arvados.git
6 years ago11454: Cache the local session token's uuid after being requested from the API.
Lucas Di Pentima [Tue, 30 Jan 2018 23:43:44 +0000 (20:43 -0300)]
11454: Cache the local session token's uuid after being requested from the API.

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

6 years agoMerge branch '13011-empty-block-error-411'
Tom Clegg [Tue, 30 Jan 2018 21:35:15 +0000 (16:35 -0500)]
Merge branch '13011-empty-block-error-411'

refs #13011

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

6 years ago13011: Fix 411 error when writing empty block to Azure storage.
Tom Clegg [Tue, 30 Jan 2018 21:04:34 +0000 (16:04 -0500)]
13011: Fix 411 error when writing empty block to Azure storage.

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

6 years ago12199: Keep SLURM's node properties up to date.
Tom Clegg [Tue, 30 Jan 2018 18:33:12 +0000 (13:33 -0500)]
12199: Keep SLURM's node properties up to date.

Change the semantics of ComputeNodeUpdateActor.sync_node so it gets
called every time a new Arvados node record appears, even if hostnames
match. The base actor's implementation now compares hostnames itself
before calling the cloud driver.

This allows the slurm update actor's sync_node method to sync SLURM
state periodically, even if hostnames don't go out of sync.

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

6 years agoMerge branch 'master' into 11454-wb-federated-search
Lucas Di Pentima [Tue, 30 Jan 2018 18:29:50 +0000 (15:29 -0300)]
Merge branch 'master' into 11454-wb-federated-search

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

6 years ago12199: Assign slot and hostname when creating/reusing a node record.
Tom Clegg [Tue, 30 Jan 2018 01:03:23 +0000 (20:03 -0500)]
12199: Assign slot and hostname when creating/reusing a node record.

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

6 years agoMerge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Fuad Muhic [Tue, 30 Jan 2018 14:02:19 +0000 (15:02 +0100)]
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk

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

6 years agoAdded error checking code to Collection and Subcollection classes
Fuad Muhic [Tue, 30 Jan 2018 14:00:40 +0000 (15:00 +0100)]
Added error checking code to Collection and Subcollection classes

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

6 years ago12764: Improve error handling around staging writable files
Peter Amstutz [Mon, 29 Jan 2018 20:58:46 +0000 (15:58 -0500)]
12764: Improve error handling around staging writable files

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

6 years ago12764: Tweak docs
Peter Amstutz [Mon, 29 Jan 2018 20:02:48 +0000 (15:02 -0500)]
12764: Tweak docs

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

6 years ago12764: Support 'dockerOutputDirectory' for containers to get to 100% conformance.
Peter Amstutz [Fri, 12 Jan 2018 20:31:09 +0000 (15:31 -0500)]
12764: Support 'dockerOutputDirectory' for containers to get to 100% conformance.

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

6 years ago12764: Update documentation.
Peter Amstutz [Fri, 12 Jan 2018 19:12:01 +0000 (14:12 -0500)]
12764: Update documentation.

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

6 years ago12764: Support empty anonymous directories by creating a .keep placeholder.
Peter Amstutz [Fri, 12 Jan 2018 19:06:06 +0000 (14:06 -0500)]
12764: Support empty anonymous directories by creating a .keep placeholder.

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

6 years ago12764: Pass one cwl test
Peter Amstutz [Wed, 10 Jan 2018 22:43:49 +0000 (17:43 -0500)]
12764: Pass one cwl test

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

6 years ago12764: Fixes
Peter Amstutz [Wed, 10 Jan 2018 21:58:29 +0000 (16:58 -0500)]
12764: Fixes

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

6 years ago12764: arvados-cwl-runner support
Peter Amstutz [Wed, 10 Jan 2018 20:44:50 +0000 (15:44 -0500)]
12764: arvados-cwl-runner support

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

6 years ago12764: Writable file/directory support wip
Peter Amstutz [Thu, 7 Dec 2017 14:51:25 +0000 (09:51 -0500)]
12764: Writable file/directory support wip

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

6 years agoMerge branch '12758-federated-id-group-sync'
Lucas Di Pentima [Mon, 29 Jan 2018 18:21:07 +0000 (15:21 -0300)]
Merge branch '12758-federated-id-group-sync'
Closes #12758

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

6 years agoMerge branch '12746-crunch2-hoststat'
Tom Clegg [Mon, 29 Jan 2018 18:10:27 +0000 (13:10 -0500)]
Merge branch '12746-crunch2-hoststat'

refs #12746

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

6 years ago12199: Derate advertised node sizes by 5%.
Tom Clegg [Mon, 29 Jan 2018 16:48:43 +0000 (11:48 -0500)]
12199: Derate advertised node sizes by 5%.

This matches nodemanager's default behavior. It aims to account for
the difference between advertised and actual memory capacity, as well
as making some room for system processes on the host.

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

6 years ago12758: Query the API server for group memberships using a
Lucas Di Pentima [Thu, 25 Jan 2018 18:32:56 +0000 (15:32 -0300)]
12758: Query the API server for group memberships using a
'like' filter to retrieve all local and remote account links to groups.
Added a remote user to the fixture and updated test to confirm
remote users are able to be added & removed from local groups by
sync-groups.

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

6 years ago12199: Log timestamps in slow integration tests.
Tom Clegg [Mon, 29 Jan 2018 15:22:26 +0000 (10:22 -0500)]
12199: Log timestamps in slow integration tests.

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

6 years agoMerge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Fuad Muhic [Mon, 29 Jan 2018 11:35:11 +0000 (12:35 +0100)]
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk

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

6 years agoImplemented custom print functions for all public classes
Fuad Muhic [Mon, 29 Jan 2018 11:33:49 +0000 (12:33 +0100)]
Implemented custom print functions for all public classes

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

6 years ago12199: Update integration tests.
Tom Clegg [Mon, 29 Jan 2018 04:04:22 +0000 (23:04 -0500)]
12199: Update integration tests.

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

6 years ago12199: Make mocks match real slurm output.
Tom Clegg [Mon, 29 Jan 2018 03:32:08 +0000 (22:32 -0500)]
12199: Make mocks match real slurm output.

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

6 years ago12199: Update slurm features when nodes come up.
Tom Clegg [Sun, 28 Jan 2018 22:22:28 +0000 (17:22 -0500)]
12199: Update slurm features when nodes come up.

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

6 years ago12199: Rename instance type features: a1.xl => instancetype=a1.xl
Tom Clegg [Sun, 28 Jan 2018 21:52:13 +0000 (16:52 -0500)]
12199: Rename instance type features: a1.xl => instancetype=a1.xl

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

6 years ago12199: Use node type X to run jobs with constraint instancetype=X.
Tom Clegg [Sun, 28 Jan 2018 21:32:22 +0000 (16:32 -0500)]
12199: Use node type X to run jobs with constraint instancetype=X.

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

6 years agoRefactor arvbox Go setup and use govendor. refs #12935
Peter Amstutz [Fri, 26 Jan 2018 20:57:29 +0000 (15:57 -0500)]
Refactor arvbox Go setup and use govendor. refs #12935

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

6 years ago12746: Don't stop hoststat until after capturing output.
Tom Clegg [Fri, 26 Jan 2018 21:30:50 +0000 (16:30 -0500)]
12746: Don't stop hoststat until after capturing output.

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

6 years ago12746: Log host cgroup stats to hoststat.txt.
Tom Clegg [Fri, 26 Jan 2018 20:44:13 +0000 (15:44 -0500)]
12746: Log host cgroup stats to hoststat.txt.

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

6 years ago12199: Refactor for more test-friendly initialization.
Tom Clegg [Fri, 26 Jan 2018 19:33:48 +0000 (14:33 -0500)]
12199: Refactor for more test-friendly initialization.

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

6 years agoUpdated unit test name to reflect changes made to getFileListing method
Fuad Muhic [Fri, 26 Jan 2018 15:09:31 +0000 (16:09 +0100)]
Updated unit test name to reflect changes made to getFileListing method

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

6 years agoUpdated test to reflect changes to getFileListing method
Fuad Muhic [Fri, 26 Jan 2018 15:04:32 +0000 (16:04 +0100)]
Updated test to reflect changes to getFileListing method

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

6 years agoMerge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Fuad Muhic [Fri, 26 Jan 2018 15:00:59 +0000 (16:00 +0100)]
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk

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

6 years agogetFileListing now returns sorted list
Fuad Muhic [Fri, 26 Jan 2018 14:59:47 +0000 (15:59 +0100)]
getFileListing now returns sorted list

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

6 years ago12199: Pass node type to sbatch --constraint argument if configured.
Tom Clegg [Fri, 26 Jan 2018 00:13:18 +0000 (19:13 -0500)]
12199: Pass node type to sbatch --constraint argument if configured.

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

6 years ago12199: Refactor to eliminate evil globals.
Tom Clegg [Fri, 26 Jan 2018 00:12:49 +0000 (19:12 -0500)]
12199: Refactor to eliminate evil globals.

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

6 years ago12199: Add SlurmNodeTypeFeatureKludge.
Tom Clegg [Fri, 26 Jan 2018 00:11:32 +0000 (19:11 -0500)]
12199: Add SlurmNodeTypeFeatureKludge.

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

6 years ago12199: Add node size calculator.
Tom Clegg [Tue, 23 Jan 2018 19:25:21 +0000 (14:25 -0500)]
12199: Add node size calculator.

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

6 years agoFix missing files needed by arvados-tests.sh refs #12935
Peter Amstutz [Thu, 25 Jan 2018 19:27:38 +0000 (14:27 -0500)]
Fix missing files needed by arvados-tests.sh refs #12935

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

6 years agoMerge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Fuad Muhic [Thu, 25 Jan 2018 14:15:04 +0000 (15:15 +0100)]
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk

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

6 years agoArvadosFile's connection method now returns curl connection instead of
Fuad Muhic [Thu, 25 Jan 2018 14:12:42 +0000 (15:12 +0100)]
ArvadosFile's connection method now returns curl connection instead of
textConnection when called with 'r' parameter

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

6 years agoMerge branch '12891-log-on-cancel'
Tom Clegg [Wed, 24 Jan 2018 15:49:21 +0000 (10:49 -0500)]
Merge branch '12891-log-on-cancel'

refs #12891

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

6 years agoMerge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Fuad Muhic [Wed, 24 Jan 2018 15:19:01 +0000 (16:19 +0100)]
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk

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

6 years agoAdded unit tests for HttpRequest class.
Fuad Muhic [Wed, 24 Jan 2018 15:17:36 +0000 (16:17 +0100)]
Added unit tests for HttpRequest class.

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

6 years ago12891: Don't wait for WaitContainer to receive loggingDone.
Tom Clegg [Tue, 23 Jan 2018 20:08:08 +0000 (15:08 -0500)]
12891: Don't wait for WaitContainer to receive loggingDone.

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

6 years ago12891: Fix some test races.
Tom Clegg [Tue, 23 Jan 2018 20:05:22 +0000 (15:05 -0500)]
12891: Fix some test races.

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

6 years ago12891: Simplify "arv-mount exits before container ends" detection.
Tom Clegg [Tue, 23 Jan 2018 19:39:26 +0000 (14:39 -0500)]
12891: Simplify "arv-mount exits before container ends" detection.

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

6 years agoMerge branch '12990-fuse-shared' refs #12990
Peter Amstutz [Tue, 23 Jan 2018 17:40:14 +0000 (12:40 -0500)]
Merge branch '12990-fuse-shared' refs #12990

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

6 years ago12990: Re-query project roots in order to get full record
Peter Amstutz [Tue, 23 Jan 2018 16:33:58 +0000 (11:33 -0500)]
12990: Re-query project roots in order to get full record

Makes the query of all projects lighter.

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

6 years agoRemoved plus sign hack from HttpRequests createFiltersQuery method
Fuad Muhic [Tue, 23 Jan 2018 16:29:08 +0000 (17:29 +0100)]
Removed plus sign hack from HttpRequests createFiltersQuery method

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

6 years agoFixed ArvadosFile/Subcollection move bug and improved http query
Fuad Muhic [Tue, 23 Jan 2018 16:16:50 +0000 (17:16 +0100)]
Fixed ArvadosFile/Subcollection move bug and improved http query
generation logic.

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

6 years ago12990: Add update lock to shared directory update.
Peter Amstutz [Tue, 23 Jan 2018 15:51:47 +0000 (10:51 -0500)]
12990: Add update lock to shared directory update.

Also limit fields returned using select.

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

6 years agoAdded additional unit tests to Arvados class
Fuad Muhic [Tue, 23 Jan 2018 11:38:18 +0000 (12:38 +0100)]
Added additional unit tests to Arvados class

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

6 years agoFactored out HttpRequest and HttpParser classes from Arvados class to
Fuad Muhic [Tue, 23 Jan 2018 09:45:28 +0000 (10:45 +0100)]
Factored out HttpRequest and HttpParser classes from Arvados class to
RESTService class

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

6 years ago11454: Conditional login to remote API servers.
Lucas Di Pentima [Mon, 22 Jan 2018 21:00:25 +0000 (18:00 -0300)]
11454: Conditional login to remote API servers.

When adding new sites to the multi site search, if the remote
site allows federated logins from the local site, created a
salted token to be able to start a session.
If not, use the classic login method.

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

6 years ago11454: (WIP) Login to remote clusters using federated identity.
Lucas Di Pentima [Mon, 22 Jan 2018 18:16:20 +0000 (15:16 -0300)]
11454: (WIP) Login to remote clusters using federated identity.

Expanded the multi site search's SessionDB to allow logins
using salted tokens.
Pending: Do the right thing on every combination of federation
settings.

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

6 years ago12891: Use docker "rm -f" instead of "stop" to cancel container.
Tom Clegg [Mon, 22 Jan 2018 15:57:18 +0000 (10:57 -0500)]
12891: Use docker "rm -f" instead of "stop" to cancel container.

"Stop" sends SIGTERM and then (after a timeout) SIGKILL to the main
process in the container. If the contained process catches SIGTERM,
the outcome depends on how much cleanup it manages to do in the
timeout period. We prefer a more predictable SIGKILL outcome.

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

6 years ago12891: Avoid flapping finalState after cancel.
Tom Clegg [Thu, 18 Jan 2018 21:41:39 +0000 (16:41 -0500)]
12891: Avoid flapping finalState after cancel.

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

6 years ago12891: Fix use of magic string.
Tom Clegg [Thu, 18 Jan 2018 21:41:14 +0000 (16:41 -0500)]
12891: Fix use of magic string.

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

6 years ago12891: Don't give up after trying once to stop the docker container.
Tom Clegg [Thu, 18 Jan 2018 21:40:59 +0000 (16:40 -0500)]
12891: Don't give up after trying once to stop the docker container.

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

6 years ago12891: Don't use SIGKILL when telling crunch-run to cancel.
Tom Clegg [Thu, 18 Jan 2018 21:39:16 +0000 (16:39 -0500)]
12891: Don't use SIGKILL when telling crunch-run to cancel.

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

6 years ago12891: Refactor slurm commands.
Tom Clegg [Thu, 18 Jan 2018 21:28:39 +0000 (16:28 -0500)]
12891: Refactor slurm commands.

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

6 years agoUpdated README to reflect current project state
Fuad Muhic [Fri, 19 Jan 2018 16:40:57 +0000 (17:40 +0100)]
Updated README to reflect current project state

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

6 years agoAdded unit tests for RESTService and HttpParser classes
Fuad Muhic [Fri, 19 Jan 2018 15:24:30 +0000 (16:24 +0100)]
Added unit tests for RESTService and HttpParser classes

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

6 years agoAdded unit tests for RESTService class
Fuad Muhic [Thu, 18 Jan 2018 14:31:02 +0000 (15:31 +0100)]
Added unit tests for RESTService class

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

6 years ago12891: Remove superfluous ThinDockerClientProxy wrapper.
Tom Clegg [Wed, 17 Jan 2018 22:21:18 +0000 (17:21 -0500)]
12891: Remove superfluous ThinDockerClientProxy wrapper.

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

6 years agoMerge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Fuad Muhic [Wed, 17 Jan 2018 16:22:31 +0000 (17:22 +0100)]
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk

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

6 years agoAdded unit test for ArvadosFile and Collection classes
Fuad Muhic [Wed, 17 Jan 2018 16:21:49 +0000 (17:21 +0100)]
Added unit test for ArvadosFile and Collection classes

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

6 years agoMerge branch '11876-r-sdk' of git.curoverse.com:arvados into 11876-r-sdk
Fuad Muhic [Wed, 17 Jan 2018 16:20:49 +0000 (17:20 +0100)]
Merge branch '11876-r-sdk' of git.curoverse.com:arvados into 11876-r-sdk

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

6 years agoFix wrong cluster label on search page when authenticated remotely.
Tom Clegg [Wed, 17 Jan 2018 15:31:04 +0000 (10:31 -0500)]
Fix wrong cluster label on search page when authenticated remotely.

Add uuid prefix to discovery doc.

refs #11453

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

6 years agoMerge branch '12934-cwl-conformance' refs #12934
Peter Amstutz [Wed, 17 Jan 2018 04:32:04 +0000 (23:32 -0500)]
Merge branch '12934-cwl-conformance' refs #12934

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

6 years ago12934: Bump cwltool version for packing fix.
Peter Amstutz [Tue, 16 Jan 2018 23:21:29 +0000 (18:21 -0500)]
12934: Bump cwltool version for packing fix.

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

6 years agoMerge branch '12479-wb-structured-vocabulary'
Lucas Di Pentima [Tue, 16 Jan 2018 21:36:27 +0000 (18:36 -0300)]
Merge branch '12479-wb-structured-vocabulary'
Closes #12479

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

6 years ago12479: Clear vocabulary.json cache every 5 minutes.
Lucas Di Pentima [Tue, 16 Jan 2018 21:21:14 +0000 (18:21 -0300)]
12479: Clear vocabulary.json cache every 5 minutes.

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

6 years ago12479: Updated example vocabulary. Attempt to show all the items
Lucas Di Pentima [Tue, 16 Jan 2018 21:07:22 +0000 (18:07 -0300)]
12479: Updated example vocabulary. Attempt to show all the items
on a given listing, using a scrolled list if necessary.
Also disabled sorting feature on awesomplete as it uses a default
sorting not suitable for our use case.

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

6 years agoMerge branch '12705-token-cache'
Tom Clegg [Tue, 16 Jan 2018 20:51:22 +0000 (15:51 -0500)]
Merge branch '12705-token-cache'

closes #12705

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

6 years ago12479: Accept tags with empty values
Lucas Di Pentima [Tue, 16 Jan 2018 20:45:46 +0000 (17:45 -0300)]
12479: Accept tags with empty values

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

6 years ago12479: Merge branch '12479-wb-structured-vocabulary' of git.curoverse.com:arvados...
Lucas Di Pentima [Tue, 16 Jan 2018 20:30:50 +0000 (17:30 -0300)]
12479: Merge branch '12479-wb-structured-vocabulary' of git.curoverse.com:arvados into 12479-wb-structured-vocabulary

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

6 years ago12479: Set dirty flag on change even when clearing input.
Tom Clegg [Tue, 16 Jan 2018 20:15:43 +0000 (15:15 -0500)]
12479: Set dirty flag on change even when clearing input.

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

6 years ago12479: Merge branch '12479-wb-structured-vocabulary' of git.curoverse.com:arvados...
Lucas Di Pentima [Tue, 16 Jan 2018 19:36:19 +0000 (16:36 -0300)]
12479: Merge branch '12479-wb-structured-vocabulary' of git.curoverse.com:arvados into 12479-wb-structured-vocabulary

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

6 years ago12479: Fix per-tag strict mode.
Tom Clegg [Tue, 16 Jan 2018 19:32:33 +0000 (14:32 -0500)]
12479: Fix per-tag strict mode.

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

6 years ago12479: Avoid tags tab reloading after saving.
Lucas Di Pentima [Tue, 16 Jan 2018 19:18:44 +0000 (16:18 -0300)]
12479: Avoid tags tab reloading after saving.

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

6 years ago12479: Open autocomplete when focusing an empty field.
Tom Clegg [Tue, 16 Jan 2018 19:18:40 +0000 (14:18 -0500)]
12479: Open autocomplete when focusing an empty field.

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

6 years ago12479: Use onupdate + stable vnode keys, let focus handle itself.
Tom Clegg [Tue, 16 Jan 2018 18:19:59 +0000 (13:19 -0500)]
12479: Use onupdate + stable vnode keys, let focus handle itself.

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

6 years agoAdded unit tests for Subcollection class
Fuad Muhic [Tue, 16 Jan 2018 13:03:41 +0000 (14:03 +0100)]
Added unit tests for Subcollection class

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

6 years ago12934: Rewrite file paths in pack instead of using "overrides"
Peter Amstutz [Tue, 16 Jan 2018 03:22:39 +0000 (22:22 -0500)]
12934: Rewrite file paths in pack instead of using "overrides"

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

6 years ago12705: Note 5 minute cache effect during user migration.
Tom Clegg [Mon, 15 Jan 2018 22:07:25 +0000 (17:07 -0500)]
12705: Note 5 minute cache effect during user migration.

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

6 years ago12705: Update authorized user when refreshing token cache.
Tom Clegg [Mon, 15 Jan 2018 21:55:56 +0000 (16:55 -0500)]
12705: Update authorized user when refreshing token cache.

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

6 years ago12934: Fix gofmt
Peter Amstutz [Mon, 15 Jan 2018 21:34:19 +0000 (16:34 -0500)]
12934: Fix gofmt

Also fix build-dev-docker-jobs-image.sh to use correct tag.

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

6 years ago12479: Re-added 'key' to the tag key div, because the lack of it
Lucas Di Pentima [Mon, 15 Jan 2018 21:16:23 +0000 (18:16 -0300)]
12479: Re-added 'key' to the tag key div, because the lack of it
produces an odd behavior when removing some existing tag using
the trash button and then trying to add a new tag.

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

6 years ago12479: Replaced selectize widget with awesomplete to solve some
Lucas Di Pentima [Mon, 15 Jan 2018 20:46:31 +0000 (17:46 -0300)]
12479: Replaced selectize widget with awesomplete to solve some
issues when navigating fields with TAB key.

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

6 years ago12934: Fix unit tests.
Peter Amstutz [Mon, 15 Jan 2018 20:22:49 +0000 (15:22 -0500)]
12934: Fix unit tests.

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

6 years agoBump version to 0.0.2
Tom Morris [Fri, 12 Jan 2018 22:09:32 +0000 (17:09 -0500)]
Bump version to 0.0.2

Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>

6 years ago12934: Remove debug log
Peter Amstutz [Fri, 12 Jan 2018 21:03:22 +0000 (16:03 -0500)]
12934: Remove debug log

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

6 years ago12934: Add .keep via manifest manipulation instead of creating real files
Peter Amstutz [Fri, 12 Jan 2018 15:53:57 +0000 (10:53 -0500)]
12934: Add .keep via manifest manipulation instead of creating real files

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

6 years agoAdded two utility functions and created unit test for them.
Fuad Muhic [Fri, 12 Jan 2018 15:25:51 +0000 (16:25 +0100)]
Added two utility functions and created unit test for them.

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

6 years agoMerge branch '12705-user-migrate-docs'
Tom Clegg [Fri, 12 Jan 2018 15:19:45 +0000 (10:19 -0500)]
Merge branch '12705-user-migrate-docs'

closes #12705

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