arvados.git
6 years agoMerge branch '11454-fix-syntax-errors' 1.1.3
Lucas Di Pentima [Thu, 8 Feb 2018 20:22:02 +0000 (17:22 -0300)]
Merge branch '11454-fix-syntax-errors'
Refs #11454

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

6 years ago11454: Syntax errors fixes.
Lucas Di Pentima [Thu, 8 Feb 2018 19:49:42 +0000 (16:49 -0300)]
11454: Syntax errors fixes.

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

6 years agoMerge branch '11454-wb-federated-search'
Lucas Di Pentima [Thu, 8 Feb 2018 16:59:10 +0000 (13:59 -0300)]
Merge branch '11454-wb-federated-search'
Refs #11454

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

6 years agoMerge branch '11876-r-sdk' refs #11876
Peter Amstutz [Tue, 6 Feb 2018 18:15:17 +0000 (13:15 -0500)]
Merge branch '11876-r-sdk'  refs #11876

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

6 years agoFix 5 failing tests
Fuad Muhic [Tue, 6 Feb 2018 15:06:39 +0000 (16:06 +0100)]
Fix 5 failing tests

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 [Tue, 6 Feb 2018 09:46:30 +0000 (10:46 +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 ago11454: Remotes listed on remoteHosts show "enable/disable" action button
Lucas Di Pentima [Mon, 5 Feb 2018 21:27:07 +0000 (18:27 -0300)]
11454: Remotes listed on remoteHosts show "enable/disable" action button
instead of "Log in/Log out".
When a listed remote rejects the salted token, the session shows as
disabled.
When a user entered (ie: not listed) remote rejects the salted token,
classic login is attempted.

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

6 years ago11454: When adding a uuid prefix on the add session box, append
Lucas Di Pentima [Mon, 5 Feb 2018 19:33:40 +0000 (16:33 -0300)]
11454: When adding a uuid prefix on the add session box, append
'.arvadosapi.com' before trying to get the API server url.
When a salted token is rejected, save the the session as logged out.

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

6 years ago11876: Add sdk/R to run-tests.sh
Peter Amstutz [Sat, 3 Feb 2018 04:11:46 +0000 (23:11 -0500)]
11876: Add sdk/R to run-tests.sh

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

6 years ago11454: On /search & /sessions page, check if the current user is
Lucas Di Pentima [Fri, 2 Feb 2018 22:29:37 +0000 (19:29 -0300)]
11454: On /search & /sessions page, check if the current user is
from a remote cluster, and if that's the case, redirect to the
proper home cluster workbench's page.

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

6 years ago11454: Add the salted token on search result links from federated
Lucas Di Pentima [Fri, 2 Feb 2018 20:49:00 +0000 (17:49 -0300)]
11454: Add the salted token on search result links from federated
remote hosts to get auto-logged in when clicking through.

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

6 years agoMerge branch '12268-libcloud-2-3-0'
Lucas Di Pentima [Fri, 2 Feb 2018 19:23:58 +0000 (16:23 -0300)]
Merge branch '12268-libcloud-2-3-0'
Refs #12268

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

6 years ago12268: Update the libcloud dependency to our forked version 2.2.2.dev4
Lucas Di Pentima [Fri, 2 Feb 2018 18:01:53 +0000 (15:01 -0300)]
12268: Update the libcloud dependency to our forked version 2.2.2.dev4
that's really 2.3.0 release candidate from the libcloud project, to
be able to do some stress testing.

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

6 years ago11454: Removed unnecessary call on migrateNonFederatedSessions()
Lucas Di Pentima [Fri, 2 Feb 2018 14:53:48 +0000 (11:53 -0300)]
11454: Removed unnecessary call on migrateNonFederatedSessions()
Added auto loading of remote hosts listed on home cluster's api discovery doc. (WIP)

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

6 years agoMerge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Fuad Muhic [Fri, 2 Feb 2018 14:45:41 +0000 (15:45 +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 agoArvados class now accepts additional parameter which specifies max
Fuad Muhic [Fri, 2 Feb 2018 14:41:44 +0000 (15:41 +0100)]
Arvados class now accepts additional parameter which specifies max
number of failed connection retries

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

6 years agoMerge branch '12902-queued-to-cancelled'
Tom Clegg [Thu, 1 Feb 2018 16:51:40 +0000 (11:51 -0500)]
Merge branch '12902-queued-to-cancelled'

refs #12902

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

6 years ago11454: Show a link to the remote workbench on the sessions page.
Lucas Di Pentima [Thu, 1 Feb 2018 16:40:17 +0000 (13:40 -0300)]
11454: Show a link to the remote workbench on the sessions page.
On page load, detect those non-federated active sessions and try to
migrate them to federated logins just in case they're stale sessions.
If the federated login doesn't succeed, keep the session's previous state.
Removed workbench remote_hosts config.

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

6 years agoMerge branch '12764-secure-tmp-parent' refs #12764
Peter Amstutz [Thu, 1 Feb 2018 16:35:30 +0000 (11:35 -0500)]
Merge branch '12764-secure-tmp-parent' refs #12764

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

6 years ago12764: Set mode on copied single files. Fix tests.
Peter Amstutz [Thu, 1 Feb 2018 16:32:33 +0000 (11:32 -0500)]
12764: Set mode on copied single files.  Fix tests.

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

6 years ago12764: Explicitly set desired permissions on copied files/dirs
Peter Amstutz [Thu, 1 Feb 2018 15:59:53 +0000 (10:59 -0500)]
12764: Explicitly set desired permissions on copied files/dirs

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

6 years ago12764: Remove CleanupTempDir. Better name for parent temp.
Peter Amstutz [Wed, 31 Jan 2018 21:59:50 +0000 (16:59 -0500)]
12764: Remove CleanupTempDir.  Better name for parent temp.

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

6 years ago12764: crunch-run temporary directories have common parent
Peter Amstutz [Wed, 31 Jan 2018 21:22:31 +0000 (16:22 -0500)]
12764: crunch-run temporary directories have common parent

Some directories created by crunch-run need to be world
readable/writable.  Apply path-based security using parent directory
with mode 0700.  Enables crunch-run to bind into the container while
avoiding making the directory trivially accessible to anyone on the
host.

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

6 years ago11454: Do federated logins by requesting the current user object
Lucas Di Pentima [Wed, 31 Jan 2018 19:37:15 +0000 (16:37 -0300)]
11454: Do federated logins by requesting the current user object
instead of the classic login flow.
When the user is inactive on the remote cluster, label the session
properly and exclude it from SessionDB.loadActive()'s results.

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

6 years agoWritable staged files/dirs need to be 0777 to match outdir mode. refs #12764
Peter Amstutz [Wed, 31 Jan 2018 19:34:26 +0000 (14:34 -0500)]
Writable staged files/dirs need to be 0777 to match outdir mode.  refs #12764

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

6 years agoFix sdk/cwl unit test refs #12934
Peter Amstutz [Wed, 31 Jan 2018 16:26:53 +0000 (11:26 -0500)]
Fix sdk/cwl unit test refs #12934

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

6 years agoMerge branch '12934-cwl-dir-output' refs #12934
Peter Amstutz [Wed, 31 Jan 2018 15:51:44 +0000 (10:51 -0500)]
Merge branch '12934-cwl-dir-output' refs #12934

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

6 years ago12902: Offer Cancel button for "on hold" containers.
Tom Clegg [Wed, 31 Jan 2018 15:17:21 +0000 (10:17 -0500)]
12902: Offer Cancel button for "on hold" containers.

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

6 years ago12902: Say "created at" instead of "started at" for a queued ctr.
Tom Clegg [Wed, 31 Jan 2018 15:09:11 +0000 (10:09 -0500)]
12902: Say "created at" instead of "started at" for a queued ctr.

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

6 years ago12902: Fix crash on null container_request name.
Tom Clegg [Wed, 31 Jan 2018 14:48:03 +0000 (09:48 -0500)]
12902: Fix crash on null container_request name.

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

6 years ago12902: Label CRs "Cancelled" if finalized with incomplete container.
Tom Clegg [Wed, 31 Jan 2018 03:41:01 +0000 (22:41 -0500)]
12902: Label CRs "Cancelled" if finalized with incomplete container.

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

6 years ago12902: Update state=Final when cancelling a container request.
Tom Clegg [Tue, 30 Jan 2018 22:56:13 +0000 (17:56 -0500)]
12902: Update state=Final when cancelling a container request.

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

6 years ago12902: Leave child CR "cancelled" (not "on hold") when parent exits.
Tom Clegg [Tue, 23 Jan 2018 15:40:21 +0000 (10:40 -0500)]
12902: Leave child CR "cancelled" (not "on hold") when parent exits.

Changing a container's priority to 0 effects "cancel" only after it
has started. Before that, it just gets held in the queue with priority
0. The child CRs of a terminated container are presumed abandoned, so
it makes more sense to finalize them.

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

6 years ago12934: Tweak output of directories to pass conformance tests
Peter Amstutz [Wed, 31 Jan 2018 14:23:57 +0000 (09:23 -0500)]
12934: Tweak output of directories to pass conformance tests

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

6 years agoReworkder HttpRequest class to use RETRY functionality
Fuad Muhic [Wed, 31 Jan 2018 13:36:57 +0000 (14:36 +0100)]
Reworkder HttpRequest class to use RETRY functionality

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 [Wed, 31 Jan 2018 09:28:51 +0000 (10:28 +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 agoMerge branch '12764-writable-file' refs #12764
Peter Amstutz [Wed, 31 Jan 2018 02:22:38 +0000 (21:22 -0500)]
Merge branch '12764-writable-file' refs #12764

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

6 years ago12764: gofmt fix
Peter Amstutz [Wed, 31 Jan 2018 02:06:54 +0000 (21:06 -0500)]
12764: gofmt fix

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

6 years ago12764: Handle empty directories. Fix test.
Peter Amstutz [Wed, 31 Jan 2018 01:46:50 +0000 (20:46 -0500)]
12764: Handle empty directories.  Fix test.

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

6 years ago12764: gofmt fix
Peter Amstutz [Wed, 31 Jan 2018 00:44:26 +0000 (19:44 -0500)]
12764: gofmt fix

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

6 years ago12764: bump cwltool version for conformance fixes
Peter Amstutz [Tue, 30 Jan 2018 23:59:15 +0000 (18:59 -0500)]
12764: bump cwltool version for conformance fixes

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

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 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 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 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 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 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 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 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>