[CWL] Pass conformance for v1.0.1

[FUSE] Hang on simple FUSE operation and when logging in again later

[Node manager] Better communication when job is unsatisfiable

[DOC] add cookbook section with code snippets

Reduce amount of parallelism in crunchstat-summary

[CWL] arv:RunInSingleContainer should take max() of ResourceRequirements of substeps

[Workbench] Remove arv-get file download fallback

Basic authenticated http health check ("ping") for each system service

[keep-web] tests hang

[Tests] Flaky test in Python SDK tests.test_events.WebsocketTest.test_subscribe_poll

[Spike] Investigate CI packaging improvements

arv-get should abort on ctrl/C

[FUSE] high memory consumption (possible leak) in long-running arv-mount

Create a CWL stress test for node manager

[Nodemanager] Fix watchdog test

Deprecate / remove arv-web

[Crunch2] crunchstat-summary --container UUID should summarize container logs

Update Pipeline Optimization wiki with CWL/Crunchv2

Nginx config should speak JSON when returning its own response for unproxyable API requests

Deprecate arv-run

[SDKs] Write integration test for when arv-put resumes from a cache with expired access tokens

Allow projects to be deleted (ie placed in the trash can)

crunchstat-summary gives invalid min_cores recommendation

Synchronize group membership with external data source

Windows file system driver for Keep (arv-mount equiv)

[arv-mount] Do not crash if /sys/fs/fuse/connections is empty

On the collections page indicate expiring collections

[CWL] arvados-cwl-runner should support tagging output collection using properties

Migrate Collections.properties to JSONB

Timeout attempting to create job for component gatk-haplotypecaller-cram-gvcf: Net::ReadTimeout

Error fetching collection (HttpError 422) during call to arvados.util.listdir_recursive

[Workbench] Update job stats to be more useful to end user

[API] Remove async permissions code

[R SDK] Create a Bioconductor/R SDK

User accounts optionally have read-only access

[Nodemanager] Improve status.json for monitoring

[Python SDK] Implement support for universal newline mode in Collections API

Support schema.org/Google structured markup for datasets

[SDKs] publish python3-arvados-python-client packages

[Workbench] Replace schizophrenic generic "groups" page with "roles" page that only creates/lists groups with group_class="role".

[Workbench] Improve user page group memberships management [to be groomed]

[Crunch2] Create workflow object for CWL runs which are initiated from the command line

Support display & reseting of expiration dates for collections

User activity page takes too long to load

[API] container_requests#update alternately responds 422 or 404 for no apparent reason

Support rendering of CWL description fields with embedded markup

[Workbench] [UNC] Copying collections also copies metadata

[API] full text search on pipeline_instances table is extremely slow (wrong index?)

[Keep] Support multiple storage tiers

[Crunch2] [Workbench] Show slurm queue position of containers submitted to slurm but not yet running

[keep-web] configurable block cache size

Switch from goamz to aws-sdk-go

[Crunch2] [API] return a more specific 422 error message when a client calls containers#unlock without having the lock

[Workbench] Support array type input parameters to Workflows

[Crunch2] Propagate error messages if sbatch command succeeds but crunch-run can't run (or can't log to the Arvados API)

[FUSE] Determine why bcl2fastq doesn't work with writable keep mount

[Node Manager] Doesn't kill itself when unhandled exceptions are raised during actor setup

[Python SDK] Document undocumented methods in RichCollectionBase

Integrate CI::Reporter to provide test output in JUnit XML format

[SDKs] `arv keep docker` supports `repo:tag` image name scheme

Add varchar_pattern_ops to all relevant PostgreSQL UUID indexes

Output glob "./" doesn't work as output from CWL workflow

[API] [Workbench] Error out when unrecognized keys appear in config files

[Go programs] Error out when unrecognized keys appear in config files

[CWL] Tries to run docker inside container where docker is not available, gives IOError

Arvados should be able to cat/zcat files in collections easily

[SDK] Writable file-like interface for collections in Go SDK

[Node Manager] Support ephemeral additional storage for Azure node types that do not have sufficient instance storage

[SSO] sso server adds multiple records without checking

Automate starting/enabling services during Workbench and API package installation

[CWL][Crunch][Crunch2] crunchrunner should ignore hidden directories when uploading to keep

[CWL][Crunch2][Crunch] crunchrunner should use CWL globs to output data to keep

[FUSE] arv-mount installation documentation not working

[FUSE] performance issues stat() in python

[FUSE] Undelete collections by moving them out of the TrashDirectory

[keep-balance] Refuse to act when planning to delete data above an admin-specified threshold

[keep-balance] Do not delete blocks referenced by collections with replication_desired=0

[SDKs] arv-put's default output includes both collection UUID and PDH

[SDKs] Improve metadata created by arv-put

[Workbench UI] Pipeline instances should have a link to view the CWL file used.

[CWL] Creating intermediate folders in working directory (fails in cwl-runner)

[Workbench] UI should advance to new step when user submits their input

[CWL] Secondary files entering into Arvados automatically

[Crunch2][Workbench] List both pipeline_templates and workflows on both pages

[keep-rsync] Rename "replications" to "replicas"

[keep-balance] "Expedited delete" tool: perform garbage collection on some specific (recently deleted) collections, bypassing usual GC race protections

[CWL] arvados-cwl-runner should reuse the most recent run

[CWL] Jobs crash when arvados/jobs:latest is not suitable to run CWL jobs

[Crunch2] crunch-dispatch-slurm can't successfully dispatch work when run from a directory it can't write to

[Crunch2] Document/fix handling of collections with non-nil expires_at field

[Data manager] Verbose reporting

[Node Manager] huge virtual memory size

[Workbench] Times out before API server loading active pipeline instances

[FUSE] rmdir on CollectionDirectory sets expires_at

[FUSE] Trash directory to list, inspect, and un-trash trashed collections

[FUSE] Don't display expiring collections in regular collection listings

[FUSE] llfuse thread can stay alive after umount, hanging tests

[FUSE] Make .arvados#collection available in collection subdirectories

[FUSE] .arvados#collection is missing or outdated after writing inside collection

[FUSE] Add timestamp to arv-mount --logfile option

add key/value support for tags

[Provenance Tracking] jobs refer to collections by uuids, not pdh

get rid of dependencies python-pyasn1 python-pyasn1-modules

[FUSE] arv-mount is too slow for strelka

[Documentation] Write a Crunch2 wiki page

[Documentation] Write a Crunch wiki page

[Node Manager] Aggressively throttles node creation requests when the cloud region is full

[NodeManager] CloudNodeListMonitorActor stopped reporting, and logs are not helpful enough to diagnose

[SDKs] PySDK fails to load CAs for SSL verification when run inside Conda

[Crunch] crunch-job can miss the final log output of a job

[FUSE] When we give up trying to write a block, the next operation on the file should fail

[Workbench] Bad URL quoting/parsing in File links from the pipeline template Components tab

[Python SDK] Add a Collection method to efficiently concatenate files

[Crunch] Limit maximum wait time between retries

[Crunch] [UX] Standard excepthook to help debug job problems

[SDKs] arv-copy fails to copy a Docker image specified with repo:tag syntax

[Workbench] The "Log" tab should have an notification that the job has been queued

[Node Manager] Less logging of tracebacks for routine exceptions

[API] Bad compute node address detection on private networks

[SDKs] WebSocketClient Exception 'NoneType' object is not callable

[Crunch] Log throttling shouldn't throttle logs from crunchstat, crunch-job

[FUSE] Add --umask, --fmask, --dmask options to control file permissions

[SDKs] Bad use of RetryLoop in events.py

[SDK] arvados.arvfile.readall_decompressed() does not return all blocks on a file

[Crunch] Job was repeatedly retried on same bad compute node until abandoned

[Docs] Many tutorial instructions are wrong outside Curoverse clusters

[Workbench] No user profile should be required in the default configuration

[Docs] Document Git 1.7.10+ dependency for shell node and HTTPS Git cloning

[Docs/Workbench] Document how to clone repositories over HTTPS

[Docs/Workbench] Improve SSH agent documentation

[Workbench] Hide file preview buttons when preview isn't possible with current keep-web config

[PySDK] API client logs a warning when you create an object without an owner_uuid

[Node Manager] Broken nodes always get shut down, exempt from all node-counting considerations

[NodeManager] Use sys.exc_clear() to release exception tracebacks

[Node Manager] Minimum idle time before node is eligible for shutdown

[Node Manager] qr1hi nodemanager can't start if ulimit is in place

[Node Manager] Doesn't convert units when determining if a job's scratch request is satisfiable

[API] Go code to connect to the API server database and make basic sense of it

[API] Go code to implement the Arvados API permissions model

[API] List queries using "distinct" option return incorrect number of items_available

[API] Should not be necessary to host git repos on the same host as API server

[FUSE] Listing a project directory is slow when there are many subprojects

[FUSE] arv-mount should detect and log any files/dirs that are still open after unmounting

[FUSE] Reset mount-tmp to the state of another collection

[SDKs] Update run-command to use arv-mount --mount-tmp instead of staging directory

[API] Job model validates that the script exists in the repository at script_version

[SDKs] Port arv-keepdocker to use the docker-py library

[SDKs] `arv keep docker` can upload an image already saved as .tar

[SDKs] `arv keep docker` can make links for an image already in a collection

[SDKs] Clients can specify which auth config file to load.

[SDKs] PySDK one_task_per_input_file should support a num_retries argument

[SDKs] arv CLI program accepts "-" and "/path/to/file" as values for parameters that expect JSON (most notably the "body" parameter)

[SDKs] arv-copy continue on error

[SDK] arv-copy better Git repository error reporting

[FUSE] arv-mount exits non-zero if any I/O errors were returned

[API] Asset pipeline does not work unless config/environments/production.rb is present at buildtime and runtime

[API] CSS+images missing on login_failure.html

[Crunch] crunch-dispatch should run the bundled version of crunch-job specified by Gemfile.lock

[API] [Workbench] config:check catches and reports YAML parsing errors

[SSO] [API] [Workbench] Have config:check sanity check secrets

[API] [Workbench] Check for nonexistent config params during rake config:check

[CRUNCH] Fail gracefully when arvados repo doesn't exists

[Keep] keepstore status.json should report runtime environment

[Workbench] Crashes with Fiddlesticks when trying to view a pipeline instance graph copied from another cluster

[Workbench] [Fiddlesticks] Live job log should show recent history

[Workbench] Doesn't explain why a job can't be cancelled

[Workbench] Show all known runtime_constraints in job status pane

[Node Manager] Detect and shut down nodes that fail provisioning in Azure

[Keep] Keepstore and keepproxy support HTTP Range requests

[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

[API] Job log cleaner should not clean logs when the job's log is the empty collection

[SDKs] Document that arv-copy accepts collection PDHs (ie content addresses) as arguments

[SDKs] Recursive pipeline instance arv-copy doesn't copy job objects, losing metadata

[Crunch] Unhelpful translation of script parameter outside script_parameters

[node manager] Upgrade to libcloud 2.0

[SSO] Template calls undefined method after fresh local accounts installation

[SDKs] Unhelpful 404 stack trace when trying to arv-copy a collection without access

[git] "git clone https://..." with a bogus token should respond 4xx, not 5xx

[Keep-store] make keep-store lookup token at runtime like keep-proxy does

[SDKs] arv-copy continues copying when a collection's content address is wrong, but warns and exits a special code

[SDK] arv-copy automatically creates new repository(ies) on the destination cluster

[SDKs] Teach arv-copy to copy whole projects

[Workbench] node visibility as admin vs ordinary user does not line up

[Keep] keepproxy should log real IP address

ubuntu package libarvados-perl should depend on libcrypt-ssleay-perl

[Docs] Refresh Google OAuth2 setup in SSO install guide

[Docs] Install guide keepstore runit script has bad syntax

[Documentation] RVM and passenger recipes are missing details

[Deployment] arvados-api-server-upgrade.sh should set up git_repositories_dir

[login-sync] Sets up settings.conf

[Documentation] Various small bugs in the CLI SDK install guide

[Documentation] Various small bugs in the install guide

[Docs] keep-web runit script depends on sudo configuration

[Documentation] Clarify PostgreSQL setup commands for Software Collections users

[Docs] Install guide missing Websockets details

[Wiki] Clean up Computation_and_Pipeline_Processing page

[Docs/Deployment] MUNGE, Nginx, PostgreSQL services don't start on boot on CentOS 6

[Documentation] Install guide incurs RVM's sudo wrath

[Docs] SSO install guide documents default_link_*

[Documentation] Install guide explains a few different deployment options

[Documentation] FUSE documentation should note granting FUSE permissions

[Documentation] Make keepproxy install guide follow nginx conventions

[Tests] Make slow tests optional (e.g., run-tests.sh --short)

[Workbench] Many shell node instructions are wrong outside Curoverse clusters

[Workbench] view log via keep-web test fails in arvbox

[API] specifying an invalid filter should result in an error

[API] Support numeric filter comparisons for numeric fields

[API] Synthetic collections include the "kind" field

[Deployment] Test distribution packages

[Workbench/API] Does not derive key name from comments with whitespace

[API] [Maybe] Update API server to support Git 1.7.2

[Node Manager] Mishandles stop signals

[Node Manager] a node filled up its /tmp which killed slurm and docker, node unusable. Node manager did not kill the node.

[API] Trying to update a collection by PDH raises a NoMethodError

[API] "order" params should be rejected or used (not silently ignored) even when they reference columns missing from the "select" param

[API] Accept collection UUID as a job's docker_image constraint

[API] Finalize and document the collections/provenance and collections/used_by API calls

[Keep] keepstore should notify sysadmin about error conditions (trying harder than just log.Print())

[SDKs] Remove ruby dependency from arv wrapper

[SDKs] arv-copy should not require --dst-git-repo when copying on the same cluster

[SDKs] Python Keep block-r/w errors should indicate which collection/file was unreadable/unwritable as a result

[SDKs] arv-put progress meter scales based on file size, rather than being fixed to MiB

[SDKs] arv-copy raises an unexpected backtrace on ^C

Out of memory when using arv-copy not handled gracefully

[SDKs] Recursive arv-copy should report progress of the entire copy, in addition to individual objects

[SDKs] Refactor arv-get/put/copy into the Python "arv" wrapper using common exception-handling and argument parsing

[SDKs] Ensure `arv keep put` replicates properly

[SDKs] Go Keep client enforces a minimum transfer rate for proxy connections

[FUSE] [SDKs] Ensure FUSE and other SDK clients work with a default replication level != 2

[SDKs] Fetch all results with the CLI `list` command

[SDKs] arv get (and edit) should support a flag that suppresses display of non-writable attributes like "status" and "writable_by"

[SDKs] Add client-side join switches to `arv foo list`

[SDKs] GoSDK arvadosclient parameters are more transparent

[SDKs] PySDK Collection class lets you iterate files and subcollections separately

[SDKs] Git credentials helper in CLI tools

[SDKs] CLI tools install tab completion aids

[SDKs] arv-copy copies all metadata associated with an object

[SDKs] Can't `arv get` a collection by PDH

[Workbench] Pagination sets limit on last page, causing unintended side effects

[Workbench] Copying jobs causes "SubmitIdReused" error if submit_id is not null

[Workbench] Project listings act like file manager directory trees, with expanding+collapsing trees

[Workbench] Remove Keep disks link?

[Workbench] Ability to create a new project when creating a new pipeline instance

[Workbench] User admin interface should show which VM(s) the user can login to

[Workbench] workbench move and copy is incomplete

[Workbench] warn user when navigation will cause input text to be lost

[Workbench] Pipeline template description display is difficult to read when making a pipeline template instance

[Workbench] Visible blanking between partial content reloads

[Workbench] Change project "Jobs and pipelines" tab to just "Pipelines"

[Workbench] Add an "invert selection" button to checklists alongside "un/select all"

[git] Should be able to clone git repositories that are shared with "anonymouspublic" without authentication

[FUSE] With --exec, expose the mount point in an environment variable

[FUSE] arv-mount usage message shows incorrect order for [--exec ...] option

[Crunch] crunch-job does not sufficiently sanitize job parameter names when putting them in the environment

[crunchstat-summary] jobs with tasks_per_node>1 need node size recommendations adjusted

[Keepstore] Support a portable data challenge API

[API] Do not accept an empty SSH key as valid

[Workbench] Project description styled differently based on whether or not the user can write to the project

[Keep] multiple response.Writeheader calls

[SDKs] `arv create` creates an object from an empty file

[Deployment] Update Rails package dependencies

[Documentation] Add Gitolite sanity check to install guide

[Docs] file_names Collection field is undocumented

[Deployment] .yml.example files should be consistent

[Documentation] Document installing the PySDK at a different PREFIX

[Documentation] A user with an older install may land in a page that requires the "latest" prerequisites.

[Workbench] Displays content at the top of the dashboard, set by the sysadmin

[Workbench] Provide an interface for the sysadmin to set Dashboard banner content

[Workbench] Provide an interface to delete files from collections

[SDKs] Provide a CLI tool to add files to an existing collection

[SDKs] Provide a CLI tool to remove files from a collection

[API] Advertise anonymous token in discovery document

[Crunch] Crunchstat and arv-mount print final stats before exiting

[Workbench] Pipeline template listings should include links to the scripts

[Workbench] Reusing ArvadosResourceList results in inconsistent results

[SDKs] CLI tools support Mac

[Keep] Write performance tests

[Performance] Compare Collection performance benchmarks across components

[API] [Workbench] Generate debconf template from config yaml

[FUSE][Performance] Job to md5sum 1TiB of 1MiB files in parallel is very slow

[FUSE] Add a --replication switch

[DRAFT] [Workbench] More encouragement for users to send feedback

[Keep] keepstore reboots GCE host under heavy load

[Workbench] Provide a GUI interface to arv-copy

[SDKs] Whenever `arv` has an invalid resource name argument, it should complain about that

[Workbench] [Webshell] Rough edges in web shell

[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

[Documentation] document installation of node manager

[Documentation] webshell installation

Port arvados-libpam to centos

[SDKs] Add runtime option to SDKs (esp Python and arv-mount) to use a filesystem directory block cache as an alternative to RAM cache.

[DRAFT] Provide one clear way for users to get data from an external source into Arvados

[Workbench] [API] Support "world-readable, but not world-searchable" permission on projects: "anyone with the link can view"

[SDKs] CLI SDK tools use Ruby SDK

[Workbench] Allow additional curation of the public projects listing

[Deployment] [Documentation] Minimize system-wide dependencies for compute node setup

[SDKs] Go SDK locator regexp (and its tests) should agree with the documented format

[Node Manager] Booting nodes shouldn't satisfy min_nodes

[FUSE] Support scaling the internal block cache based on number of open files

[Workbench] Public project listing should exclude subprojects

[API] [Workbench] Home project should be a real object (group with group_class="project"), not current_user.