Arvados Future Sprints

Due in about 19 months (01/02/2020) (Sprint start date 01/01/2020)

A pseudo-version to collect tickets from multiple projects

7%

998 issues   (112 closed886 open)

Future sprints

Arvados Contributor Wiki

This wiki has information related to the open source project. It's a work in progress, so come back often for updates and feel free to become a contributor.

Platform Overview

Release Notes

Key Components

Using Arvados

Contributing and hacking

Community

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Time tracking
Estimated time 27.00 hours
Issues by
Bug

41/479

Feature

12/181

Task

46/135

Story

13/203

Related issues
# Subject Story Points
Bug #13609 Copying files using the R SDK results in 0 byte files
Story #13571 Review dependencies to make sure that they meet requirements
Story #10511 [Crunch2] [API] Specify which user's credentials should be used by a container
Feature #13493 Federated record retrieval 2.0
Story #11740 [Workbench] Support display & reseting of expiration dates for collections 2.0
Story #13198 [Keep-web] Add metrics endpoint 3.0
Feature #13403 [crunch-run] Cancel container on FUSE error 2.0
Feature #13382 [keepstore] Write new blocks to appropriate storage class 1.0
Story #13219 Allow user to specify time limit for submitted jobs 3.0
Bug #13351 Benchmark container_request creation and see if there are opportunities for optimization
Story #13255 Provide account activation configuration options for federated logins 2.0
Story #13146 [API] Endpoint to get projects shared with me 3.0
Story #13484 [API] Support multiple load-balanced API server nodes 1.0
Bug #13343 arvbox warn if running as root or on OS X
Bug #13322 keepstore -help entry for -dump-config is unclear
Story #13048 Refactor crunch2 logging 2.0
Feature #12444 Compute nodes monitor the tmpdir space over time 1.0
Story #12191 Support SLURM parameter passthrough from CWL jobs 2.0
Bug #13006 is_a filter doesn't work with remote objects 1.0
Story #11942 [CWL] arvados-cwl-runner should support tagging output collection using properties 1.0
Bug #13142 crunch-dispatch-slurm uses a surprising number of file descriptors, and stops dispatching when it gets a "too many open files" error
Bug #12251 [API] Strict checks for "@@" filter operand 1.0
Story #13096 Investigate packrat to lock down R package dependencies
Story #13077 R SDK submit to Bioconductor
Story #13046 Provide configuration knob to disallow external access through keep-proxy
Bug #12994 Can't create user group with the same name as a top level project
Bug #12990 [FUSE] Access shared/ is inefficient
Bug #12880 [Composer] Production build fails to load
Bug #12859 keepstore no longer functioning with repeated errors: http: Accept error: accept tcp [::]:25107: accept4: too many open files; retrying in 1s
Bug #12834 [Crunch2] Node record's crunch_worker_state field is not populated
Bug #12558 [Workbench] Bad dashboard time formatting - 60m == 1h
Bug #12510 [API] Don't create an index if it exists already. Will break install if we manually added it,
Bug #12465 [crunchv2] Improve crunch-run environment reporting
Story #12704 [API] Associate multiple identity_url from SSO with same user
Feature #12090 Collections/data access API
Bug #12410 Different help listing for 'arvados-cwl-runner'
Bug #11519 arv-get should abort on ctrl/C
Story #12527 [Composer] Refactor to separate vendor-specific pieces and all them to be replaced
Bug #12606 Symlink in output points to invalid location -- no such file or directory
Bug #12077 [Workbench] Description column doesn't contain descriptions 1.0
Story #12409 [cwl] cwl-tool conditional implementation
Bug #12360 Document how to add EBS tmp disk to nodemanager configuration
Bug #12358 Document requirements for nodemanager token scope
Bug #12295 [nodemanager] Only looking at first 100 queued jobs
Bug #12331 [CWL] Does not distinguish between keep references to File and Directory when selected in Workbench template
Story #12289 Migrate to Slurm API
Story #12288 Status endpoint aggregator
Story #12239 Allow templating of the collection sharing web page
Bug #12198 Copying a project with a docker image doesn't copy the docker metadata
Bug #11794 Deprecate / remove arv-web
Story #11285 Update Pipeline Optimization wiki with CWL/Crunchv2
Bug #12170 crunch-run handling non-group readable files in output directory
Bug #12113 mandatory keep_web configuration missing from workbench install instructions
Story #12089 Javascript SDK
Bug #12082 [SDKs] Improve wording of Keep error messages in Python SDK
Bug #12058 [node manager] failing test
Bug #12051 lost job log
Feature #12028 Be able to create a new collection based on a subdirectory in workbench
Bug #12026 [crunchstat-summary] gives invalid min_cores recommendation
Feature #12009 Find arvados-cwl-runner version easier in a container request
Story #11983 On the collections page indicate expiring collections
Bug #11917 Error fetching collection (HttpError 422) during call to arvados.util.listdir_recursive
Bug #10584 [FUSE] high memory consumption (possible leak) in long-running arv-mount
Story #10679 [Workbench] Update job stats to be more useful to end user
Story #11705 [API] Remove async permissions code 0.5
Story #11875 User accounts optionally have read-only access
Story #11871 [Workbench] Add a "Browse" tab that links to tree/master in repository#Show page
Story #11884 Convert Collection properties column type to JSONB
Bug #11863 [Go] CLI programs should exit 0 after giving -help
Bug #11844 [Workbench] incorrect text about log messages on empty collection
Story #11836 [Nodemanager] Improve status.json for monitoring 0.5
Story #11770 [Python SDK] Implement support for universal newline mode in Collections API
Feature #11745 Support schema.org/Google structured markup for datasets
Story #11748 Standard convention for Nagios-compatible health check scripts kept alongside source for services
Bug #11724 Import Docker images without requiring Docker on client
Bug #11716 [Workbench] The sort order of items on /pipeline_instances and /container_requests page is incorrect
Bug #11692 CWL Expression Tool Javascript issue when using str.includes
Bug #11691 Using cwl, when you obtain files (file objects) from a directory listing they lose some fields when compare to files listed in cwl doc
Bug #11680 [Workbench] Provenance graph consolidates scatter steps
Bug #11679 [Workbench] Logs containers with undefined exit code
Bug #11669 [Crunch2] crunch-dispatch-slurm hits scancel too much
Feature #11668 [SDKs] Exceptions raised by Python SDK should include the "error token" if provided in the API response
Story #11657 [SDKs] publish python3-arvados-python-client packages 1.0
Bug #5076 [Workbench] Replace schizophrenic generic "groups" page with "roles" page that only creates/lists groups with group_class="role".
Bug #11627 [node manager] not assigning weights
Bug #11621 Example CWL code for cwl-runner doesn't work
Bug #11609 [Workbench] A cancelled container request page should show the "Re-run" button
Feature #11605 arv-put detects symlinks to common files and directories to avoid duplicated uploads
Bug #11594 [API] [Wrokbench] set a default config.log_level
Bug #11593 [API] [Workbench] config option serve_static_assets to serve_static_files 1.0
Bug #11581 a-c-r should log the command used to run the pipeline
Feature #11582 [API] Delete old job/container logs in main server process, instead of rake tasks invoked from cron jobs
Bug #11584 [CWL] Allow "keep:" references on command line.
Bug #11561 [API] Limit number of lock/unlock cycles for a given container
Story #9441 [Workbench] Improve user page group memberships management [to be groomed]
Feature #11515 [CWL] [Workbench] Support for copying/moving pipelines
Bug #11556 occasional API server badness: 'incomplete response received from application'
Story #11741 [Crunch2] Create workflow object for CWL runs which are initiated from the command line
Story #11558 [FUSE] Integration test using real programs with complex write patterns.
Feature #11555 [API] Webhook callbacks for server-to-server communication
Bug #11553 [FUSE] Writable fuse creating conflicts with itself
Bug #11548 workbench needs to handle API server timeouts better
Bug #11547 [API] Excessive memory and time consumed by API and dispatch when container fields (like "mounts") are large
Bug #11531 [API] clean up stale/conflicting dns data from deleted node records
Story #11524 Implement disk usage reporting for the administrator
Bug #11523 User activity page takes too long to load
Bug #11520 "arv collection list" command parsing allows invalid lines
Feature #11508 HTTP 503 status for planned downtime
Bug #11495 bcbio NA12878 validation runs: job re-use failure with non-existant collection
Bug #11494 bcbio NA12878 validation runs: failed steps due to being unable to setup container
Story #11452 Support rendering of CWL description fields with embedded markup
Bug #11460 [SDK] avoid interfering with socket open/close - use pycurl sockoptfunction instead of opensocketfunction
Feature #11442 [SDK] Resolve symbolic names to uuid/pdh (cwl + other tools)
Story #11421 [Workbench] UUIDs & PDHs should be hyperlinked
Feature #11419 [SDKs] support text-mode open() in Python 3
Feature #11410 [SDK] tool for copying CWL file + input collections 0.5
Bug #11405 [arv-put] Lumpy / slow upload
Bug #11396 Network saturation
Feature #10123 [Workbench] [UNC] Copying collections also copies metadata
Bug #11296 [arv-put] bad progress indicator
Bug #11257 [CWL] Fails with $schemas referencing remote resources.
Bug #11261 [API] full text search on pipeline_instances table is extremely slow (wrong index?)
Bug #11260 [API] "arv group contents" produces a 404 error (seems to POST instead of GET?)
Story #11251 [Tests] Make workbench integration tests finish faster (at least in Jenkins)
Bug #11238 job_task creation fails with ApiError - HttpError 422 - ActiveRecord::StatementInvalid: PG::InternalError: ERROR: invalid memory alloc request size 1718630765
Bug #11222 Docker load time on compute node is too long
Feature #11183 [Deployment] Use consul to report health of services/components
Story #11171 [Nodemanager] Packaging for compute node setup scripts
Story #11163 [GA4GH] Participate in DREAM workflow interoperability activities
Story #11161 [GA4GH] Support task execution API using crunch v2 containers
Story #11160 [GA4GH] Expose workflow records via tool registry API
Story #11159 [GA4GH] Import from tool registry API
Bug #11157 [arv-put] When debug mode is active, report the cache file name being to be used
Bug #11155 [Docs] Document keepstore S3 volume configuration
Bug #11154 [Docs] Migrate install docs from command line flags to YAML configs (keepstore, keepproxy, keep-web)
Feature #11153 [API] create_token script should allow operator to provide token scopes and opaque comment
Bug #11148 [Crunch2] Propagate dispatch error messages (e.g., sbatch fails) to user via logs/websocket
Story #11147 Write scalability test which can be used periodically as needed
Feature #11146 [Crunch2] [Workbench] Show slurm queue position of containers submitted to slurm but not yet running 3.0
Bug #11137 apt-get upgrade arvados-api-server on Ubuntu 12.04 did not update crunch-job
Bug #11093 "arv keep_service create" should go to an editor.
Bug #11075 Trying to copy a pipeline template to 9tee4 fails
Bug #11026 "Run a example test" Button.
Bug #10008 [SDKs] [Python] When reading data through Collection et al., signatures should refresh automatically when needed
Story #11016 Document how to choose a suitable blob signature TTL
Bug #11013 [WB] 'Used by' tab empty when no graph is available
Feature #10998 [keep-web] configurable block cache size 0.5
Bug #10978 [CWL] Avoid using "+" char in mount paths 0.5
Bug #10955 arvados-cli gem dependency error
Bug #10948 [Workbench] Live stats should use consistent coloring for graphs
Story #10477 Switch from goamz to aws-sdk-go 2.0
Bug #10705 [Crunch2] [API] return a more specific 422 error message when a client calls containers#unlock without having the lock
Bug #10946 [Docs] [SDKs] Mention in API docs and discovery doc that destroy=delete and index=list
Story #10904 [Spike] virtualenv arvados-cwl-runner
Bug #10898 [Documentation] we should not use github.com copy of arvados in the tutorial
Bug #10881 [cwl] arvados-cwl-runner submitted job fails due to missing dependency futures>=3.0.5 in docker/jobs image
Feature #10865 [Crunch2] [Crunch1] Disable crunch1 APIs by default on new installs 0.5
Story #10849 [API] [SDKs] When client and server versions differ, the server must either implement the API the client expects, or return an error.
Feature #10830 [Workbench] Support array type input parameters to Workflows
Bug #10809 [Workbench] Don't create manifest with 0 length chunk
Bug #10794 [keepstore] Refactor volume Get/Put funcs to BlockReader/BlockWriter interfaces
Bug #10729 [Crunch2] Propagate error messages if sbatch command succeeds but crunch-run can't run (or can't log to the Arvados API)
Feature #10763 [arvbox] [arvados-ws] Make arvbox use the new arvados-ws 0.5
Bug #10756 [Workbench] pipeline_instance#show page should offer “Copy to project” and “Move pipeline instance” options like most other show pages
Bug #10718 add a --user-script option to install-arvados-jobs-image
Bug #10721 [Docs] Missing docker_image link classes from API docs 0.5
Bug #10715 [Workbench] "Public pipelines" on help menu links to wiki, not local public pipelines
Story #10717 Deprecate arv-run
Bug #10708 [Crunch2] crunch-run fails trying to set swappiness on ubuntu 1204 kernel
Bug #10689 Crunch1 jobs should still work on a slurm setup configured for Crunch2
Bug #10035 [FUSE] Determine why bcl2fastq doesn't work with writable keep mount 1.0
Bug #8871 [Node Manager] Doesn't kill itself when unhandled exceptions are raised during actor setup
Bug #10650 [Python SDK] Document undocumented methods in RichCollectionBase 0.5
Bug #10643 Unable to build arvados-cwl-runner in 9tee4 environment
Bug #10614 [CWL] a-c-r maximum recursion depth exceeded error
Bug #10573 apps/workbench_functionals test failing
Bug #10571 services/nodemanager test_time_timout failing
Bug #10570 [crunchstat-summary] should not report 0% CPU and 0 RAM in cases where stats were not reported at all
Bug #10566 arvbox destroy fails because some files are owned by root
Bug #10561 sometimes `arvbox reboot test` gets stuck asking for a sudo password
Bug #10554 Collection file count & size information don't get dynamically updated on collection update
Bug #10552 arvados-git-httpd returns error '500' (Internal Server Error) when a request is not authorized
Bug #10545 arvbox loops forever when something goes wrong
Bug #10543 implement approximate (estimated) counts for API list method
Story #10537 [Workbench] Add support for Trash Bin
Feature #10541 [Keep] Share buffers between overlapping/consecutive GET requests for the same block 2.0
Bug #10535 test suite hangs (in arvbox) in sdk/python test_callback
Bug #10532 Multiple links with the same relevant information can be created
Bug #10531 [crunchstat-summary] HTML plots should be a superset of text format output
Story #10525 Integrate CI::Reporter to provide test output in JUnit XML format
Bug #10514 [crunch-run] use docker instead of docker.io 0.5
Feature #10493 [Python SDK] Provide more control over pre-fetch behavior
Bug #10469 Multiple virtual machines with the same hostname can be created
Bug #10458 Document crunchstat-summary
Bug #10445 [SDKs] Fix memory leak in Python SDK Collection class
Bug #10444 [Performance][Workbench] While in a resource #show page, switching between tabs results in fetching the object again from API server. This can cause unacceptable amount of latency for large objects such as large pipeline instances and also to collections.
Bug #10408 4xphq keep balance api request causes oom on api server
Feature #10403 Node manager should fetch pricing information from cloud APIs
Story #10405 [API] Remove unimplemented fields from api_client_authorization
Story #10402 [CWL] Reduce redundant work with subworkflow RunInSingleContainer
Bug #10390 crunchstat-summary should explain why "(no report generated)" when possible
Story #10388 Request collections that don't (yet) exist via fuse interface
Story #10387 Faster downloading using arv-get
Bug #10386 In the arvados sso database, multiple identical clients can be created
Story #10354 Add varchar_pattern_ops to all relevant PostgreSQL UUID indexes
Story #10358 Get list of Arvados configuration parameters in puppet that could be published by Consul
Story #10355 [Workbench] Enable refresh for "small" pipelines
Story #10344 [Workbench] Import CWL workflow
Bug #10337 remove the need of yum reinstall from the installation/upgrade of Rails based components
Bug #10327 arvados-cwl-runner fails to find secondaryFiles
Bug #10320 [Workbench] Don't assume Switchyard config for SSH explanation
Bug #10319 [Workbench] list of logins in the admin page isn't showing all logins
Feature #10328 [CWL] a-c-r option to resubmit failed jobs
Feature #10313 [Crunch2] crunch-run config option to use arv-mount for output dir
Feature #10309 [Workbench] add a configuration flag to hide compute nodes
Bug #10308 Output glob "./" doesn't work as output from CWL workflow
Bug #10298 [Crunch2] [API] Accept collection UUID or PDH as container_image in a container request
Bug #10296 [Centos7] [google_api_python_client] packaging with wrong permissions
Feature #10594 [API] [Workbench] Error out when unrecognized keys appear in config files 0.5
Bug #10282 [Go programs] Error out when unrecognized keys appear in config files
Bug #10265 [Workbench] Pipeline instance shows wrong button labels in tab area
Bug #10696 [CWL] Tries to run docker inside container where docker is not available, gives IOError
Feature #10268 [SDK] Convenience method for resolving project/file paths
Story #10245 [Performance][Workbench] Computing user notifications in topnav is expensive. Can the user's properties be used instead?
Story #10242 [Performance] Fetching the pipeline instance qr1hi-d1hrv-jl9fvzy3x8sdj8v seems to take too long
Feature #10217 [Crunch1] Log the node properties at the start of a job
Story #10213 Efficient queries for notification menu items
Bug #10206 [CWL] arvados-cwl-runner may not be handling input files on keep mount correctly
Feature #10191 Arvados should be able to cat/zcat files in collections easily
Feature #10183 [Node Manager] Support ephemeral additional storage for Azure node types that do not have sufficient instance storage
Bug #10182 Provide more reasonable error messages for memory issues during container dispatch
Feature #10181 Crunch job output logging improvement stories 2.0
Bug #10177 Confusing job duration reporting
Bug #10167 [SSO] sso server adds multiple records without checking
Bug #10170 [Workbench] Jobs on dashboard say "No output" even when they have output
Feature #10164 Additional Crunch job logging controls
Story #9960 Automate starting/enabling services during Workbench and API package installation
Feature #10141 [Packaging] Include sample config file (/etc/arvados/foo/foo.example.yml) with each configurable package 2.0
Bug #10127 [API] In each request log entry, report time spent getting current permission graph
Bug #10120 [Crunch] crunch-dispatch log throttling should not apply to its own stderr
Bug #10097 Python RichCollectionbase's find_or_create() method callers may assume that found object is of "create_type" type
Bug #10096 RichCollectionBase's _get_src_target method would crash if "source" argument is not basestring and "target_path" is empty.
Bug #10084 keep-balance reporting large numbers of replicas lost
Bug #10083 queued jobs in Paused pipeline instances start running anyway
Bug #10080 pipeline_instance state can be changed from `Complete` to `Paused`
Bug #10040 [Workbench] ContainerRequest#show crashes "undefined method `each' for nil:NilClass"
Story #10027 Move Container related documentation from wiki to code
Bug #10018 [Workbench] Double-clicking "show version" link causes modal deadlock
Bug #10007 [Workbench] Retrieve all log content directly from API instead of pre-rendering in Rails
Bug #9989 [SDKs] Python SDK should use a more recent version of the google api client library
Bug #9985 [Testing] TestErrorDuringRsync_FakeDstKeepservers
Bug #9984 [Testing] test_shutdown_declined_when_idle_and_job_queued flaky
Bug #9969 [Crunch2] [API] Permit container [request] with empty command (run default docker command)
Feature #9968 [Crunch2] [API] Support container request expiry (expires_at)
Bug #9965 [CWL][Crunch][Crunch2] crunchrunner should ignore hidden directories when uploading to keep
Bug #9964 [CWL][Crunch2][Crunch] crunchrunner should use CWL globs to output data to keep
Bug #9870 [FUSE] arv-mount installation documentation not working
Bug #9732 [FUSE] performance issues stat() in python
Story #9591 [FUSE] Undelete collections by moving them out of the TrashDirectory
Story #8179 [keep-balance] Refuse to act when planning to delete data above an admin-specified threshold
Bug #9967 [keep-balance] Do not delete blocks referenced by collections with replication_desired=0
Story #9958 login-sync config file & systemd unit
Story #9959 nodemanager systemd unit
Story #9945 [SDK] Package Python apps as virtualenvs
Story #9937 [Workbench] file upload should provide progress bar for overall upload, not just individual files
Bug #9936 Workbench file upload should allow the selection of directories
Bug #9929 [SDK] portable_manifest_text() normalizes manifest, breaks CollectionReader() round trip
Bug #9921 [SDKs] Python SDK duplicates resource attributes in top level of params
Feature #8415 [SDKs] arv-put's default output includes both collection UUID and PDH
Feature #3311 [SDKs] Improve metadata created by arv-put
Feature #9802 [Workbench UI] Pipeline instances should have a link to view the CWL file used.
Bug #9755 [CWL] Creating intermediate folders in working directory (fails in cwl-runner)
Bug #9750 [Workbench] UI should advance to new step when user submits their input
Feature #9747 [CWL] Secondary files entering into Arvados automatically
Story #9839 [Crunch2][Workbench] List both pipeline_templates and workflows on both pages 2.0
Bug #9588 [CWL] cwl-runner parses nested arrays repetively
Bug #10142 [Workbench] Ability to add group from Groups admin page
Bug #9443 [keep-rsync] Rename "replications" to "replicas" 0.5
Feature #9364 [keep-balance] "Expedited delete" tool: perform garbage collection on some specific (recently deleted) collections, bypassing usual GC race protections 3.0
Bug #9362 [CWL] arvados-cwl-runner should reuse the most recent run
Bug #9659 [CWL] Jobs crash when arvados/jobs:latest is not suitable to run CWL jobs
Bug #9630 [Crunch2] crunch-dispatch-slurm can't successfully dispatch work when run from a directory it can't write to 0.5
Story #9278 [Crunch2] Document/fix handling of collections with non-nil expires_at field 1.0
Story #8912 [Data manager] Verbose reporting 0.5
Bug #8798 [Node Manager] huge virtual memory size
Bug #8504 [Workbench] Times out before API server loading active pipeline instances 0.5
Story #9592 [FUSE] rmdir on CollectionDirectory sets expires_at
Story #9590 [FUSE] Trash directory to list, inspect, and un-trash trashed collections
Story #9584 [FUSE] Don't display expiring collections in regular collection listings
Feature #9245 [FUSE] Make .arvados#collection available in collection subdirectories
Bug #9244 [FUSE] .arvados#collection is missing or outdated after writing inside collection
Bug #8685 [FUSE] Add timestamp to arv-mount --logfile option
Feature #8641 add key/value support for tags
Story #8573 crunchstat-summary should calculate averages of all metrics
Bug #8317 [Provenance Tracking] jobs refer to collections by uuids, not pdh
Bug #8254 Add Gantt chart for pipeline optimization
Bug #7977 get rid of dependencies python-pyasn1 python-pyasn1-modules
Bug #7747 [FUSE] arv-mount is too slow for strelka
Story #7543 [Documentation] Write a Crunch2 wiki page 1.0
Story #7542 [Documentation] Write a Crunch wiki page 1.0
Bug #7479 [Node Manager] Aggressively throttles node creation requests when the cloud region is full
Bug #11027 [Crunchv2] python thread error after job success
Bug #7667 [NodeManager] CloudNodeListMonitorActor stopped reporting, and logs are not helpful enough to diagnose 1.0
Bug #8669 [SDKs] PySDK fails to load CAs for SSL verification when run inside Conda
Bug #8721 [Crunch] crunch-job can miss the final log output of a job
Bug #8148 [FUSE] When we give up trying to write a block, the next operation on the file should fail
Bug #9156 [Workbench] Bad URL quoting/parsing in File links from the pipeline template Components tab
Feature #9136 [Python SDK] Add a Collection method to efficiently concatenate files
Story #8774 [Crunch] Limit maximum wait time between retries
Feature #7328 [Crunch] [UX] Standard excepthook to help debug job problems 1.0
Bug #8315 [SDKs] arv-copy fails to copy a Docker image specified with repo:tag syntax 0.5
Bug #8901 [Workbench] The "Log" tab should have an notification that the job has been queued
Story #8894 [Node Manager] Less logging of tracebacks for routine exceptions
Bug #8346 [API] Bad compute node address detection on private networks
Bug #8388 [SDKs] WebSocketClient Exception 'NoneType' object is not callable 0.5
Story #8552 [Crunch] Log throttling shouldn't throttle logs from crunchstat, crunch-job
Story #7831 [FUSE] Add --umask, --fmask, --dmask options to control file permissions 1.0
Bug #9141 [SDKs] Bad use of RetryLoop in events.py
Bug #7156 [SDK] arvados.arvfile.readall_decompressed() does not return all blocks on a file
Bug #8869 [Crunch] Job was repeatedly retried on same bad compute node until abandoned
Bug #8387 [Docs] Many tutorial instructions are wrong outside Curoverse clusters
Bug #8830 [Workbench] No user profile should be required in the default configuration 0.5
Story #8778 [Docs] Document Git 1.7.10+ dependency for shell node and HTTPS Git cloning
Story #8781 [Docs/Workbench] Document how to clone repositories over HTTPS
Story #8775 [Docs/Workbench] Improve SSH agent documentation
Bug #7743 [Workbench] Hide file preview buttons when preview isn't possible with current keep-web config 1.0
Story #8885 [PySDK] API client logs a warning when you create an object without an owner_uuid
Story #7980 [Node Manager] Broken nodes always get shut down, exempt from all node-counting considerations
Story #8000 [Node Manager] Shut down nodes in SLURM 'down' state
Bug #8541 [NodeManager] Use sys.exc_clear() to release exception tracebacks
Feature #8551 [Node Manager] Minimum idle time before node is eligible for shutdown
Bug #8686 [Node Manager] qr1hi nodemanager can't start if ulimit is in place
Bug #8084 [Node Manager] Doesn't convert units when determining if a job's scratch request is satisfiable 0.5
Story #8565 [API] Go code to connect to the API server database and make basic sense of it
Story #8566 [API] Go code to implement the Arvados API permissions model
Bug #8638 [API] List queries using "distinct" option return incorrect number of items_available
Bug #6772 [API] Should not be necessary to host git repos on the same host as API server 2.0
Bug #8189 [FUSE] Listing a project directory is slow when there are many subprojects
Feature #8163 [FUSE] arv-mount should detect and log any files/dirs that are still open after unmounting
Story #7973 [FUSE] Reset mount-tmp to the state of another collection
Feature #7847 [SDKs] Update run-command to use arv-mount --mount-tmp instead of staging directory
Story #7621 [API] Job model validates that the script exists in the repository at script_version 1.0
Story #9428 [SDKs] Port arv-keepdocker to use the docker-py library
Story #9045 [SDKs] `arv keep docker` can upload an image already saved as .tar
Story #9147 [SDKs] `arv keep docker` can make links for an image already in a collection
Story #3897 [SDKs] Clients can specify which auth config file to load. 0.5
Bug #7660 [SDKs] PySDK one_task_per_input_file should support a num_retries argument
Feature #8212 [SDKs] arv CLI program accepts "-" and "/path/to/file" as values for parameters that expect JSON (most notably the "body" parameter) 0.5
Story #8314 [SDKs] arv-copy continue on error
Story #8313 [SDK] arv-copy better Git repository error reporting
Feature #8363 [FUSE] arv-mount exits non-zero if any I/O errors were returned 0.5
Bug #6753 [API] Asset pipeline does not work unless config/environments/production.rb is present at buildtime and runtime
Bug #7312 [API] CSS+images missing on login_failure.html
Bug #7880 [Crunch] crunch-dispatch should run the bundled version of crunch-job specified by Gemfile.lock 0.5
Bug #8195 [API] [Workbench] config:check catches and reports YAML parsing errors
Bug #7323 [SSO] [API] [Workbench] Have config:check sanity check secrets
Feature #7694 [API] [Workbench] Check for nonexistent config params during rake config:check 0.5
Bug #8121 [CRUNCH] Fail gracefully when arvados repo doesn't exists
Feature #7024 [Keep] keepstore status.json should report runtime environment
Bug #7008 [Workbench] Crashes with Fiddlesticks when trying to view a pipeline instance graph copied from another cluster 0.5
Feature #5846 [Workbench] [Fiddlesticks] Live job log should show recent history 2.0
Bug #8399 [Workbench] Doesn't explain why a job can't be cancelled
Story #8091 [Workbench] Show all known runtime_constraints in job status pane
Feature #8515 [Node Manager] Detect and shut down nodes that fail provisioning in Azure
Feature #3734 [Keep] Keepstore and keepproxy support HTTP Range requests 2.0
Feature #8228 [SDKs] [FUSE] Python SDK and arv-mount use Range requests when a caller requests part of a block that has been ejected from the cache 2.0
Feature #7127 [API] Job log cleaner should not clean logs when the job's log is the empty collection
Feature #7818 [SDKs] Document that arv-copy accepts collection PDHs (ie content addresses) as arguments 0.5
Bug #7001 [SDKs] Recursive pipeline instance arv-copy doesn't copy job objects, losing metadata
Bug #7600 [Crunch] Unhelpful translation of script parameter outside script_parameters 1.0
Bug #6868 [SSO] Template calls undefined method after fresh local accounts installation
Bug #7418 [SDKs] Unhelpful 404 stack trace when trying to arv-copy a collection without access
Bug #6780 [git] "git clone https://..." with a bogus token should respond 4xx, not 5xx 0.5
Bug #7725 [Keep-store] make keep-store lookup token at runtime like keep-proxy does 1.0
Bug #6968 [SDKs] arv-copy continues copying when a collection's content address is wrong, but warns and exits a special code 2.0
Feature #5676 [SDK] arv-copy automatically creates new repository(ies) on the destination cluster
Story #6840 [SDKs] Teach arv-copy to copy whole projects
Bug #7400 [Workbench] node visibility as admin vs ordinary user does not line up
Bug #7120 [Keep] keepproxy should log real IP address 0.5
Bug #7823 ubuntu package libarvados-perl should depend on libcrypt-ssleay-perl
Bug #8330 [Docs] Refresh Google OAuth2 setup in SSO install guide 0.5
Bug #8348 [Docs] Install guide keepstore runit script has bad syntax
Bug #7129 [Documentation] RVM and passenger recipes are missing details 0.5
Bug #6883 [Deployment] arvados-api-server-upgrade.sh should set up git_repositories_dir
Feature #8344 [login-sync] Sets up settings.conf
Bug #7170 [Documentation] Various small bugs in the CLI SDK install guide
Bug #7356 [Documentation] Various small bugs in the install guide
Bug #8349 [Docs] keep-web runit script depends on sudo configuration
Story #8331 [Documentation] Clarify PostgreSQL setup commands for Software Collections users 0.5
Bug #8372 [Docs] Install guide missing Websockets details 0.5
Bug #8621 [Wiki] Clean up Computation_and_Pipeline_Processing page
Bug #8683 [Docs/Deployment] MUNGE, Nginx, PostgreSQL services don't start on boot on CentOS 6
Bug #7575 [Documentation] Install guide incurs RVM's sudo wrath 0.5
Story #8329 [Docs] SSO install guide documents default_link_* 0.5
Bug #7342 [Documentation] Install guide explains a few different deployment options 2.0
Bug #7230 [Documentation] FUSE documentation should note granting FUSE permissions 0.5
Bug #6919 [Documentation] Make keepproxy install guide follow nginx conventions 0.5
Feature #9017 [Tests] Make slow tests optional (e.g., run-tests.sh --short)
Bug #8386 [Workbench] Many shell node instructions are wrong outside Curoverse clusters
Bug #8223 [Workbench] view log via keep-web test fails in arvbox
Bug #7166 [API] specifying an invalid filter should result in an error
Bug #6992 [API] Support numeric filter comparisons for numeric fields
Story #9150 [API] Synthetic collections include the "kind" field
Bug #7184 [Deployment] Test distribution packages
Bug #8538 [Workbench/API] Does not derive key name from comments with whitespace
Bug #6922 [API] [Maybe] Update API server to support Git 1.7.2
Bug #7026 [Node Manager] Mishandles stop signals
Bug #6996 [Node Manager] a node filled up its /tmp which killed slurm and docker, node unusable. Node manager did not kill the node.
Bug #9143 [API] Trying to update a collection by PDH raises a NoMethodError
Bug #6240 [API] "order" params should be rejected or used (not silently ignored) even when they reference columns missing from the "select" param 0.5
Bug #7695 [API] Accept collection UUID as a job's docker_image constraint 0.5
Story #9148 [API] Finalize and document the collections/provenance and collections/used_by API calls
Bug #7232 [Keep] keepstore should notify sysadmin about error conditions (trying harder than just log.Print())
Bug #4730 [SDKs] Remove ruby dependency from arv wrapper 1.0
Bug #4431 [SDKs] arv-copy should not require --dst-git-repo when copying on the same cluster 0.5
Bug #6276 [SDKs] Python Keep block-r/w errors should indicate which collection/file was unreadable/unwritable as a result 1.0
Story #6387 [SDKs] arv-put progress meter scales based on file size, rather than being fixed to MiB
Bug #6959 [SDKs] arv-copy raises an unexpected backtrace on ^C
Bug #8065 Out of memory when using arv-copy not handled gracefully
Feature #8379 [SDKs] Recursive arv-copy should report progress of the entire copy, in addition to individual objects
Story #5468 [SDKs] Refactor arv-get/put/copy into the Python "arv" wrapper using common exception-handling and argument parsing 2.0
Story #7476 [SDKs] Ensure `arv keep put` replicates properly
Story #7477 [SDKs] Go Keep client enforces a minimum transfer rate for proxy connections
Story #7473 [FUSE] [SDKs] Ensure FUSE and other SDK clients work with a default replication level != 2
Feature #8502 [SDKs] Fetch all results with the CLI `list` command
Feature #8213 [SDKs] arv get (and edit) should support a flag that suppresses display of non-writable attributes like "status" and "writable_by" 1.0
Feature #8501 [SDKs] Add client-side join switches to `arv foo list`
Feature #8498 [SDKs] GoSDK arvadosclient parameters are more transparent
Story #8838 [SDKs] PySDK Collection class lets you iterate files and subcollections separately
Story #8780 [SDKs] Git credentials helper in CLI tools
Story #8022 [SDKs] CLI tools install tab completion aids
Story #7394 [SDKs] arv-copy copies all metadata associated with an object
Bug #9144 [SDKs] Can't `arv get` a collection by PDH
Bug #7385 [Workbench] Pagination sets limit on last page, causing unintended side effects
Bug #6439 [Workbench] Copying jobs causes "SubmitIdReused" error if submit_id is not null 0.5
Story #8562 [Workbench] Project listings act like file manager directory trees, with expanding+collapsing trees
Bug #6920 [Workbench] Remove Keep disks link? 0.5
Story #8560 [Workbench] Ability to create a new project when creating a new pipeline instance
Story #7830 [Workbench] User admin interface should show which VM(s) the user can login to
Bug #7002 [Workbench] workbench move and copy is incomplete
Bug #7003 [Workbench] warn user when navigation will cause input text to be lost
Bug #6436 [Workbench] Pipeline template description display is difficult to read when making a pipeline template instance
Bug #6363 [Workbench] Visible blanking between partial content reloads
Feature #8486 [Workbench] Change project "Jobs and pipelines" tab to just "Pipelines"
Feature #8221 [Workbench] Add an "invert selection" button to checklists alongside "un/select all"
Feature #8318 [git] Should be able to clone git repositories that are shared with "anonymouspublic" without authentication
Story #7990 [FUSE] With --exec, expose the mount point in an environment variable
Bug #8294 [FUSE] arv-mount usage message shows incorrect order for [--exec ...] option
Bug #7404 [Crunch] crunch-job does not sufficiently sanitize job parameter names when putting them in the environment
Bug #8151 [crunchstat-summary] jobs with tasks_per_node>1 need node size recommendations adjusted 0.5
Story #8181 [Keepstore] Support a portable data challenge API
Story #8180 [Keepstore] Don't trash/delete blocks until they appear on multiple trash lists
Bug #6601 [API] Do not accept an empty SSH key as valid 0.5
Bug #6571 [Workbench] Project description styled differently based on whether or not the user can write to the project
Bug #6991 [Keep] multiple response.Writeheader calls
Bug #6921 [SDKs] `arv create` creates an object from an empty file 0.5
Story #8058 [Documentation] Add Gitolite sanity check to install guide
Bug #8873 [Docs] file_names Collection field is undocumented
Story #8328 [Deployment] .yml.example files should be consistent 0.5
Bug #7158 [Documentation] Document installing the PySDK at a different PREFIX 0.5
Bug #6886 [Documentation] A user with an older install may land in a page that requires the "latest" prerequisites.
Story #7468 [Workbench] Displays content at the top of the dashboard, set by the sysadmin
Story #7469 [Workbench] Provide an interface for the sysadmin to set Dashboard banner content
Story #7470 [Workbench] Provide an interface to delete files from collections
Story #7471 [SDKs] Provide a CLI tool to add files to an existing collection
Story #7472 [SDKs] Provide a CLI tool to remove files from a collection
Bug #7141 [API] Advertise anonymous token in discovery document
Feature #7845 [Crunch] Crunchstat and arv-mount print final stats before exiting 1.0
Feature #7411 [Workbench] Pipeline template listings should include links to the scripts
Bug #7100 [Workbench] Reusing ArvadosResourceList results in inconsistent results
Story #7439 [SDKs] CLI tools support Mac
Story #8773 [GATK Queue] Support a mechanism to redirect stderr for children
Bug #7000 [Docker] API server starts before PostgreSQL is ready
Bug #7007 [Docker] Bootstrap font fails to load in Workbench Docker image
Bug #7006 [Docker] Fix SSO configuration in published images
Bug #7005 [Docker] API server uses omniauth.rb for SSO configuration, not application.yml
Bug #6998 [Docker] Workbench image doesn't serve HTTPS
Story #6783 [Performance] Compare Collection performance benchmarks across components
Feature #6782 [API] [Workbench] Generate debconf template from config yaml
Bug #6762 [FUSE][Performance] Job to md5sum 1TiB of 1MiB files in parallel is very slow
Bug #6651 "This website is under heavy load" error causes a parsing error
Story #7474 [FUSE] Add a --replication switch
Story #6570 [DRAFT] [Workbench] More encouragement for users to send feedback
Bug #6997 [Keep] keepstore reboots GCE host under heavy load
Bug #6606 [Workbench] Provide a GUI interface to arv-copy
Bug #6599 [SDKs] Whenever `arv` has an invalid resource name argument, it should complain about that 0.5
Feature #6574 [Workbench] [Webshell] Rough edges in web shell 2.0
Bug #6677 [Workbench] Anonymous user is listed in the "Share with users" popup when anonymous viewing is disabled, while "Share with groups" popup omits the anonymous group
Bug #6635 [Documentation] document installation of node manager
Bug #6649 [Documentation] webshell installation 1.0
Feature #6517 Port arvados-libpam to centos
Story #3640 [SDKs] Add runtime option to SDKs (esp Python and arv-mount) to use a filesystem directory block cache as an alternative to RAM cache. 2.0
Story #5914 [DRAFT] Provide one clear way for users to get data from an external source into Arvados
Feature #6442 [Workbench] [API] Support "world-readable, but not world-searchable" permission on projects: "anyone with the link can view"
Bug #7099 [SDKs] CLI SDK tools use Ruby SDK
Story #6405 [Workbench] Allow additional curation of the public projects listing
Feature #6348 [Deployment] [Documentation] Minimize system-wide dependencies for compute node setup 1.0
Bug #6318 [SDKs] Go SDK locator regexp (and its tests) should agree with the documented format 0.5
Story #6313 [Node Manager] Booting nodes shouldn't satisfy min_nodes 1.0
Story #6311 [Maybe] [SDKs] Support caching Keep blocks in memcached
Feature #6310 [FUSE] Support scaling the internal block cache based on number of open files
Story #6307 [Workbench] Public project listing should exclude subprojects 0.5
Bug #6274 [API] [Workbench] Home project should be a real object (group with group_class="project"), not current_user. 2.0
Bug #6175 [Workbench] Add social sharing buttons to public projects [and other data?] 1.0
Bug #6174 [Workbench] Propagate old search engine meta tags in sync with Open Graph data 0.5
Bug #6173 [Workbench] Make public data crawlable
Bug #6172 [Workbench] Breadcrumbs can occupy multiple rows when the screen is narrow 0.5
Bug #6130 [Workbench] Support searching collections by their collection name
Story #6642 [API] Include a mechanism to automatically trust some clients
Bug #6076 [API] walk api server installations and ensure modified_at for collections is unique + ensure modified_at is enforced to be unique at the api level.
Story #5098 [Keep] Design: using Arvados to browse, and run jobs on, input data that is stored remotely (not on local Keep disks) 0.5
Feature #5414 [Keep] Use data stored remotely (not in local keepstore) 3.0
Bug #6025 [SSO] Authenticate users with OAuth2
Bug #6020 [Workbench] The collection information box values for content address and content size should be updated automatically after new file(s) are added via browser upload.
Bug #6019 [FUSE] `ls` in a large home directory (4400+ items) takes too long
Feature #6015 [SSOs] Support authentication against multiple backend LDAP servers
Feature #5962 [Keep] Use bufferpool in keepproxy to limit memory use when there are many concurrent PUTs 1.0
Bug #5952 Slow to log-in to Workbench
Bug #5949 [DRAFT] [Workbench] Users can be notified about changes to important pipelines
Bug #5947 [Workbench] Provide additional guidance to users running their first pipeline
Bug #5946 [Workbench] "other collections have the same content" page is confusing
Bug #5945 arv-get is slow for this collection
Feature #5928 Syntax highlighting of viewing source in workbench
Bug #5919 Keep errors
Bug #5923 Fiddlesticks when trying to view a log file
Bug #5907 [SDKs] PySDK's internal decorators lose method metadata 0.5
Bug #5908 [Workbench] collection#show performing too many unnecessary API server requests when accessing qr1hi-4zz18-zn1m6s2le7dqjfs.
Bug #5906 [API] crunch-dispatch should mark a job failed when its repository cannot be fetched 1.0
Bug #5905 [SDKs] Improve certificate validation in Python SDK
Bug #5902 [Workbench] collection#show is unresponsive for a large collection
Bug #5901 [API] Improve performance of large requests in parallel
Feature #5900 [SDK] Implement arvados.gettaskparam(*args) to match arvados.getjobparam(*args)
Bug #5897 [FUSE] Catch and recover from any API client exceptions
Bug #5896 [FUSE] Ensure all I/O errors properly distinguish "not found" and other API errors
Bug #5892 [Workbench] collections#index returns 504 Gateway Timeout
Bug #5878 [Workbench] PipelineInstancesTest#test_Create_and_run_a_pipeline is not reliable
Bug #5876 [Docker] Needs smarter dependency ordering when restarting existing containers
Bug #5874 [Workbench] Mobile menus lack contrast (gray text on aubergine) 0.5
Story #5865 [Crunch] Run a local job using a docker image directly from the shell VM (without writing the docker image to Keep) 2.0
Story #5781 [API] [DRAFT] Provide API methods for manipulating and combining collections 2.0
Bug #5850 All clients authenticate directly against SSO server without going through API server
Bug #5523 [Crunch] crunchstat should not report errors during normal timing races 0.5
Feature #5840 [API] Relax repository name constraints to permit [-_.] -- ideally allow anything github allows 0.5
Feature #5828 [Workbench] Create new collection with selected files copy streams as well as files
Story #5788 [SDKs] [refactor] Dry up KeepService get() and put() in arvados/keep.py 0.5
Feature #4223 [SDKs] arv keep docker --download to get image from Arvados 0.5
Feature #5782 [Workbench] Support entering boolean script_parameters when editing a pipeline instance 0.5
Feature #5769 [OPS] Routinely check for stale Gemfile.lock 0.5
Feature #5767 [API] Websockets subscribe API should accept a start timestamp, so clients don't have to miss any events logged between the given start time and websocket connection success. 1.0
Bug #5841 [Workbench] Link to script sources on github when repository is a github url 0.5
Bug #3989 [Workbench] [DRAFT] Fix clock/node time reporting on Workbench pipeline page
Feature #5740 [OPS] Add diagnostics script for shell nodes
Bug #5736 [Node Manager] Reuse node records after shutting down the cloud node set up with them 1.0
Bug #5743 [Workbench] Replace type-specific #index pages with generic code 2.5
Story #6058 [Workbench] Provide a guided workflow to new users who want to upload data and run a public pipeline 2.5
Bug #5662 [FUSE] cd/ls sometimes takes too long on su92l
Bug #5713 [FUSE] File access sometimes takes too long on su92l
Feature #5035 [Documentation] Document the minimum docker image / Dockerfile that can be used to run a job. 1.0
Bug #4696 [SDKs] one_task_per_input_stream fails due to unsupported APIs. Remove it from docs, examples, and SDK. 0.5
Bug #5820 [Workbench] Missing link target in iframe error message 0.5
Bug #5669 [Workbench] Make Dashboard contents filterable
Feature #5668 [Workbench] Favorite projects, pipelines, collections
Bug #5667 [Workbench] Indicate related pipeline instances
Bug #5665 [Workbench] Link to log from pipeline and/or job summary page
Bug #5614 [Workbench] 504 error returned when trying to create a large new collection
Bug #5235 [Workbench] Pipeline instance "Re-run with latest" button occasionally returns Not found page
Feature #5778 [FUSE] Support efficient copy at command line 2.0
Feature #4835 [Workbench] Log Graph - Feature requests
Feature #5415 [Workbench] Improve presentation of anonymously-viewed collections (via both "sharing link" and regular copy-and-pasted Location) 2.5
Story #5624 [API] [Workbench] [Performance] Use object caching to improvement performance (such as memcache).
Bug #5560 [DRAFT] [API] Good API for accessing the old_ and new_attributes in Logs table properties column 2.0
Bug #4943 [Workbench] [Performance] Combining big collections should start returning a response faster (currently you can get a 502 proxy error even if the collection still combines)
Bug #5381 [Crunch] Node went away unexpectedly during pipeline run. 0.5
Story #5621 [Documentation] Improve SDK documentation
Bug #3040 [API] Replace is_trusted attribute with a per-{user,client} flag which is set by the user on first login to a given client
Feature #5582 [API] [Workbench] Add read-only ("locked") flag to projects 2.0
Feature #5118 [OPS] Use packer to generate docker images for our various services 2.0
Feature #5511 [Workbench] Workbench should support viewing VCF files
Feature #5510 [DRAFT] [Crunch] User can configure task retries
Feature #5495 [Workbench] Change "recent pipelines" to curated selection of "public pipelines"
Feature #5494 [Documentation] Run an uncommitted script straight from a working directory using arv-run-pipeline-instance --run-here
Feature #5459 [Crunch] Job logs include node-level resource usage statistics (cpu, ram, swap, etc)
Feature #5413 [DRAFT] [API/SSO] Use externally-defined (e.g., LDAP) groups as permission groups
Story #5428 [Tests] Enhance keep testing to support signed locators. 2.0
Bug #5137 [SDKs] Add Python version test 2.7 <= sys.version_info < 3 0.5
Bug #5515 Job failure due to 'arv-put' 'ConnectionError'?
Bug #5127 [Docs] Note apt key information in Python package READMEs
Bug #5327 [SDK] CLI tools should catch socket errors like "Connection refused" 0.5
Feature #5201 [SDKs] arv-put --description X --properties P should set respective attrs on new collection. 0.5
Bug #5267 [Node Manager] add one integration test for node manager 0.5
Bug #4957 [SDKs] arv keep put blows up when trying to put a danging symlink 0.5
Feature #5119 [OPS] Write a wrapper script that calls packer to generate customized docker images for a new installation (with IP ranges, hostnames, etc preseeded) 2.0
Bug #5451 [Documentation] Fix Go SDK comments so they look reasonable in godoc 0.5
Feature #5138 [SDKs] arv-run-pipeline-instance should accept project and title parameters 0.5
Feature #5245 [Documentation] Show footer with date last updated 0.5
Bug #3625 [Workbench] API token provided in query string should not be ignored just because the session already has a token. 0.5
Feature #5439 [Tests] Provide a docker image, based on puppet/packer process, that can run the entire test suite quickly.
Feature #5387 [DRAFT] [Workbench] Improve provenance/used-by graphs so they are legible even for large pipelines / long provenance trails 2.0
Feature #5384 [DRAFT] [Workbench] Improve display of pipelines and jobs 2.0
Story #3022 Improvements to sortable log viewer 2.0
Feature #5297 [Workbench] Enable users to share with any other user
Feature #5382 [Documentation] arvados VM simulator, demonstrating how it looks to use Arvados from CLI 2.0
Feature #5316 [DRAFT] [Workbench] Browse change history for records
Feature #5284 [Docker] Auto setup as much as possible for new users
Feature #5391 [SDK] Go KeepClient offers a "read block" API that recovers from transmission errors by attempting alternate servers.
Bug #5541 [Workbench] Buttons should have consistent ctrl-click and right-click behavior
Bug #5147 [Docker] Make API server root URL in discovery document easier to resolve 0.5
Bug #5307 [Workbench] Additional settings for ssh/config from Manage Account page 0.5
Feature #5296 [Workbench] Extend Sharing tab to collections
Feature #5260 [Tests] Implement long-running keepstore services in run-tests, similar to what api got in #3021 1.0
Feature #5259 [Tests] Reduce dependency on integration tests 2.0
Feature #5193 [Workbench] Public project page should encourage visitors to try using Arvados themselves 1.0
Feature #5237 [Workbench] Pipeline re-run dialog should offer docker image choices (latest/same), similar to script version choices 1.0
Bug #5134 [SDKs] CLI tools fail or warn when current working directory is gone
Story #5142 [DRAFT] [API] Enrich supported dataclass values for pipeline templates
Feature #5032 [Workbench] User can trash and un-trash items 2.0
Feature #5139 [SDKs] arv-get should support getting multiple files by shell glob
Feature #5133 [Crunch] Use uncommitted code in a git work tree to run a dockerized crunch job in a VM (using crunch-job or arv-run-pipeline-instance --run-jobs-here) 2.5
Bug #4048 [Crunch] arv-run-pipeline-instance --run-jobs-here cannot run jobs with local script path in script_version. 0.5
Feature #4561 [SDKs] Refactor run-command so it can be used as an SDK by scripts in a git tree 2.0
Feature #5097 [SDKs] CLI tools support project paths in addition to uuids 2.0
Feature #5036 [arv-mount] Change default mount type from "fuse" to "fuse.arvados" 0.5
Bug #4938 [Workbench] improve error reporting for failed AJAX calls 1.0
Bug #3691 [Workbench] Suppress "ajax failed" error messages when ajax fails due to browser navigation event. 1.0
Bug #4989 [Deployment] Switchyard should behave correctly when one SSH key has access to multiple VMs using different usernames. 0.5
Bug #3948 [SDKs] File access on keep mount giving I/O error 0.5
Bug #5233 [Tests] Eliminate system globals in test suites 1.0
Bug #4770 [Workbench] after file upload, the files tab should refresh immediately (overriding the 15 second throttle) 0.5
Bug #5026 [API] Prohibit leaving jobs in an inconsistent state (e.g., state=queued with non-null log or output) 1.0
Bug #4821 [SDKs] CLI tests should be better isolated from user configuration 0.5
Bug #4805 [Workbench] Workbench provenance graph tabs appear empty when graph is very large 0.5
Bug #5068 [Docker] fix @_NOT_FOUND_@ hack in config.rb 0.5
Story #3532 [Keep] Keepstore queries API server to verify tokens 2.0
Story #4744 [Workbench] Merge "user agreement" and "required profile fields" into a single page 2.0
Feature #5064 [Crunch] Automatically restart jobs after internal/intermittent errors
Bug #5025 [Docker] Make it easy to add data from the host system to containers
Story #5007 [Workbench] Pilot material design theme 1.0
Story #5094 [Workbench] Make pipeline rerun UI more like jobs'
Bug #5065 [Node Manager] EC2 driver creates nodes configured to terminate on shutdown 0.5
Bug #4129 [Node Manager] Don't reuse node table records 1.0
Bug #3573 [Workbench] When showing a shared project, do not include "Home" in breadcrumbs. 0.5
Feature #4935 [Crunch] Choose worker nodes where the desired docker image is already available.
Bug #4358 [Tests] When comparing pipelines, the graph should highlight the differences by using different colors for pipeline A/B/both. 0.5
Bug #5021 [Workbench] Page for downloading collections with anonymous sharing link does not have any styling.
Feature #4906 [Documentation/FUSE] Document '.arvados#collection' in shell VM keep mount
Feature #5033 [SDKs] `arv keep docker` should pipe the data directly to Keep instead of store-and-forward, and provide some progress feedback up front in any case. 1.0
Bug #4881 [Workbench] Make "Compute and job status" pane update dynamically 0.5
Bug #5020 [Workbench] File upload should start immediately, not wait for user to press "Start" 0.5
Story #4833 [Crunch] Quick turnaround time when updating a docker image in order to re-run a job 2.0
Bug #4841 [Workbench] When using "Run pipeline" button at the top of project A, the pipeline template chooser should start out showing project A, not "All projects". 0.5
Bug #4923 [Workbench] Editable "name" column is presented but not actually available for "other" objects such as Human and Specimen.
Bug #4952 [SDKs] [DRAFT] arv-get with just one locator argument should download the entire collection
Bug #4771 [Workbench] Collection content hash should stay up-to-date (e.g., while uploading files) 0.5
Bug #4726 [Crunch] run-command should show helpful error message when task.foreach argument is not a list 0.5
Bug #4767 [API] Discovery doc should fix its incorrect "list" method description to be identical to "index" 0.5
Feature #4579 [Documentation] Run-command docs should remind user how & why to exit non-zero on failure. 0.5
Bug #4669 [SDKs] arv-put should assume --no-resume when --raw is given 0.5
Bug #4635 [Tests] Diagnostics suite tests that live logs are displayed while jobs are running. 0.5
Bug #4692 [API] Prompt user when logging in to a client for the first time. 2.0
Bug #4690 [DRAFT] [Workbench] Prevent CSRF and XSS attacks 1.0
Bug #3224 [Workbench] Search box on collections page should use infinite scroll instead of (broken) page number links 2.0
Story #3490 [Workbench] Create and edit pipeline templates 2.0
Feature #4647 [Workbench] Projects dropdown should have a free text filter box 0.5
Bug #4750 [Crunch] crunch-dispatch's Bundler environment infects non-Docker jobs 0.5
Bug #4729 [API] Remove success and running attributes from job data model, since we are now using the state attribute. 0.5
Bug #4700 [Workbench] Websocket client should only subscribe to events about relevant objects, not all events. 2.0
Feature #4530 [Workbench] Show more (earlier) log entries for a running job 2.0
Story #4566 [Documentation] Introduce compute workflow / pipeline concepts in user guide 1.0
Feature #4508 [Documentation] Best practices for getting the most out of job re-use 1.0
Feature #4531 [Documentation] Set of introductory tutorials each focused on accomplishing a simple task 2.0
Feature #3223 [Documentation] Tutorial for adding a crunch script wrapper for an existing tool that is already hosted on github. 2.0
Bug #4460 [Workbench] Sortable column headings (filename, size) in collections#show 1.0
Bug #3387 [Workbench] Disable auto-refresh on tabs with infinite-scroll or editable content. 0.5
Bug #4494 [Crunch] Do more error-checking and show more diagnostic info when installing a Docker image 1.0
Feature #3980 [SDKs] CLI tool to view real time logs from running jobs/pipelines, much like the Log tab of the Workbench PipelineInstance#show page 1.0
Feature #4808 [Workbench] "Add data from another project" modal supports regex filtering
Feature #4503 [SDKs] Option to watch logs (instead of exiting) when queuing a job or pipeline instance using arv job create, arv pipeline run, etc. 1.0
Feature #4642 [Workbench] "Download" / "Save as" button for provenance graph 0.5
Feature #3928 [Workbench] Reveal log collection ID in pipeline/job summary and job Log tab 0.5
Feature #3284 [Workbench] Project show page should have buttons to add objects besides Collections
Feature #4650 [API] API method and CLI shortcut for refreshing the signatures on some block locators (without creating a collection) 0.5
Feature #4393 [Workbench] Display portable data hash, parent project, file count in Collection tables
Feature #4539 [Workbench] Job detail page should show the job status when the job is not running or has completed running (button that shows 'queued', 'not ready', 'failed', 'complete', etc) 0.5
Story #4919 [API] Arvados clients can use standard OAuth2 protocol instead of custom token handling mechanism 2.0
Bug #4427 [Workbench] Each active job/pipeline on the dashboard should show how many worker nodes are allocated to it. 1.0
Bug #4289 [Workbench] Job view should include the relevant component name(s) from each pipeline where the job was used 0.5
Bug #4514 [Workbench] Pipelines that are in New or Ready state should show up somewhere on the dashboard, (e.g., in "Active pipelines" or "Recent pipelines" table). 0.5
Bug #4394 [Workbench] Make duplicate name error message more user-friendly 0.5
Feature #4446 [Workbench] Provide feedback on dashboard to indicate that NodeManager is booting a node. 1.0
Feature #4502 [SDKs] "arv recent [objectType]" lists recently modified objects 1.0
Feature #4302 [Crunch] Pipelines should not fail immediately after one job failure, but continue running as much as possible
Bug #4500 [OPS] Improve and automate non-shared VM configuration 0.5
Bug #4452 [Workbench] Report a Problem" menu item does not like being opened in a new tab/window. 0.5
Feature #4516 [Workbench] Don't show empty projects/collections when using the chooser dialog to select pipelines, files, etc. 0.5
Feature #3101 [Tests] Websockets should work out of the box in test/development modes, even when using an ssh tunnel and a self-signed certificate. 2.0
Bug #3037 [API] websocket clients should not put API tokens in path or query string 1.0
Story #4442 [API] [Workbench] Site-wide regex searching 1.0
Feature #3125 [Workbench] Add a "docker images" page to Workbench that lists available docker images 1.0
Feature #4404 [API] [SDKs] Include provenance information for uploaded Collections
Bug #4182 [Workbench] [API] "Manage" permission should be sufficient to delete subprojects 1.0
Story #4350 [Workbench] Order by Collections "Name" column puts "folders" (collections containing files) at the top
Feature #4349 [SDKs] When editing a template in arv-edit and faced with a parse error, when trying again, it should automatically take you to the line/column of the error
Bug #4175 [API] API method and interface to check if a bugfix is deployed on a cluster 2.0
Feature #2897 [OPS] Implement new deploy procedure 3.0
Feature #4343 [SDKs] arv create needs --project-uuid and --name parameters for appropriate classes
Bug #4324 [Docker] Fix supervisor.conf to supervise services instead of running init.d start script and hoping everything is OK 0.5
Bug #4009 [Crunch] run_command should use SDK's retry support 0.5
Bug #4273 [API] as admin user, permission denied canceling a job (started by another user) 0.5
Bug #4265 [Workbench] default .ssh/config instructions should specify cluster name 0.5
Bug #4438 [DRAFT] [SDKs] arv-keepdocker should be smarter about caching the image to upload
Feature #3829 [Crunch] Email notification when pipeline finishes, depending on user prefs flag 1.0
Feature #3226 [Workbench] Project chooser dialog should have a "create new project" button. 1.0
Story #4237 [Documentation] Update and expand user/tutorials/tutorial-keep-mount.html to show practical ways of finding data via FUSE mount. 1.0
Bug #4256 [API] Jobs that sit in the front of the queue for a long time without running should be cancelled 1.0
Feature #4193 [SDK] Make arv keep docker smarter about storing docker layers, thus making uploads of changed images (much) faster 2.0
Bug #4309 [SDK] arv-copy collection copy performance 2.0
Story #4255 [SDKs] Implement "arv keep less" and "arv keep check" natively instead of hoping whless and whcheck are installed. 1.0
Bug #4118 [API] Link model validation allows only Users and Groups to get can_read, can_write, can_manage 0.5
Bug #4191 [Keep] "Shared" directory in arv-mount doesn't show non-project groups that own projects 1.0
Bug #4116 [Workbench] Users activity page link is gone for non-admin users with read-only admin permissions. Users activity page only shows own activity for non-admin users with read-only admin permissions. 0.5
Bug #4288 [API] api server docker_images endpoint
Bug #3976 [API] Non-admin users should see all nodes with crunch_worker_state busy/idle, regardless of ping age. 0.5
Bug #3974 [SDKs] CLI 'arv pipeline run --run-pipeline-here' should change instance state from 'ready' (or 'not running'?) to 'RunningOnClient' 0.5
Story #4128 [Workbench] [refactor] JavaScript refactoring
Bug #3834 [Workbench] pipeline instance that is RunningOnClient should be rendered as Running, not Ready. 0.5
Bug #3973 [Workbench] After cloning a pipeline instance, the new instance should not have any cancelled jobs/components 0.5
Bug #4041 [SDKs] arv pipeline_instance --help should work even if api server is not running / reachable. 0.5
Story #4030 [SDK] Command line tool to manipulate collection manifests
Feature #3964 [SDKs] Command-line diagnostic suite reveals problems on a shell VM (e.g., arv-mount, SDK version skew) 1.0
Bug #3817 [API] Discovery document schema does not include generated fields like job dependencies 1.0
Feature #3892 [SDKs] Install man pages for CLI tools (auto generate from the --help content) 2.0
Story #3298 [Workbench] Rearrange collection chooser to show a preview (file list) inline instead of in a separate preview pane. See [[Workbench UI images]] 2.0
Story #3815 [SDK] arv-put supports --ignore-symlinks 0.5
Feature #3818 [API] Discovery document schema should include whether field on resource is writable or read-only. 1.0
Bug #3622 [API] [refactor] Move system_group, system_user, etc to class methods in Group and User 0.5
Story #3365 [SDK] Show the Workbench URI for the job when running a job or pipeline from the command line 0.5
Feature #3445 [Workbench] Improve chooser preview for collections, and add previews for objects that don't have any yet (pipeline instances, templates, jobs, projects) 2.0
Story #3279 [Workbench] Link to OFTC web chat on version/bugreport modal 0.5
Bug #3437 "Choose folder" dialog when running a pipeline displays folders you can't write to
Bug #3416 [API] Clean up exception raise/rescue usage, use 4xx and 5xx appropriately 1.0
Story #3355 [SDK] Show the API server URI for the new pipeline instance when running a pipeline from the command line. 0.5
Bug #4409 [Workbench] Want to remove projects from Home 1.0
Bug #3391 [Workbench] Can see job information but cannot access output collection
Feature #3336 [Docker] use local docker install for additional testing 2.0
Story #3163 [Tests] Non-destructive test script suitable for running on a production VM/server in order to verify correct operation of basic features. 2.0
Bug #3165 [Crunch] Queued and running jobs do not get cancelled when a pipeline instance gets cancelled. 1.0
Bug #3073 [Workbench] Progress bar not fully green when all jobs/tasks complete successfully 0.5
Bug #3164 [Workbench] resolve race condition in displaying logs from newly-completed jobs 1.0
Bug #3172 [Workbench] Moving a pipeline instance from a private project to a shared project does not also effectively share the component jobs. 2.0
Story #3199 [SDK] Keep clients (e.g., arv-put and crunch-job) ask API to refresh blob signatures if expiry times are sooner than ETA of collection.create 3.0
Story #3179 "Dump core" option when running a job (or every job in a pipeline): save the state of a failed task's container before tearing it down. 2.0
Bug #3086 AJAX behaves strangely if login token expires 1.0
Story #3711 [Docs] Update Arvados permissions model in docs 1.0
Bug #3978 [SDKs] Pipelines started from the CLI should set status to "Paused" when aborted 1.0
Feature #4823 [SDKs] Good Collection API for Python SDK 1.0
Feature #5375 [workbench] Enable in-browser preview for text files in collections 0.5
Feature #5646 [Workbench] Display duration on pipeline instance listings
Feature #4456 [Workbench] Provide more feedback about when a queued job is likely to start. 1.0
Story #5793 [Workbench] Add search filter to "/links" page
Story #2992 [Workbench] Support "display_order" (integer) key for pipeline template components. Obey when rendering pipeline summary/details in Workbench. 0.5
Bug #5738 [API] Validate that selected columns are selectable, and return an error if not 0.5
Bug #5913 [Workbench] Should validate that a job's repository actually exists before rendering the link to avoid fiddlesticks
Bug #4706 [Workbench] Re-connect to websockets when the connection drops; use "last_log_id" so nothing is missed. 1.0
Bug #3629 [Workbench] Display timestamps in user's local timezone using class="localized-time" 0.5
Story #9046 [Crunch2] Can issue container request to pull and import Docker images 2.0
Story #8332 [Docs] Fix flow of Rails servers' install guides 1.0
Story #9952 crunch-dispatch-local config file and systemd unit
Story #10244 [Performance][Workbench] Computing notifications in topnav is expensive. Can the users properties be used instead?
Story #12917 Users should be able to see if a container failed from the container_request method 2.0
298.0