arvados.git
6 years ago13497: Rename SystemNodes to NodeProfiles in config.
Tom Clegg [Fri, 15 Jun 2018 19:26:24 +0000 (15:26 -0400)]
13497: Rename SystemNodes to NodeProfiles in config.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Abort startup if Rails API cannot be found.
Tom Clegg [Fri, 15 Jun 2018 19:08:59 +0000 (15:08 -0400)]
13497: Abort startup if Rails API cannot be found.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Support "run-tests.sh --only go".
Tom Clegg [Fri, 15 Jun 2018 19:06:02 +0000 (15:06 -0400)]
13497: Support "run-tests.sh --only go".

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Bump version numbers for Go packages when lib/ changes.
Tom Clegg [Fri, 15 Jun 2018 19:05:17 +0000 (15:05 -0400)]
13497: Bump version numbers for Go packages when lib/ changes.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Quote file paths in test suite nginx.conf.
Tom Clegg [Thu, 14 Jun 2018 21:03:24 +0000 (17:03 -0400)]
13497: Quote file paths in test suite nginx.conf.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Suppress nginx "info" logs from console.
Tom Clegg [Thu, 14 Jun 2018 21:02:10 +0000 (17:02 -0400)]
13497: Suppress nginx "info" logs from console.

(unless ARVADOS_DEBUG is set)

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Send test server logs to {workspace}/tmp/*.log.
Tom Clegg [Thu, 14 Jun 2018 20:29:11 +0000 (16:29 -0400)]
13497: Send test server logs to {workspace}/tmp/*.log.

Don't send them to console unless ARVADOS_DEBUG is set.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Add systemd unit to arvados-controller package.
Tom Clegg [Thu, 14 Jun 2018 19:37:13 +0000 (15:37 -0400)]
13497: Add systemd unit to arvados-controller package.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Accept host key on command line.
Tom Clegg [Thu, 14 Jun 2018 19:23:08 +0000 (15:23 -0400)]
13497: Accept host key on command line.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Add controller to health check.
Tom Clegg [Thu, 14 Jun 2018 17:34:58 +0000 (13:34 -0400)]
13497: Add controller to health check.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Set usable path for nginx request body buffering.
Tom Clegg [Wed, 13 Jun 2018 20:59:52 +0000 (16:59 -0400)]
13497: Set usable path for nginx request body buffering.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Remove alternate integration test glue in Workbench.
Tom Clegg [Wed, 13 Jun 2018 20:43:41 +0000 (16:43 -0400)]
13497: Remove alternate integration test glue in Workbench.

Expect run-tests.sh to have set everything up correctly instead.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Route API traffic through controller in test suites.
Tom Clegg [Wed, 13 Jun 2018 19:51:30 +0000 (15:51 -0400)]
13497: Route API traffic through controller in test suites.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Don't propagate connection-oriented headers when proxying.
Tom Clegg [Wed, 13 Jun 2018 19:51:07 +0000 (15:51 -0400)]
13497: Don't propagate connection-oriented headers when proxying.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Send request body when proxying.
Tom Clegg [Wed, 13 Jun 2018 19:49:26 +0000 (15:49 -0400)]
13497: Send request body when proxying.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Add timeout for proxy requests.
Tom Clegg [Tue, 12 Jun 2018 20:39:41 +0000 (16:39 -0400)]
13497: Add timeout for proxy requests.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Proxy requests to Rails API.
Tom Clegg [Tue, 12 Jun 2018 20:00:07 +0000 (16:00 -0400)]
13497: Proxy requests to Rails API.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Move common system service code to lib/service.
Tom Clegg [Tue, 12 Jun 2018 15:10:12 +0000 (11:10 -0400)]
13497: Move common system service code to lib/service.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Build arvados-server and arvados-controller packages.
Tom Clegg [Thu, 7 Jun 2018 19:23:05 +0000 (15:23 -0400)]
13497: Build arvados-server and arvados-controller packages.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13427: More symlink hack
Tom Clegg [Wed, 6 Jun 2018 19:25:45 +0000 (15:25 -0400)]
13427: More symlink hack

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Add arvados-server command.
Tom Clegg [Thu, 7 Jun 2018 14:20:29 +0000 (10:20 -0400)]
13497: Add arvados-server command.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Use basename($0) as subcommand, if it is one.
Tom Clegg [Thu, 7 Jun 2018 13:33:20 +0000 (09:33 -0400)]
13497: Use basename($0) as subcommand, if it is one.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13497: Add controller, proxy to Rails API.
Tom Clegg [Thu, 7 Jun 2018 04:46:47 +0000 (00:46 -0400)]
13497: Add controller, proxy to Rails API.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoMerge branch '13456-phantomjs-died'
Tom Clegg [Tue, 5 Jun 2018 19:56:57 +0000 (15:56 -0400)]
Merge branch '13456-phantomjs-died'

refs #13456

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoMore gopath symlink hacks.
Tom Clegg [Tue, 5 Jun 2018 19:11:38 +0000 (15:11 -0400)]
More gopath symlink hacks.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoMerge branch '13431-keepproxy-storage-classes-headers'
Lucas Di Pentima [Tue, 5 Jun 2018 19:10:11 +0000 (16:10 -0300)]
Merge branch '13431-keepproxy-storage-classes-headers'
Closes #13431

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years ago13456: Restart driver after each test.
Tom Clegg [Tue, 5 Jun 2018 19:08:42 +0000 (15:08 -0400)]
13456: Restart driver after each test.

Shot in the dark from https://github.com/teampoltergeist/poltergeist/issues/232

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13431: Removes commented code
Lucas Di Pentima [Tue, 5 Jun 2018 18:43:40 +0000 (15:43 -0300)]
13431: Removes commented code

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years ago13431: Fixes unrelated test
Lucas Di Pentima [Tue, 5 Jun 2018 18:37:05 +0000 (15:37 -0300)]
13431: Fixes unrelated test

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years ago13431: Adds test confirming that keepproxy propagates X-Keep-Storage-Classes
Lucas Di Pentima [Tue, 5 Jun 2018 18:22:18 +0000 (15:22 -0300)]
13431: Adds test confirming that keepproxy propagates X-Keep-Storage-Classes

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years agoMerge branch '13164-cr-locking'
Tom Clegg [Tue, 5 Jun 2018 16:57:23 +0000 (12:57 -0400)]
Merge branch '13164-cr-locking'

refs #13164

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13164: Remove locking. Clean up after races in background instead.
Tom Clegg [Tue, 5 Jun 2018 14:56:22 +0000 (10:56 -0400)]
13164: Remove locking. Clean up after races in background instead.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13431: Make keepproxy propagate X-Keep-Storage-Classes headers
Lucas Di Pentima [Tue, 5 Jun 2018 00:39:18 +0000 (21:39 -0300)]
13431: Make keepproxy propagate X-Keep-Storage-Classes headers

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years ago13431: Adds storage class support to Keepclient.
Lucas Di Pentima [Mon, 4 Jun 2018 20:24:57 +0000 (17:24 -0300)]
13431: Adds storage class support to Keepclient.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years agoMerge branch '12061-nm-integration-tests'
Tom Clegg [Mon, 4 Jun 2018 13:22:13 +0000 (09:22 -0400)]
Merge branch '12061-nm-integration-tests'

refs #12061

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoMerge branch '13559-ciso8601-pin'
Lucas Di Pentima [Mon, 4 Jun 2018 13:20:29 +0000 (10:20 -0300)]
Merge branch '13559-ciso8601-pin'
Closes #13559

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years ago13559: Pin ciso8601 to version <2.0.0 due to API changes.
Lucas Di Pentima [Fri, 1 Jun 2018 21:12:43 +0000 (18:12 -0300)]
13559: Pin ciso8601 to version <2.0.0 due to API changes.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years ago12061: Disable nodemanager integration tests.
Tom Clegg [Fri, 1 Jun 2018 17:35:10 +0000 (13:35 -0400)]
12061: Disable nodemanager integration tests.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12061: Remove unreliable check.
Tom Clegg [Fri, 1 Jun 2018 17:36:43 +0000 (13:36 -0400)]
12061: Remove unreliable check.

"Shutdown because state=down" is possible during a race, when
nodemanager logs "Shutdown success" and polls sinfo again before the
test suite has finished updating the sinfo stub.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12061: Reduce per-test timeout.
Tom Clegg [Fri, 1 Jun 2018 16:50:02 +0000 (12:50 -0400)]
12061: Reduce per-test timeout.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12061: Fix nodes marked busy while expecting shutdown decision.
Tom Clegg [Fri, 1 Jun 2018 16:49:42 +0000 (12:49 -0400)]
12061: Fix nodes marked busy while expecting shutdown decision.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12061: Use shorter retry-after sleeps in integration test.
Tom Clegg [Thu, 31 May 2018 21:17:33 +0000 (17:17 -0400)]
12061: Use shorter retry-after sleeps in integration test.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12061: Don't wait around for test daemon to shutdown gracefully.
Tom Clegg [Thu, 31 May 2018 21:07:13 +0000 (17:07 -0400)]
12061: Don't wait around for test daemon to shutdown gracefully.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12061: Poll aggressively in integration tests.
Tom Clegg [Thu, 31 May 2018 21:06:32 +0000 (17:06 -0400)]
12061: Poll aggressively in integration tests.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12061: Allow sub-second poll times and sub-minute shutdown windows.
Tom Clegg [Thu, 31 May 2018 21:01:15 +0000 (17:01 -0400)]
12061: Allow sub-second poll times and sub-minute shutdown windows.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoMerge branch '13517-buffer-leak'
Tom Clegg [Thu, 31 May 2018 19:05:47 +0000 (15:05 -0400)]
Merge branch '13517-buffer-leak'

refs #13517

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoMerge branch '12061-flaky-tests'
Tom Clegg [Thu, 31 May 2018 18:39:41 +0000 (14:39 -0400)]
Merge branch '12061-flaky-tests'

refs #12061

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12061: Explicitly join actor thread after stopping.
Tom Clegg [Thu, 31 May 2018 18:26:59 +0000 (14:26 -0400)]
12061: Explicitly join actor thread after stopping.

Fixes the "nonfatal" test case the same way the "fatal" test case was
fixed in 6706c6d46c6cfb080371b147b60fcaa191bd55a6.

Since the nonfatal case just tests that kill_mock did *not* get
called, the race condition used to make the test ineffectual
occasionally, instead of failing occasionally.

The race condition became visible only after the status reporting test
was added.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13517: Fix leaked goroutine and buffer on failed S3 write.
Tom Clegg [Thu, 31 May 2018 17:44:18 +0000 (13:44 -0400)]
13517: Fix leaked goroutine and buffer on failed S3 write.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12061: Don't round down to 1s in timestamp parser.
Tom Clegg [Wed, 30 May 2018 20:32:20 +0000 (16:32 -0400)]
12061: Don't round down to 1s in timestamp parser.

ComputeNodeMonitorActor.offer_arvados_pair() pairs nodes only if

  first_ping_time >= cloud_node_start_time

However, first_ping_time is passed through arvados_timestamp() before
this comparison, which was truncating the subsecond part -- so the
comparison was effectively

  floor(first_ping_time) >= cloud_node_start_time

When FPT and CNST differed only in the subsecond part, this comparison
failed, and the nodes could never be paired. This caused sporadic
failures in tests, where the two values are often separated by less
than a second.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12061: Change busywait approach to preserve assertion messages.
Tom Clegg [Wed, 30 May 2018 20:30:45 +0000 (16:30 -0400)]
12061: Change busywait approach to preserve assertion messages.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoMerge branch '11162-wes-support' refs #11162
Peter Amstutz [Wed, 30 May 2018 11:39:30 +0000 (07:39 -0400)]
Merge branch '11162-wes-support' refs #11162

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years agoMerge branch '13513-balance-deadlock'
Tom Clegg [Tue, 29 May 2018 20:05:27 +0000 (16:05 -0400)]
Merge branch '13513-balance-deadlock'

fixes #13513

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago11162: Remove debugging check
Peter Amstutz [Tue, 29 May 2018 17:16:55 +0000 (13:16 -0400)]
11162: Remove debugging check

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago13513: Fix deadlocked workers.
Tom Clegg [Tue, 29 May 2018 13:46:04 +0000 (09:46 -0400)]
13513: Fix deadlocked workers.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoFix crunch_script for jobs api refs #13516
Peter Amstutz [Sat, 26 May 2018 02:04:21 +0000 (22:04 -0400)]
Fix crunch_script for jobs api refs #13516

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years agoReplace unicode copyright character with ASCII in README.Rmd
Peter Amstutz [Sat, 26 May 2018 01:49:14 +0000 (21:49 -0400)]
Replace unicode copyright character with ASCII in README.Rmd

Fix documentation generation

no issue #

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago11162: Add tests for http_to_keep.
Peter Amstutz [Fri, 25 May 2018 20:45:12 +0000 (16:45 -0400)]
11162: Add tests for http_to_keep.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago11162: Add test for --submit-request-uuid
Peter Amstutz [Fri, 25 May 2018 14:16:07 +0000 (10:16 -0400)]
11162: Add test for --submit-request-uuid

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago11162: Fix tests.
Peter Amstutz [Fri, 25 May 2018 13:55:13 +0000 (09:55 -0400)]
11162: Fix tests.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago11162: Bump cwltool for fix in generating basename from url
Peter Amstutz [Wed, 23 May 2018 20:56:40 +0000 (16:56 -0400)]
11162: Bump cwltool for fix in generating basename from url

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago11162: Smarter http downloads.
Peter Amstutz [Wed, 23 May 2018 19:23:44 +0000 (15:23 -0400)]
11162: Smarter http downloads.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago11162: Add logging about checking cache
Peter Amstutz [Wed, 23 May 2018 17:17:40 +0000 (13:17 -0400)]
11162: Add logging about checking cache

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago11162: Set a default cache time of 24 hours for files fetched over http.
Peter Amstutz [Wed, 23 May 2018 16:52:22 +0000 (12:52 -0400)]
11162: Set a default cache time of 24 hours for files fetched over http.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago11162: Add progress for http data download.
Peter Amstutz [Wed, 23 May 2018 00:45:58 +0000 (20:45 -0400)]
11162: Add progress for http data download.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago11162: Add --submit-request-uuid
Peter Amstutz [Tue, 22 May 2018 20:53:16 +0000 (16:53 -0400)]
11162: Add --submit-request-uuid

Allows container request to be created separately from initialization
that occurs prior to actually committing the container to run.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago11162: Handle missing git
Peter Amstutz [Mon, 14 May 2018 16:02:51 +0000 (12:02 -0400)]
11162: Handle missing git

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago11162: Support public http and https file references
Peter Amstutz [Fri, 11 May 2018 20:36:54 +0000 (16:36 -0400)]
11162: Support public http and https file references

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago2411: Merge branch '2411-another-pass'
Ward Vandewege [Thu, 24 May 2018 15:30:58 +0000 (11:30 -0400)]
2411: Merge branch '2411-another-pass'

refs #2411

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

6 years ago2411: Add a bunch of exceptions to .licenseignore for our R sdk
Ward Vandewege [Thu, 24 May 2018 02:26:25 +0000 (22:26 -0400)]
2411: Add a bunch of exceptions to .licenseignore for our R sdk

refs #2411

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

6 years ago2411: Add license header to sdk/R/README.Rmd
Ward Vandewege [Thu, 24 May 2018 02:26:05 +0000 (22:26 -0400)]
2411: Add license header to sdk/R/README.Rmd

refs #2411

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

6 years ago2411: add copyright headers to our R files.
Ward Vandewege [Thu, 24 May 2018 02:17:25 +0000 (22:17 -0400)]
2411: add copyright headers to our R files.

refs #2411

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

6 years ago2411: Add support for R source files to build/check-copyright-notices
Ward Vandewege [Thu, 24 May 2018 02:16:58 +0000 (22:16 -0400)]
2411: Add support for R source files to build/check-copyright-notices

refs #2411

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

6 years ago2411: another pass at adding copyright headers where missing.
Ward Vandewege [Wed, 23 May 2018 21:50:16 +0000 (17:50 -0400)]
2411: another pass at adding copyright headers where missing.

refs #2411

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

6 years agoAdd Veritas Genetics to the AUTHORS file.
Ward Vandewege [Wed, 23 May 2018 14:04:13 +0000 (10:04 -0400)]
Add Veritas Genetics to the AUTHORS file.

No issue #

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

6 years agoMerge branch '13430-allow-storage-classes'
Fuad Muhic [Wed, 23 May 2018 13:07:39 +0000 (15:07 +0200)]
Merge branch '13430-allow-storage-classes'

refs #13430

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoMerge branch '13453-r-sdk-incorrect-rest-call-fix'
Fuad Muhic [Wed, 23 May 2018 10:15:31 +0000 (12:15 +0200)]
Merge branch '13453-r-sdk-incorrect-rest-call-fix'

refs #13453

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoAdded test that checks that saving a committed collection updates the storage_classes...
Fuad Muhic [Wed, 23 May 2018 10:05:41 +0000 (12:05 +0200)]
Added test that checks that saving a committed collection updates the storage_classes_desired

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoTweak arvados-cwl-runner subprocess32 version dependency refs #13516
Peter Amstutz [Wed, 23 May 2018 01:25:58 +0000 (21:25 -0400)]
Tweak arvados-cwl-runner subprocess32 version dependency refs #13516

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years agoFix tests refs #13516
Peter Amstutz [Tue, 22 May 2018 23:19:21 +0000 (19:19 -0400)]
Fix tests refs #13516

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years agoMerge branch '13516-fix-cwl-tests' refs #13516
Peter Amstutz [Tue, 22 May 2018 21:08:13 +0000 (17:08 -0400)]
Merge branch '13516-fix-cwl-tests' refs #13516

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago13516: Bump cwltool, cwltest and subprocess32 versions
Peter Amstutz [Tue, 22 May 2018 17:55:54 +0000 (13:55 -0400)]
13516: Bump cwltool, cwltest and subprocess32 versions

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years agoUpdated save method of Collection class to always update when
Fuad Muhic [Tue, 22 May 2018 16:08:36 +0000 (18:08 +0200)]
Updated save method of Collection class to always update when
storage_classes is specified.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoAdded tests and documentation for save and save_new methods in
Fuad Muhic [Tue, 22 May 2018 15:40:15 +0000 (17:40 +0200)]
Added tests and documentation for save and save_new methods in
Collection class.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years ago9918: Merge branch '9918-index-timeout'
Ward Vandewege [Tue, 22 May 2018 13:58:52 +0000 (09:58 -0400)]
9918: Merge branch '9918-index-timeout'

refs #9918

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

6 years ago9918: Merge branch 'master' into 9918-index-timeout
Ward Vandewege [Tue, 22 May 2018 13:47:40 +0000 (09:47 -0400)]
9918: Merge branch 'master' into 9918-index-timeout

refs #9918

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

6 years agoAdded tests to arv-put to cover storage classes feature.
Fuad Muhic [Tue, 22 May 2018 10:25:28 +0000 (12:25 +0200)]
Added tests to arv-put to cover storage classes feature.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoMerge branch '12995-wb-merge-acct' refs #12995
Peter Amstutz [Mon, 21 May 2018 17:54:19 +0000 (13:54 -0400)]
Merge branch '12995-wb-merge-acct' refs #12995

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago12995: Fix tests
Peter Amstutz [Mon, 21 May 2018 16:29:19 +0000 (12:29 -0400)]
12995: Fix tests

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years agoAdded --storage-classes argument to arv-put.
Fuad Muhic [Mon, 21 May 2018 15:18:37 +0000 (17:18 +0200)]
Added --storage-classes argument to arv-put.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years ago12995: Add username to link_accounts page.
Peter Amstutz [Mon, 21 May 2018 15:08:17 +0000 (11:08 -0400)]
12995: Add username to link_accounts page.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago12995: Add user and admin documentation pages.
Peter Amstutz [Mon, 21 May 2018 14:59:47 +0000 (10:59 -0400)]
12995: Add user and admin documentation pages.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago12995: Do nested logout/login to workaround SSO session.
Peter Amstutz [Fri, 18 May 2018 20:57:21 +0000 (16:57 -0400)]
12995: Do nested logout/login to workaround SSO session.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago12995: Bugfix to support following chained user uuid redirection.
Peter Amstutz [Fri, 18 May 2018 20:28:44 +0000 (16:28 -0400)]
12995: Bugfix to support following chained user uuid redirection.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago9918: Add RequestTimeout config for keep-balance.
Tom Clegg [Fri, 18 May 2018 19:50:15 +0000 (15:50 -0400)]
9918: Add RequestTimeout config for keep-balance.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12995: Don't let admins lose admin privs by linking a non-admin account.
Peter Amstutz [Fri, 18 May 2018 19:37:23 +0000 (15:37 -0400)]
12995: Don't let admins lose admin privs by linking a non-admin account.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years agoMerge branch '13164-container-deadlock'
Tom Clegg [Fri, 18 May 2018 19:10:53 +0000 (15:10 -0400)]
Merge branch '13164-container-deadlock'

refs #13164

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12995: Add testing
Peter Amstutz [Fri, 18 May 2018 18:34:43 +0000 (14:34 -0400)]
12995: Add testing

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago13164: Lock tables in order when locking a container.
Tom Clegg [Fri, 18 May 2018 18:29:34 +0000 (14:29 -0400)]
13164: Lock tables in order when locking a container.

Locking involves assigning auth_uuid, which involves looking up
container requests, so both tables must be locked in order to avoid
deadlock.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago13164: Lock tables in order for container updates.
Tom Clegg [Fri, 18 May 2018 18:02:29 +0000 (14:02 -0400)]
13164: Lock tables in order for container updates.

Otherwise, a container update can lock a container row, then perform
container request queries, which can deadlock with another thread that
locked container_requests first.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>