[ARVADOS] updated: ebb2559b3a09636ff687316bbe512e0e8a86b168
Git user
git at public.curoverse.com
Wed Dec 21 10:08:54 EST 2016
Summary of changes:
.../controllers/container_requests_controller.rb | 28 +
.../controllers/pipeline_instances_controller.rb | 2 +-
.../application/_extra_tab_line_buttons.html.erb | 0
.../views/application/_title_and_buttons.html.erb | 3 +
.../_extra_tab_line_buttons.html.erb | 10 +
apps/workbench/config/application.default.yml | 5 +
apps/workbench/config/routes.rb | 1 +
apps/workbench/lib/tasks/config_dump.rake | 6 +
.../container_requests_controller_test.rb | 27 +
.../test/diagnostics/container_request_test.rb | 49 ++
apps/workbench/test/diagnostics/pipeline_test.rb | 45 +-
apps/workbench/test/diagnostics_test_helper.rb | 43 +
build/libcloud-pin | 2 +-
build/run-build-packages-one-target.sh | 1 -
build/run-build-packages.sh | 11 +-
build/run-tests.sh | 16 +-
doc/_config.yml | 10 +-
doc/_includes/_register_cwl_workflow.liquid | 21 -
doc/install/install-ws.html.textile.liquid | 204 +++++
doc/user/cwl/cwl-extensions.html.textile.liquid | 56 ++
.../cwl/cwl-run-options.html.textile.liquid} | 44 +-
doc/user/cwl/cwl-runner.html.textile.liquid | 206 ++---
doc/user/cwl/cwl-style.html.textile.liquid | 2 +
.../examples/crunch-examples.html.textile.liquid | 2 +
.../getting_started/workbench.html.textile.liquid | 2 +-
.../reference/job-pipeline-ref.html.textile.liquid | 2 +
doc/user/topics/arv-docker.html.textile.liquid | 12 +-
doc/user/topics/run-command.html.textile.liquid | 2 +
...nning-pipeline-command-line.html.textile.liquid | 2 +-
...nning-workflow-command-line.html.textile.liquid | 17 -
.../running-external-program.html.textile.liquid | 2 +-
.../tutorial-submit-job.html.textile.liquid | 2 +-
.../writing-cwl-workflow.html.textile.liquid | 186 ++++-
sdk/cli/test/test_arv-keep-put.rb | 8 +-
sdk/cwl/arvados_cwl/__init__.py | 28 +-
sdk/cwl/arvados_cwl/arvcontainer.py | 102 ++-
sdk/cwl/arvados_cwl/arvjob.py | 15 +-
sdk/cwl/arvados_cwl/crunch_script.py | 1 +
sdk/cwl/arvados_cwl/fsaccess.py | 84 ++
sdk/cwl/arvados_cwl/pathmapper.py | 2 +
sdk/cwl/arvados_cwl/runner.py | 12 +-
sdk/cwl/setup.py | 7 +-
sdk/cwl/tests/test_container.py | 12 +-
sdk/cwl/tests/test_job.py | 31 +-
sdk/cwl/tests/test_submit.py | 212 ++++-
sdk/cwl/tests/test_urljoin.py | 56 ++
sdk/cwl/tests/wf/expect_arvworkflow.cwl | 24 +
sdk/cwl/tests/wf/expect_packed.cwl | 2 +-
.../wf/{submit_wf.cwl => submit_keepref_wf.cwl} | 13 +-
sdk/dev-jobs.dockerfile | 2 +-
sdk/go/arvados/client.go | 97 ++-
sdk/go/arvados/log.go | 25 +
sdk/go/arvadosclient/arvadosclient.go | 43 +-
sdk/go/config/load.go | 5 +
sdk/go/crunchrunner/crunchrunner.go | 20 -
sdk/go/ctxlog/log.go | 59 ++
sdk/go/keepclient/keepclient.go | 3 +-
sdk/go/logger/logger.go | 204 -----
sdk/go/logger/util.go | 20 -
sdk/go/stats/duration.go | 35 +
sdk/go/stats/duration_test.go | 23 +
sdk/go/util/util.go | 34 -
sdk/python/arvados/arvfile.py | 8 +
sdk/python/arvados/collection.py | 13 +-
sdk/python/arvados/commands/put.py | 492 ++++++++----
sdk/python/arvados/keep.py | 4 +-
sdk/python/arvados/util.py | 2 +
sdk/python/setup.py | 1 -
sdk/python/tests/nginx.conf | 16 +
sdk/python/tests/run_test_server.py | 71 +-
sdk/python/tests/test_arv_put.py | 155 +++-
sdk/python/tests/test_arvfile.py | 21 +
sdk/python/tests/test_collections.py | 2 +
sdk/python/tests/test_events.py | 29 +-
services/api/app/models/arvados_model.rb | 7 +-
services/api/app/models/job.rb | 4 +
services/api/config/application.default.yml | 1 +
.../20161213172944_full_text_search_indexes.rb | 32 +
services/api/db/structure.sql | 18 +-
services/api/lib/tasks/config_dump.rake | 6 +
services/crunch-run/crunchrun.go | 19 +
services/crunch-run/crunchrun_test.go | 34 +-
services/datamanager/collection/collection.go | 408 ----------
services/datamanager/collection/collection_test.go | 202 -----
services/datamanager/collection/testing.go | 61 --
services/datamanager/datamanager.go | 220 -----
services/datamanager/datamanager_test.go | 732 -----------------
services/datamanager/experimental/datamanager.py | 887 ---------------------
.../datamanager/experimental/datamanager_test.py | 41 -
services/datamanager/keep/keep.go | 551 -------------
services/datamanager/keep/keep_test.go | 278 -------
services/datamanager/loggerutil/loggerutil.go | 52 --
services/datamanager/summary/canonical_string.go | 30 -
services/datamanager/summary/file.go | 115 ---
services/datamanager/summary/pull_list.go | 215 -----
services/datamanager/summary/pull_list_test.go | 272 -------
services/datamanager/summary/summary.go | 277 -------
services/datamanager/summary/summary_test.go | 220 -----
services/datamanager/summary/trash_list.go | 62 --
services/datamanager/summary/trash_list_test.go | 76 --
services/fuse/arvados_fuse/__init__.py | 30 +-
services/fuse/arvados_fuse/command.py | 2 +
services/fuse/tests/mount_test_base.py | 2 +
services/fuse/tests/test_retry.py | 2 +-
services/keepstore/logging_router.go | 22 +-
services/nodemanager/arvnodeman/launcher.py | 5 +-
.../keepproxy.service => ws/arvados-ws.service} | 6 +-
services/ws/config.go | 40 +
services/ws/doc.go | 55 ++
services/ws/event.go | 65 ++
services/ws/event_source.go | 216 +++++
services/ws/handler.go | 235 ++++++
services/ws/main.go | 67 ++
services/ws/permission.go | 94 +++
services/ws/router.go | 140 ++++
services/ws/session.go | 33 +
services/ws/session_v0.go | 295 +++++++
services/ws/session_v1.go | 14 +
118 files changed, 3534 insertions(+), 5623 deletions(-)
copy tools/crunchstat-summary/tests/__init__.py => apps/workbench/app/views/application/_extra_tab_line_buttons.html.erb (100%)
create mode 100644 apps/workbench/app/views/container_requests/_extra_tab_line_buttons.html.erb
create mode 100644 apps/workbench/lib/tasks/config_dump.rake
create mode 100644 apps/workbench/test/diagnostics/container_request_test.rb
delete mode 100644 doc/_includes/_register_cwl_workflow.liquid
create mode 100644 doc/install/install-ws.html.textile.liquid
create mode 100644 doc/user/cwl/cwl-extensions.html.textile.liquid
rename doc/{_includes/_arvados_cwl_runner.liquid => user/cwl/cwl-run-options.html.textile.liquid} (51%)
delete mode 100644 doc/user/topics/running-workflow-command-line.html.textile.liquid
create mode 100644 sdk/cwl/tests/test_urljoin.py
create mode 100644 sdk/cwl/tests/wf/expect_arvworkflow.cwl
copy sdk/cwl/tests/wf/{submit_wf.cwl => submit_keepref_wf.cwl} (70%)
create mode 100644 sdk/go/arvados/log.go
create mode 100644 sdk/go/ctxlog/log.go
delete mode 100644 sdk/go/logger/logger.go
delete mode 100644 sdk/go/logger/util.go
create mode 100644 sdk/go/stats/duration.go
create mode 100644 sdk/go/stats/duration_test.go
delete mode 100644 sdk/go/util/util.go
create mode 100644 services/api/db/migrate/20161213172944_full_text_search_indexes.rb
create mode 100644 services/api/lib/tasks/config_dump.rake
delete mode 100644 services/datamanager/collection/collection.go
delete mode 100644 services/datamanager/collection/collection_test.go
delete mode 100644 services/datamanager/collection/testing.go
delete mode 100644 services/datamanager/datamanager.go
delete mode 100644 services/datamanager/datamanager_test.go
delete mode 100755 services/datamanager/experimental/datamanager.py
delete mode 100755 services/datamanager/experimental/datamanager_test.py
delete mode 100644 services/datamanager/keep/keep.go
delete mode 100644 services/datamanager/keep/keep_test.go
delete mode 100644 services/datamanager/loggerutil/loggerutil.go
delete mode 100644 services/datamanager/summary/canonical_string.go
delete mode 100644 services/datamanager/summary/file.go
delete mode 100644 services/datamanager/summary/pull_list.go
delete mode 100644 services/datamanager/summary/pull_list_test.go
delete mode 100644 services/datamanager/summary/summary.go
delete mode 100644 services/datamanager/summary/summary_test.go
delete mode 100644 services/datamanager/summary/trash_list.go
delete mode 100644 services/datamanager/summary/trash_list_test.go
copy services/{keepproxy/keepproxy.service => ws/arvados-ws.service} (55%)
create mode 100644 services/ws/config.go
create mode 100644 services/ws/doc.go
create mode 100644 services/ws/event.go
create mode 100644 services/ws/event_source.go
create mode 100644 services/ws/handler.go
create mode 100644 services/ws/main.go
create mode 100644 services/ws/permission.go
create mode 100644 services/ws/router.go
create mode 100644 services/ws/session.go
create mode 100644 services/ws/session_v0.go
create mode 100644 services/ws/session_v1.go
via ebb2559b3a09636ff687316bbe512e0e8a86b168 (commit)
via c1a8e01539932e2f0153cfb2ffc4eaa2c3dc00f1 (commit)
via 53468cf5e609c4456d1bfd24aeb74c326ff6a8b7 (commit)
via 5fe2a0ab78c82b67b92434596d554bedda1d4259 (commit)
via a092ab09fab941057e5cc44d93886676d542bdd6 (commit)
via ad0712ccdb7ad3d01ab4fc0d4f1a15dc7443b18a (commit)
via 965565ddc62635928a6b043158fd683738961c8c (commit)
via 697e73b0605b6c182f1051e97ed370d5afa7d954 (commit)
via ffd4738242c61fa5acd423f927339f836dfb0ffb (commit)
via a619c2ce3c6d5bc00b9898dd084ac0e2efc2ee76 (commit)
via 005cb811d937fe52cee11d76484252ed7167f9a8 (commit)
via 6a370a002d008dffaf9f47b7db3da47b40e57254 (commit)
via dcca309415bc0683f57f38ad65c30b539d80e191 (commit)
via 28db15c830a8f129283f43682727b470862572d8 (commit)
via 409d130ddcc4b76def5fa8d61d2584725c61152a (commit)
via f987de07f96595851187ed2a4e0212fa0e10e999 (commit)
via ba57b6537679889b42693ecd839a94d59c716aaf (commit)
via 57170c25230cf56c99c5b2cbc795f4599cbda87f (commit)
via 9676ee85d8f8fc64dfd4149cea5999de54e827a7 (commit)
via c856cb5095e454c1733bd6f0053e59e2b884d644 (commit)
via f3e02106cfc33ffe333af9e303a9e68f3ecfb2e4 (commit)
via 08e03489e053779f7bbc168677deeebd86d6249c (commit)
via 7e931b4355800f1715b614e7a01212a1b1791a30 (commit)
via cc1dbda8f559ab43f326c77595d4af87e8ca7a33 (commit)
via 55e9587e140e1621dcd374afcf30ee0aec2c6d24 (commit)
via 738ecb0cd43e2ae728b04534697198d11d6bd85f (commit)
via 80d4b6ebb20393507be7ecd0dcf888ebda623a35 (commit)
via 7df118ca0c58dd65f3ec83e94941976d5073ff45 (commit)
via 386248b68c309b890f9cb257360a62d28cb8706b (commit)
via b94b54c25a57a26925eaf739dcf59a4ff94238ae (commit)
via 18c3e601c065e5afd526b29e214b497fad04ce32 (commit)
via 0b898bf7c9337ac0f2385159329d2f3e6a1694ec (commit)
via aa94204c3e88f5386d14cb90e3e13a5e9caaf251 (commit)
via e1fb30fb49c337c7711e51fa3f6c3c81650b228c (commit)
via efb3422f119be36e133ffbd14519c5d6c74addc8 (commit)
via c668e7499c3b2a1561389a06910e33112e7d171d (commit)
via 23cdaa559272388135e1a5c3d1cc64cfe6e422d5 (commit)
via 49a647b963d16c7035d514ea6a09a11afe3a5d19 (commit)
via 3da0fb0eef35b665c9c427fa9acf9b932dd45062 (commit)
via 83a4e42fb15030a9108e76dcf01a1a7d6c14cda5 (commit)
via e54cce12bbda235dcaebf3b7565804cd8c296100 (commit)
via f2e2487ddba3944d3acd46fae3424a87fc624be9 (commit)
via ae9c556899557f64acaa54b339a62c9f5c5966c9 (commit)
via d13cc16ebbe287fe81d06c5faa1d15fe588bcf16 (commit)
via 474ed0b55fcf7f8c9d6c195df829ef9b2ecac798 (commit)
via 62d8f575a93374a235097b88499fa65eef2f56ec (commit)
via ccc1201e103e168b04801b135b662577d7ea475b (commit)
via 190e6d0b21800dcaec1c5d0b2346d2c2bf43eeea (commit)
via 50a3cf5df8624618cc00308159fde643dd8d6f28 (commit)
via b5af6347690934f0a0fba10b79b6d8dcf2c84243 (commit)
via 9f2fccd1c01823a762044c8a73e6fa0f7ed9086b (commit)
via 8e8b3d8dd81e4fd9c910e6739c74998f3b6ed288 (commit)
via d070d1e50551b9c84e4705406a435b1b50f84a08 (commit)
via 3265a76b23fc57ae22ddce95a589c019abce503c (commit)
via 20d7a8b075490d434b6513eea24e99ff257601e6 (commit)
via 5646f9476220ef151d1811acb4eff88ebe8ef530 (commit)
via ba1ec0f0b59ab871b6e4faf5e8ae87809fdb85b6 (commit)
via b9f0177e6a477a518fd5a89156fafde57f2dddf8 (commit)
via bdb92619b5f6d920119b8c32c3027cf4b751ed16 (commit)
via 5d843ab702bd516257dda1a872d45755e5170678 (commit)
via c86fec0e51f30b2771c9ae95152f76b438db6542 (commit)
via 2e104941dbf1e4bf92e0632cadeb946be0595d67 (commit)
via 8be35986ae62ce39691c4c6d491601012255b1ba (commit)
via 1c96d4eb740dc4285d9f30ba0ce73499f7b7d59e (commit)
via 4a71cc82448046d28600d9788f523ece07649e2f (commit)
via 199da9e541e23ed6648ae0abd0cbd38866d3e85f (commit)
via a62e41101a75e01f9b0dd7124eef81714443d8a1 (commit)
via 47a5c66948792602f657e5e1157bfd172d23c546 (commit)
via 05f0eefbaa31ef430a6ac71e4b8eb066f195d9df (commit)
via 0d62edcb9d25bf4dcdb20d8872ea7b438e12fc59 (commit)
via 13f7a114f9c03b1efa0d6f696a7f6034b6cc2677 (commit)
via ae61fc4e1e7c1cbd4695bb3cc715eba5492c2b20 (commit)
via a175a62538e4db86296e49e5412be41e026e73b6 (commit)
via 8303a85b6c3fed92710a590fa5653557b73439cf (commit)
via 90de410ff977f3669d33f532adf0cb71ac8ac261 (commit)
via 0479c53c53a4a458b2759b067ae2cb928cbbf051 (commit)
via 2a1978f10b7dff4f239eb868648f404f070fccc3 (commit)
via ed9be4cc10c12051bdb1a65210726ab1d688108c (commit)
via 24f455da9cb2bf7a3c519912abbc15292a414655 (commit)
via 9a9850ac59958f1aa1b5f97ff8479c29d073e964 (commit)
via b4422bbdb475f689cc46cfc12f037db1e888f521 (commit)
via 2a62b82e96a6f56357e913117e04c36b1ccf7585 (commit)
via 2ec950c960fa8e95de9593fdf09f40833861c36e (commit)
via 324ffadbac85457cba901c7c195b8a20a32a8c4d (commit)
via aaa964ac44f923985d6a6eb40c179f62c13ca8ce (commit)
via 83ec78f608d67622ccc87b67cc16276a48a0430a (commit)
via 7ef471d9d0513b0b06cf0007e575f16eda93ec29 (commit)
via 45dd8543ac140a3326e6a8063bd43bd6c4ad05c8 (commit)
via d63601c63f651ab9fe4fefb5a7e8d76bf0495da3 (commit)
via 8595030d0314e6f88a245e66f90cce0a306b6867 (commit)
via deac6ece295b9c2049f8c91e1492324a97bf1b01 (commit)
via dd2320c6877939365caf79767b5244d86a288437 (commit)
via fd717a88835be62ae1b5c4b1ecd74c21cab0e744 (commit)
via ebf7f34bfd6d20273f8a5f8fded07c3f0387b39f (commit)
via 9f0854e394baf712f1fbcf3ebd21af215276c0fb (commit)
via 0f1fca27f3b4b40ff8f6be729e12f2feeba05f8f (commit)
via cc0cd658d3db6820fba9daf380da4fa177b38f5c (commit)
via 44702d2cdc6f6f76c16d9d5da9ae3225ab07de2f (commit)
via 15aca78766bda903480e327340d67d3d882ee69f (commit)
via 2eaa77dc327c024f2faa3fbd322e7054454b6442 (commit)
via 8c014223e42683d308798475c021bad7a794e998 (commit)
via 2225be2cb92613495450528ba24a9ca14f232748 (commit)
via 50128b53da4003912635b03fb27b5be2c5beaca1 (commit)
via 0d2d039368f65490e9479bd7500a1f8bdf30849c (commit)
via fd7db907627aac75dae62430b6f2fa948719a3af (commit)
via 161a519439dcad4d77ca400ec48bb58cb685b54a (commit)
via b0ba939812720869fca0a75b07d42518d4953345 (commit)
via 05666b170533c79800bea1d472c284e23c9ec5e0 (commit)
via 88ab51c83676a75efbb7b83e7d17927816ecaac4 (commit)
via 74d5bfb293b2acf76d639df12ff8769bc333a5f2 (commit)
via 3c1b51391b320539eb4cfbc02ea9e9363df1b370 (commit)
via 53d8d85b53e445ffb8c16eed86145adee2ff9e37 (commit)
via 261b9d42a367704e4815f3d59565467b98853787 (commit)
via c52c3788fbbf161db40118261c4cfff52ebf8ceb (commit)
via 5413abe433a089f11f7ea595073a6a20ffa371de (commit)
via bfabb2a8fd5fc3914035a7e2be6bd29d14fc7850 (commit)
via a6d6a57a908b1cac8ebcc5bc4261b7c906d249a4 (commit)
via 259252b7b9418c931e59d67257e50632c83261c5 (commit)
via 1a17734f7264bc74463e1e6fe115cdad6ec4c521 (commit)
via d3a6d626ab4534865a14e8a34295a65e92036f37 (commit)
via ec5ec8c10756217482930b0ad763ff174b7843fd (commit)
via f675fb2c202516021b961b5aa2de4528ba9f0d1f (commit)
via 17b7582b6116a4891a27769ee06f9a604bbabdd7 (commit)
via dfb995ab9ea0f1d8808c812870db717164ac95f4 (commit)
via 567269bca35ce82045643f86d38992f45d75f435 (commit)
via 8e37378b2955346c2b4a3c1e38fcdfb2e74b7e07 (commit)
via bc4dd2d01cda24a71f95b62ae1fa72aa9fb1226d (commit)
via 5ffb79040668114c58bf35c3e18a8302b8d94445 (commit)
via d6b6b39bfe67926490506125c88f3567e45e7dcc (commit)
via 7ae5533a074d80882171b33f7b659c9bcace1bd3 (commit)
via 0c6cbd8a07e31decd703ef7fd9eca591e5661c32 (commit)
via f6f8feeada332a55d1a966e9f4a240d99dc58b55 (commit)
via 5a420beeb6c64efc3ca0ef13d4ab9ac6c654c3ab (commit)
via 3e39ed33427a0c3000ed41b4826fcfa182934f71 (commit)
via e12c0414039f7e818e31aa4765a5e69666333069 (commit)
via f224b7ff4c38027309292a01516cd1df9f158a3e (commit)
via 53b116a7dac30b01f4080ea2832a68e7b885db51 (commit)
via 2a4aae5d6b865e959b97386b84386358e56ebd50 (commit)
via bbf8780255b9c04d0aaa95ef055cb8e777df11be (commit)
via 87363153b74c9137b6113a5c62da475e02908d9a (commit)
via 54aa46e52ff46fa667ec333e6bbaa00e0382f6f4 (commit)
via 0f2a62815c97a47b610b76a748a7d092c89e3e7b (commit)
via 83f085a0c405695d9840a0542eb9746e7b5d3f6f (commit)
via f1c316086c32a0c19cfbf4ac7bb122d3e8cd049b (commit)
via 0040a5a5b2e82f20641278584ecae835c1c537d3 (commit)
via da44904bb64303db2ae01aa9978188c20d453445 (commit)
via f517492fccb7cec138621cd0e710668877be57ce (commit)
via 104b2b5a46844e94a37c332b4ddd5a861dd8d63d (commit)
via dcb82d1101219a76df671a4f61738b764841d8dd (commit)
via f9eb135e4420352198729534f115f233cda8c261 (commit)
via 39b1824cff7cae632a19dbe9c011b8b5d8fb9375 (commit)
via 219daa3b227f147cb628a27b823b9b4e1f8d32b1 (commit)
via 6e2b2d15e8c3b7926cd7b300660698fa23644efc (commit)
via 7cb536fa58d8cc837b4cb59680c7355a1687648b (commit)
via 1e094e23db422cabe013ecbf7a0b465c4b096e12 (commit)
via 2dec79b036796df75885abf4e1a977958f9c541d (commit)
via a3d45597b1f4ea9443d35370ebfa7925fdd5ce90 (commit)
via 3885bc2e043ce123929acceaaa8dbbf20dbb8c12 (commit)
via 3dec7045b24acdd53dc054bddcfd4c7f77739f00 (commit)
via 845d6e6521b284a111534447919a6bc594573ee1 (commit)
via 391a1d8378b4bc6b17b71904b3d6494160b51627 (commit)
from d0dc273718a2f657643a2b2800d984c7a3a62f78 (commit)
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 ebb2559b3a09636ff687316bbe512e0e8a86b168
Merge: d0dc273 c1a8e01
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Dec 21 10:08:44 2016 -0500
10467: Merge branch 'master' into 10467-client-disconnect
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list