crunchutil/subst.py | 102 -
crunch_scripts/crunchutil/vwd.py | 107 -
crunch_scripts/cwl-runner | 117 -
crunch_scripts/decompress-all.py | 64 -
crunch_scripts/file-select | 18 -
crunch_scripts/grep | 24 -
crunch_scripts/hash | 37 -
crunch_scripts/pgp-survey-import | 119 -
crunch_scripts/pgp-survey-parse | 22 -
crunch_scripts/picard-gatk2-prep | 211 --
crunch_scripts/pyrtg.py | 75 -
crunch_scripts/rtg-fasta2sdf | 27 -
crunch_scripts/rtg-fastq2sdf | 45 -
crunch_scripts/rtg-map | 41 -
crunch_scripts/rtg-snp | 34 -
crunch_scripts/run-command | 458 ----
crunch_scripts/split-fastq.py | 70 -
crunch_scripts/test/task_output_dir | 19 -
doc/_config.yml | 22 +-
doc/_includes/_arv_run_redirection.liquid | 27 -
doc/admin/upgrading.html.textile.liquid | 10 +-
doc/api/crunch-scripts.html.textile.liquid | 2 +
doc/api/execution.html.textile.liquid | 7 -
doc/api/methods/humans.html.textile.liquid | 2 +
doc/api/methods/job_tasks.html.textile.liquid | 2 +
doc/api/methods/jobs.html.textile.liquid | 4 +-
.../methods/pipeline_instances.html.textile.liquid | 2 +
.../methods/pipeline_templates.html.textile.liquid | 2 +
doc/api/methods/specimens.html.textile.liquid | 2 +
doc/api/methods/traits.html.textile.liquid | 2 +
.../install-compute-node.html.textile.liquid | 112 -
.../install-crunch-dispatch.html.textile.liquid | 207 --
doc/sdk/cli/subcommands.html.textile.liquid | 95 -
.../crunch-utility-libraries.html.textile.liquid | 228 --
.../examples/crunch-examples.html.textile.liquid | 102 -
.../reference/job-pipeline-ref.html.textile.liquid | 14 -
doc/user/topics/arv-run.html.textile.liquid | 163 --
.../crunch-tools-overview.html.textile.liquid | 70 -
doc/user/topics/run-command.html.textile.liquid | 319 ---
...nning-pipeline-command-line.html.textile.liquid | 58 -
.../topics/tutorial-parallel.html.textile.liquid | 85 -
.../tutorial-trait-search.html.textile.liquid | 278 ---
.../running-external-program.html.textile.liquid | 85 -
.../tutorial-firstscript.html.textile.liquid | 112 -
.../tutorial-submit-job.html.textile.liquid | 95 -
lib/cli/external.go | 6 +-
lib/config/config.default.yml | 30 +-
lib/config/export.go | 5 -
lib/config/generated_config.go | 30 +-
sdk/cli/arvados-cli.gemspec | 6 +-
sdk/cli/bin/arv | 10 -
sdk/cli/bin/arv-crunch-job | 6 -
sdk/cli/bin/arv-run-pipeline-instance | 781 ------
sdk/cli/bin/crunch-job | 2577 --------------------
sdk/cli/test/test_arv-run-pipeline-instance.rb | 37 -
sdk/cli/test/test_crunch-job.rb | 141 --
sdk/cwl/tests/test_container.py | 2 -
sdk/go/arvados/config.go | 9 +-
sdk/go/arvadosclient/arvadosclient_test.go | 50 -
sdk/go/crunchrunner/crunchrunner.go | 439 ----
sdk/go/crunchrunner/crunchrunner_test.go | 478 ----
sdk/go/crunchrunner/upload.go | 241 --
sdk/go/crunchrunner/upload_test.go | 152 --
sdk/python/arvados/commands/run.py | 185 +-
sdk/python/bin/arv-run | 7 -
sdk/python/setup.py | 1 -
sdk/python/tests/test_arv_run.py | 28 -
sdk/python/tests/test_pipeline_template.py | 62 -
sdk/python/tests/test_retry_job_helpers.py | 31 -
.../controllers/arvados/v1/job_tasks_controller.rb | 5 +
.../app/controllers/arvados/v1/jobs_controller.rb | 104 +-
.../arvados/v1/pipeline_instances_controller.rb | 10 +-
.../arvados/v1/pipeline_templates_controller.rb | 5 +
.../api/app/helpers/commit_ancestors_helper.rb | 6 -
services/api/app/helpers/commits_helper.rb | 263 ++
services/api/app/models/commit.rb | 272 ---
services/api/app/models/commit_ancestor.rb | 44 -
services/api/app/models/job.rb | 214 +-
services/api/app/models/job_task.rb | 10 +
services/api/app/models/pipeline_instance.rb | 35 +-
services/api/app/models/pipeline_template.rb | 11 +
services/api/config/arvados_config.rb | 5 -
....rb => 20190808145904_drop_commit_ancestors.rb} | 4 +-
...s.rb => 20190809135453_remove_commits_table.rb} | 4 +-
services/api/db/structure.sql | 115 +-
services/api/lib/can_be_an_owner.rb | 2 +
services/api/lib/crunch_dispatch.rb | 981 --------
services/api/lib/enable_jobs_api.rb | 12 +
services/api/script/crunch-dispatch.rb | 20 +-
services/api/script/crunch_failure_report.py | 222 --
services/api/script/fail-jobs.rb | 21 -
.../arvados/v1/job_reuse_controller_test.rb | 702 ------
.../functional/arvados/v1/jobs_controller_test.rb | 307 +--
.../v1/pipeline_instances_controller_test.rb | 44 -
services/api/test/helpers/git_test_helper.rb | 8 +-
.../api/test/integration/crunch_dispatch_test.rb | 47 -
services/api/test/integration/jobs_api_test.rb | 83 -
services/api/test/integration/pipeline_test.rb | 36 -
.../test/integration/serialized_encoding_test.rb | 21 -
services/api/test/unit/commit_test.rb | 70 +-
services/api/test/unit/crunch_dispatch_test.rb | 218 --
services/api/test/unit/fail_jobs_test.rb | 83 -
services/api/test/unit/job_task_test.rb | 11 -
services/api/test/unit/job_test.rb | 406 +--
services/api/test/unit/pipeline_instance_test.rb | 106 -
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 2 +-
tools/arvbox/lib/arvbox/docker/crunch-setup.sh | 40 -
.../service/crunch-dispatch0/log/main/.gitstub | 0
.../arvbox/docker/service/crunch-dispatch0/log/run | 1 -
.../lib/arvbox/docker/service/crunch-dispatch0/run | 1 -
.../docker/service/crunch-dispatch0/run-service | 6 -
.../service/crunch-dispatch1/log/main/.gitstub | 0
.../arvbox/docker/service/crunch-dispatch1/log/run | 1 -
.../lib/arvbox/docker/service/crunch-dispatch1/run | 1 -
.../docker/service/crunch-dispatch1/run-service | 7 -
144 files changed, 480 insertions(+), 15230 deletions(-)
delete mode 100755 crunch_scripts/GATK2-VariantFiltration
delete mode 100755 crunch_scripts/GATK2-bqsr
delete mode 100755 crunch_scripts/GATK2-merge-call
delete mode 100755 crunch_scripts/GATK2-realign
delete mode 100755 crunch_scripts/arvados-bcbio-nextgen.py
delete mode 100644 crunch_scripts/arvados_bwa.py
delete mode 100644 crunch_scripts/arvados_gatk2.py
delete mode 100644 crunch_scripts/arvados_ipc.py
delete mode 100644 crunch_scripts/arvados_picard.py
delete mode 100644 crunch_scripts/arvados_samtools.py
delete mode 100755 crunch_scripts/bwa-aln
delete mode 100755 crunch_scripts/bwa-index
delete mode 100755 crunch_scripts/collection-merge
delete mode 100755 crunch_scripts/crunchrunner
delete mode 100644 crunch_scripts/crunchutil/__init__.py
delete mode 100644 crunch_scripts/crunchutil/robust_put.py
delete mode 100644 crunch_scripts/crunchutil/subst.py
delete mode 100644 crunch_scripts/crunchutil/vwd.py
delete mode 100755 crunch_scripts/cwl-runner
delete mode 100755 crunch_scripts/decompress-all.py
delete mode 100755 crunch_scripts/file-select
delete mode 100755 crunch_scripts/grep
delete mode 100755 crunch_scripts/hash
delete mode 100755 crunch_scripts/pgp-survey-import
delete mode 100755 crunch_scripts/pgp-survey-parse
delete mode 100755 crunch_scripts/picard-gatk2-prep
delete mode 100644 crunch_scripts/pyrtg.py
delete mode 100755 crunch_scripts/rtg-fasta2sdf
delete mode 100755 crunch_scripts/rtg-fastq2sdf
delete mode 100755 crunch_scripts/rtg-map
delete mode 100755 crunch_scripts/rtg-snp
delete mode 100755 crunch_scripts/run-command
delete mode 100755 crunch_scripts/split-fastq.py
delete mode 100755 crunch_scripts/test/task_output_dir
delete mode 100644 doc/_includes/_arv_run_redirection.liquid
delete mode 100644 doc/install/install-compute-node.html.textile.liquid
delete mode 100644 doc/install/install-crunch-dispatch.html.textile.liquid
delete mode 100644 doc/sdk/python/crunch-utility-libraries.html.textile.liquid
delete mode 100644 doc/user/examples/crunch-examples.html.textile.liquid
delete mode 100644 doc/user/reference/job-pipeline-ref.html.textile.liquid
delete mode 100644 doc/user/topics/arv-run.html.textile.liquid
delete mode 100644 doc/user/topics/crunch-tools-overview.html.textile.liquid
delete mode 100644 doc/user/topics/run-command.html.textile.liquid
delete mode 100644 doc/user/topics/running-pipeline-command-line.html.textile.liquid
delete mode 100644 doc/user/topics/tutorial-parallel.html.textile.liquid
delete mode 100644 doc/user/topics/tutorial-trait-search.html.textile.liquid
delete mode 100644 doc/user/tutorials/running-external-program.html.textile.liquid
delete mode 100644 doc/user/tutorials/tutorial-firstscript.html.textile.liquid
delete mode 100644 doc/user/tutorials/tutorial-submit-job.html.textile.liquid
delete mode 100755 sdk/cli/bin/arv-crunch-job
delete mode 100755 sdk/cli/bin/arv-run-pipeline-instance
delete mode 100755 sdk/cli/bin/crunch-job
delete mode 100644 sdk/cli/test/test_arv-run-pipeline-instance.rb
delete mode 100644 sdk/cli/test/test_crunch-job.rb
delete mode 100644 sdk/go/crunchrunner/crunchrunner.go
delete mode 100644 sdk/go/crunchrunner/crunchrunner_test.go
delete mode 100644 sdk/go/crunchrunner/upload.go
delete mode 100644 sdk/go/crunchrunner/upload_test.go
delete mode 100755 sdk/python/bin/arv-run
delete mode 100644 sdk/python/tests/test_arv_run.py
delete mode 100644 sdk/python/tests/test_pipeline_template.py
delete mode 100644 services/api/app/helpers/commit_ancestors_helper.rb
delete mode 100644 services/api/app/models/commit.rb
delete mode 100644 services/api/app/models/commit_ancestor.rb
copy services/api/db/migrate/{20130315183626_add_log_to_jobs.rb => 20190808145904_drop_commit_ancestors.rb} (57%)
copy services/api/db/migrate/{20130315183626_add_log_to_jobs.rb => 20190809135453_remove_commits_table.rb} (58%)
delete mode 100644 services/api/lib/crunch_dispatch.rb
delete mode 100755 services/api/script/crunch_failure_report.py
delete mode 100755 services/api/script/fail-jobs.rb
delete mode 100644 services/api/test/integration/crunch_dispatch_test.rb
delete mode 100644 services/api/test/unit/crunch_dispatch_test.rb
delete mode 100644 services/api/test/unit/fail_jobs_test.rb
delete mode 100755 tools/arvbox/lib/arvbox/docker/crunch-setup.sh
delete mode 100644 tools/arvbox/lib/arvbox/docker/service/crunch-dispatch0/log/main/.gitstub
delete mode 120000 tools/arvbox/lib/arvbox/docker/service/crunch-dispatch0/log/run
delete mode 120000 tools/arvbox/lib/arvbox/docker/service/crunch-dispatch0/run
delete mode 100755 tools/arvbox/lib/arvbox/docker/service/crunch-dispatch0/run-service
delete mode 100644 tools/arvbox/lib/arvbox/docker/service/crunch-dispatch1/log/main/.gitstub
delete mode 120000 tools/arvbox/lib/arvbox/docker/service/crunch-dispatch1/log/run
delete mode 120000 tools/arvbox/lib/arvbox/docker/service/crunch-dispatch1/run
delete mode 100755 tools/arvbox/lib/arvbox/docker/service/crunch-dispatch1/run-service
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commit 35658af99f09f2f6768583d65246429f789fc5a2
Merge: 9f912f75b d7a5e6e37
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Mon Aug 12 10:36:31 2019 -0400
Merge branch '15133-remove-jobs-api' refs #15133
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
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