Arvados v1.4 - Q1/Q2 2019


  • New Arvados Workbench implementation as a single page web app using the React framework (Beta)
  • New Java SDK
  • Rails 5 support in API Server & Workbench 1
  • Prometheus metrics support in a number of components
  • arvados-cwl-runner updated to support Python 3. Arvados will be ready for Python 2.x retirement at end of 2019.
  • all Arvados utilities written in Python now packaged with their own virtualenv to minimize dependency issues
  • Support for Ubuntu 18.04
  • Support for Python 3.7 in Python SDK


Release Backlog

# Tracker Subject Story Points

Closed Sprints

2018-12-12 Sprint


# Tracker Subject Story Points
14594 Bug [CWL] Update cwltool / schema-salad
14584 Bug API] Do not disqualify container from reuse due to different runtime_user/scopes
14538 Feature [keep-web] Do not block writes while flushing blocks to Keep
14574 Bug Workflow deadlocked
14343 Story Design for Group/Cluster favorites/library 1.0
14476 Bug CommandLineTool hanging in unexpected limbo state between
14181 Bug [keep-web] [Documentation] Increase client_max_body_size for WebDAV requests

2018-12-21 Sprint


# Tracker Subject Story Points
14640 Bug [API][Workbench] Security vulnerability on activejob
14012 Bug arv-put does not check cached signatures when resuming
14495 Bug [crunch2] include space required to download/unpack docker image in tmp disk request
13006 Bug is_a filter doesn't work with remote objects 1.0
14596 Bug [crunch-dispatch-slurm] Abandoned container starts again instead of being cancelled
14595 Bug [API] logs.event_at has wrong timestamp
11419 Story [SDKs] support text-mode open() in Python 3
14327 Bug [CWL] Don't make any create/list API calls when preprocessed inputs turn out to be identical to original inputs
14360 Story [crunch-dispatch-cloud] Merge incomplete implementation 1.0
14510 Bug [e51c5] scheduling happens every 5 minutes.
14617 Support Migrate public channel to gitter
14439 Story Write configuring federation admin documentation 0.5

2019-01-16 Sprint


# Tracker Subject Story Points
14703 Bug [SSO] Login fails when configured with only the local provider
14660 Story [Workbench 2] Investigate feature parity with Workbench 1 3.0
14324 Feature [crunch-dispatch-cloud] Azure driver 3.0
14691 Bug Update suggested .ssh/config section in documentation and workbench

2019-01-30 Sprint


# Tracker Subject Story Points
14718 Feature [API] Option to issue salted token in login procedure 2.0
14739 Story [GA4GH] Review DRS for Arvados 2.0
14482 Bug [SDKs] Handle "." empty directory placeholder in manifests in Ruby SDK
14733 Bug Secrets example

2019-02-13 Sprint


# Tracker Subject Story Points
14725 Story [GA4GH] Support WES 1.0 0.5
13306 Story arvados-cwl-runner supports Python 3
14806 Bug [crunch1] unescape filenames when parsing manifests in crunch-job
14325 Feature [crunch-dispatch-cloud] Dispatch containers to cloud VMs directly, without slurm or nodemanager 1.0
14326 Bug Our custom-compiled `python-future` and `python3-future` packages can't be installed together and have precedence
14539 Bug [SDKs] [arv-mount] Use "." placeholder to persist empty directories
9945 Story [SDK] Package Python apps as virtualenvs 1.0

2019-02-27 Sprint


# Tracker Subject Story Points
12958 Feature [Federation] Workbench login chooser
14383 Bug [API] Java SDK double slash bug with arvados-controller
14853 Feature Merge chapmanb py3k-subprocess32 pull request
14841 Story Link from Workbench 2 to Workbench 1 0.5
14794 Story Link from Workbench 1 to Workbench 2
14804 Bug [keepstore] Return 5xx (not 4xx) if block is not found due to transient backend device failure
14720 Feature [Federation] Workbench2 login chooser 1.0
11561 Bug [API] Limit number of lock/unlock cycles for a given container 2.0
14845 Bug [controller] Fix flaky test
14745 Bug [crunch-dispatch-cloud] Azure cloud driver fixups 3.0
14828 Bug [crunch-dispatch-cloud] Fix flaky test

2019-03-13 Sprint


# Tracker Subject Story Points
13593 Bug [API] Sequence of "create group" requests runs slowly, and can crash API server 3.0
14784 Bug [node manager] not shutting down all nodes
14920 Bug [crunch-dispatch-cloud] New Azure instances always have state=unknown instead of state=booting
13937 Story [keepstore] Move legacy metrics to prometheus /metrics endpoint 1.0
14938 Bug [crunch-dispatch-cloud] flaky test in lib/dispatchcloud/worker
14936 Bug ImportError: No module named future_builtins
14880 Bug arv-keepdocker is very picky about the order of its command line arguments and crashes with an obscure error if the order is wrong
14870 Story [API] Access logs from previous attempts after auto-retrying a container request 2.0
14886 Bug Recursion runtime error in arvados.cwl-runner running on su92l
14819 Feature Upgrade the arvados/jobs image to Debian Stretch
14885 Bug Review and merge chapmanb's ciso and conda packaging pull request
14291 Feature [crunch-dispatch-cloud] AWS driver 2.0
9865 Bug [CWL] Fix undefined behavior after ignoring an unhandled exception
14382 Story Review Java SDK PR
14911 Bug [dispatch-cloud] Azure driver panic at startup
14844 Bug [dispatch-cloud] Azure driver bugs discovered in trial run 1.0
13823 Story Package Arvados for Ubuntu Bionic Beaver 18.04 LTS 0.5
14884 Bug arv-put doesn't handle non-ASCII filenames correctly

2019-03-27 Sprint


# Tracker Subject Story Points
15007 Bug [dispatch-cloud] Azure driver panic in Address() (missing nic?)
14606 Story [CWL] CWL v1.1 spec work and support 1.0
14900 Bug [arv-put] when reusing a local cache, arv-put does not check if the blocks exist and blindly creates the collection
14322 Feature [CWL] Accept collection uuid in input 2.0
12026 Bug [crunchstat-summary] gives invalid min_cores recommendation
10570 Bug [crunchstat-summary] should not report 0% CPU and 0 RAM in cases where stats were not reported at all
14451 Bug crunchstat-summary recommends 563 TB Keep cache (or more!)
14807 Story [arvados-dispatch-cloud] Features/fixes needed before first production deploy
14645 Story [arv-mount] Report FUSE operation latency 3.0
14669 Story [Java] Merge into main Arvados repo
14977 Bug [arvados-dispatch-cloud] kill crunch-run procs for containers that are deleted or have state=Cancelled when dispatcher starts up
14947 Feature [Tests] --interactive
14966 Bug [API] Fix hanging test - suspect permission changes

2019-04-10 Sprint


# Tracker Subject Story Points
15040 Bug Fix federation tests
14873 Story [API] Update to Rails 5 2.0
14484 Story [API Server] Return collection size and number of files in collection record 1.0
14796 Story [crunch-dispatch-cloud] Document installation / migration from c-d-slurm + node manager 1.0
15044 Bug [Tests] Update tests to work on base debian:9 image
15050 Bug Limit number of containers crunch-dispatch-local runs at one time

2019-04-24 Sprint


# Tracker Subject Story Points
14627 Bug [crunchstat-summary] job elapsed time wrong for crunch2 jobs 0.5
14939 Story Update crunchstat-summary to Python 3 1.0
14835 Story Update cluster configuration wiki from scratch doc
15109 Bug [Documentation] Add details about logs table purging on the Admin section
15002 Story [API] Admin can prevent reuse by cancelling a completed container 1.0
13996 Story [API] Migrate RailsAPI to new cluster config file 3.0
14573 Feature [Spike] [API] Fully functional filename search 2.0
14723 Bug [CWL] File that should appear multiple times in output collection only appears once
15092 Bug [SSO] [c6coi] [q2] Support for non-email login in LDAP
15058 Bug [SSO] "Not found. Authentication passthru" when using local account authentication

2019-05-08 Sprint


# Tracker Subject Story Points
15180 Story [Spike] Test migration on production database 0.5
15164 Bug Container request not finalized
14670 Story [Java] Write / merge Java SDK documentation

2019-05-22 Sprint


# Tracker Subject Story Points
15241 Bug [a-c-r] crashing using collection in writable initialWorkDir
15230 Bug [wb2] Crash loading federated collection
15232 Bug [config] BlobSigningTTL should be expressable with a suffix
15064 Feature [Workbench2] Use long-lived cookies to improve login chooser defaults 1.0
15227 Bug [API][Workbench] Adding tags via workbench1's tag editor saves the JSON string to properties
15167 Bug Complete logs table management docs with unlogged_attributes setting
15088 Story [Workbench2] Replicate Workbench1 merge account feature 2.0
14988 Story [Workbench] Upgrade to Rails 5 0.5
15225 Bug [API] installation gives error: Creating git_internal_dir ''...mkdir: cannot create directory ‘’: No such file or directory
15161 Bug Dev clusters are failing: uninitialized constant ArInternalMetadatum (NameError)
8189 Bug [FUSE] Listing a project directory is slow when there are many subprojects

2019-06-05 Sprint


# Tracker Subject Story Points
15275 Bug [API] Collection DELETE call fail when versioning is active
15258 Bug [Workbench] Report problem/Show version popup failing