[ARVADOS] created: 2.0.3
Git user
git at public.arvados.org
Fri Jun 12 21:03:39 UTC 2020
at abd5a3e7b092627c8a22c955f473b18d2f018662 (tag)
tagging db83f805e4ccf82eef22fe2c9a3db38ebd772a83 (commit)
replaces 1.3.0
tagged by Ward Vandewege
on Fri Jun 12 11:58:23 2020 -0400
Release 2.0.3, release notes at https://arvados.org/release-notes/2.0.3/
Dante Tsang (1):
Fixed FetchAll method for Container queue in order to make use of preemptible instance
Eric Biagiotti (229):
13306: Changes to arvados-cwl-runner code after running futurize --stage2
13306: Fixed formatting for newly introduced imports
13306: Fix for sdk/cwl tests.test_job.TestJob.test_run
13306: Fix for test_job.TestJob.test_done and test_done_use_existing_collection
13306: Fixed test_submit.TestCreateTemplate encoding
13306: Added py2 and 3 compatible 'next' for test_job.TestWorkflow.test_run
13306: Updated use of built in 'sorted' and a test_util bytestring
13306: Adding py2 and py3 compatible byte objects for literals
13306: test_submit fixes for py2 unicode support
13306: test_submit additional fixes for py2 unicode support
13306: Adding py2/3 unicode support to the test_job tests
13306: Updates ArvCwlExecutor to properly convert objects to JSON in unicode
13306: Updating depreciated warn function
13306: Updating depreciated assertEquals
13306: Updating get_current_container to raise when not a 404
13306: Removing unneeded try/except statements in the acr submit tests
13306: Prevents multiple RunTimeStatusLoggingHandlers from being added
13306: Removes a log handler added during a test, breaking subsequent tests.
13306: Adds test for when get_current_container results in a 404
13306: Updating dict value iteration to be more efficient with py2
13306: Updating dict keys as a list to ensure py2/3 compatibility
13306: Updating dict values as a list to improve py2 performance
13306: Fixing previous commit to use viewvalues instead of listvalues
13306: Updating dict items as lists to improve py2 performance
13306: Removing list wrapping added by futurize to PathMapper objects
13306: Removing old_div to simplify division operations
13306: Unicode fixes for the conformance tests
13306: Unicode fix for docker image generation in py3 environment
13306: Adding support for building the dev docker jobs image with py3
13306: Removing debug echo
Merge branch 'master' into 13306-arvados-cwl-runner-py3-support
13306: Fixes futurize mistakes regarding PathMapper items()
13306: Additional dict item iteration improvements
13306: Improved py2/3 str compatibility
13306: fixes test_with_arvados.sh pip executable with python2
13306: Adds declaration of py2/3 support to arvados cwl and python sdks
Merge branch '13306-arvados-cwl-runner-py3-support'
13306: Removing unneeded import statements
Merge branch 'master' into 13306-arvados-cwl-runner-py3-support
Merge branch '13306-arvados-cwl-runner-py3-support'
14745: Makes the azure driver its own package
14745: Adds gocheck hook to go test for azure dirver
14745: Updates config keys, documentation, and addresses golint suggestions
14745: Makes DeleteDanglingResourcesAfter an arvados.Duration
14745: Un-exports identifiers
14745: Updates drivers to use json.RawMessage instead of map[string]interface
14745: Updates StubDriver to match driver interface and updates vendor.json
14745: Replaces debug println with proper return and doc clean up
14745: Adds back param loading to StubDriver InstanceSet
14745: Removes unneeded file and debug code and improves Duration comments
14745: Improves azure driver exported var comment
14745: Adds support for passing nil params to StubDriver InstanceSet
14745: Removes unnecessary test parameter
Merge branch '14745-azure-cloud-driver-fixups'
14853: Adds os.name check for subprocess conditional import
Merge branch '14853-chapmanb-subprocess-merge'
9865: Simplifies ACR exception handling
9865: Removes handling of exceptions derived from BaseException
9865: Executor exception improvement
9865: Adds stack trace to API server state check exception
14885: Updates sdk/cwl and services/fuse ciso8601 dependency
Merge branch 'master' into 14885-ciso-and-conda-packaging-pr
14885: Removes as_naive datetime parsing distinction
14885: Adds python2 conditional pytz import
9865: Removes trailing whitespace
Merge branch '9865-cwl-fix-ignored-exceptions'
Merge branch '14885-ciso-and-conda-packaging-pr'
14886: Adds a test that reproduces the error
14886: Simplifies test mocking
14886: Adds flag to stop infinite logs
14886: Updates test to fail for the more specific case
14886: Fixes mock issue between tests
14886: Fixes typo
Merge branch '14886-acr-recursion-runtime-error'
14885: Reverts back to parse_datetime_as_naive
Merge branch '14885-ciso-and-conda-packaging-pr'
14645: Adds FUSE ops timing using prometheus
14645: Adds FUSE ops time to crunchstat output
Merge remote-tracking branch 'origin/master' into 14645-fuse-operations-reporting
14645: Adds prometheus_client dependency
14645: Adds individual ops time output
14645: Adds op counts to reporting
14645: Updates crunchstat format for fuse ops
Merge remote-tracking branch 'origin/master' into 14645-fuse-operations-reporting
Merge branch '14645-fuse-operations-reporting'
14484: Adds migration file for collection file count and size
14484: Updates the db structure after db:migrate
14484: Adds functionality and test for pdh grouping in the container model
14484: Fixes bug in pdh transaction grouping
14484: Adds migration for collection file count and total size
14484: Changes file token to match the one used in collection.rb model
14484: Fixes grouping bug by simplifying nested pdhs arrays
14484: Adds file count and size callback to the collection model
14484: Updates the migration to use the sdk for manifest parsing
14484: Makes quotation marks consistent
14484: Simplifies pdh transaction grouping, keeps SQL in the migration
14484: Adds test for pdh grouping functionality in the container model
14484: Fixes tests that intentionally pass in invalid manifests
14484: Fixes performance test by changing file_size_total to bigint
14484: Updates collection documentation to include the new file stats
14484: Adds tests for Collection model and makes file attributes readonly
14484: Moves pdh grouping into a lib module
14484: Moves test for grouping pdhs to its own file
14484: Moves the file count and total size callback to after_validation
14844: Adds collections controller tests and updates collection model tests
14484: Update collection model to overwrite file stats if a change is attempted
14484: Improves test coverage and attribute setting performance
14484: Adds test for updating a collection with file stats and manifest changes
Merge remote-tracking branch 'origin/master' into 14484-collection-record-update
Merge branch '14484-collection-record-update'
14723: Mapping each target destination to an input file WIP
14723: Fixes literal mapping and name conflict resolution
14723: Adds tests for multiple file targets and literal name resolution
14723: Fixes trailing whitespace
15002: Adds admin feature for cancelling completed containers
Merge branch '15002-cancel-completed-container'
14723: Adds comments for the changes to StagingPathMapper
Merge branch 'master' into 14723-cwl-multiple-file-targets
Merge branch '14723-cwl-multiple-file-targets'
15106: Adds trigram index migration
Merge branch 'master' into 15106-trgm-text-search
15106: Adds trigram search to the api
15106: Fix for trgm non-string operators
15106: Adds test to verify the trgm index exists on the correct columns
15106: Adds exception handling to the trgm migration
15106: Arvbox update to be able to run the trgm migration
Merge remote-tracking branch 'origin/master' into 15106-trgm-text-search
15106: Updates install and upgrade docs to include trgm prerequisites
14965: Updates fuse tests with futurize stage1
15106: Fixes arvbox to update an existing arvados user to superuser
14965: Updates fuse tests with futurize stage2
15106: Adds trigram support for "like" queries
14965: Updates fuse code with futurize stage1
15295: Updates fuse code with futurize stage2 and fixes tests
Merge branch '15106-trgm-text-search'
14865: Fixes test mount type test
14965: Fix for inflexible llfuse function parameter
14965: Fixes subprocess.check_output parsing
15396: Improves trgm update and installation docs
Merge branch '15396-trgm-docs'
14965: Fixes read operation encoding
Merge remote-tracking branch 'origin/master' into 14965-arv-mount-py-three
14965: Fixes the create operation encoding
15380: Adds documentation for text search filtering
14965: Fixes test for checking the arvmount version
14965: Fixes unlink operation encoding
15380: Improves list filter search documentation
14865: Reverts change to read op and fixes StringFile
14965: Fix for default command args test
14965: Adds net-tools to arvbox for run-test-server.py netstat update
14965: Fixes netstat regex string
14965: Fixes crunchstat test assertion
14965: Fixes magic directory test data
14965: Fixes replace test encoding
14965: Fixes token expiry time mock, byte data, and open mock
Merge branch '15380-full-text-search-docs'
14965: Fixes mkdir name encoding
14965: Fixes rmdir and rename op encoding
14965: Fixes FuseMountTest encoding
14965: Simplifies previous fix to FuseMagicTest
14965: Adds encoding to keep.put argument
14965: Mocks FreshBase _poll_time to avoid comparing mock and int
14965: Cleans up test output by reducing resource warnings
14965: Report python 3 compatibility
14965: Clarifies decoding in pdh test
14965: Fixes port waiting regex
14965: Fixes py2 installation
Merge branch 'master' into 14965-arv-mount-py-three
Removes python-llfuse package from arvbox base
14965: Removes python-llfuse package from arvbox base
Merge branch '14965-arv-mount-py-three' of git.curoverse.com:arvados into 14965-arv-mount-py-three
Merge branch 'master' into 14965-arv-mount-py-three
14965: Fixes resource warning when resetting run_test_server
14965: Fixes assertRegexpMatch deprecation warning
14965: Optimizes dict iteration
14965: Improves inode item view
Merge branch '14965-arv-mount-py-three'
14813: Adds ClusterID to config export
14813: Fixes cluster config whitelist merge
Merge branch '14813-wb2-config'
14715: Adds keepproxy to cluster config loading
14715: Keepproxy uses cluster config
14715: Fixes tests and removes PID creation
15522: Adds correct name decoding to fuse ops
14715: Updates arvbox with new keepproxy cluster config
14715: Fixes keepproxy tests
14715: Adds legacy config test
Merge branch '15522-arvmount-ops-encoding'
14715: Updates keepproxy documentation
14715: keepproxy.service checks for cluster config
Merge branch 'master' into 14715-keepprox-config
14715: Fixes error handling
14715: Moves legacy config test to lib/config
14715: Fixes install and config migration docs
14715: Fixes keepproxy config migration doc
14715: Adds config option warning to upgrade notes
Merge branch '14715-keepprox-config'
14712: Adds arv-git-httpd to cluster config loading
14712: arv-git-httpd uses cluster config
14712: Updates arvbox and run_test_server with arv git cluster config
14712: Cleans up arv-git arvbox setup
14712: Fixes tests
14712: Tests use cluster config
14712: Adds legacy config test
14712: Updates arv-git-httpd documentation
14712: Fixes default config and install doc
Merge branch '14712-git-httpd-config'
15583: Adds more with_counts to queries
Merge branch '15583-no-count'
14714: Adds keep-balance to cluster config loading
14714: keep-balance uses cluster config
14714: Tests use cluster config
14714: Removes context from Server functions. Adds sync.Once to setup
14714: Sets the token on the arvados client
14714: Uses lib/cmd prometheus registry
14714: Updates/adds keep-balance docs
14714: Adds missing doc
14714: Updates KeepServiceTypes legacy mapping and error messages
14714: Simplifies server startup and removes globals
Merge remote-tracking branch 'origin/master' into 14714-keep-balance-config
14714: Removes metrics serving
Merge branch '14714-keep-balance-config'
14714: Improves error message when using the legacy keep-balance config
14714: Corrects keepstore service distinction in the upgrade notes
Merge branch '14714-keep-balance-config'
15655: Fixes logtail encoding
Merge branch '15655-logtail-encoding'
Removes old config assertions
Removes arvados-docker-cleaner commented out service file assert
Evgeny Sabirov (1):
Redesign OkHttpClientFactory:
Fernando Monserrat (23):
no issue # Fix and update rvm GPG Key signature issue
no issue # Fix and update rvm GPG Key signature issue on test dockerfiles
issue #14891 upload rcs to testing repo
issue #14891 upload rcs . Add verbose
issue #14891 Update to receive param rc to build for release candidates
issue #14891 remove -x
issue #14891 fix spaces and initialize RC
refs #14891 .Merge branch '14891-upload-to-testing-repo'
no issue # Remove jessie-updates from sources.list as it is no longer supported
issue #15041 Updates adding versioning for java sdk and gradle task to build and publish it. gradle publish include push to sonatype \nArvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat at veritasgenetics.com>
Merge branch '14670-new-java-sdk-docs' of git.curoverse.com:arvados into 14670-new-java-sdk-docs
issue #15041 Updates adding versioning for java sdk and gradle task to build and publish it. gradle publish include push to sonatype \nArvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat at veritasgenetics.com>
issue #15041 Updates adding groupID org.arvados to the settings and install to script to deploy to staging repo \nArvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat at veritasgenetics.com>
issue #15041 Fix gradle command \nArvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat at veritasgenetics.com>
issue #15041 Split test and upload. uploadArchives passed as parameter to publish artifact \nArvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat at veritasgenetics.com>
15412: update to bash 4.4.12 on centos7 containers
15612: Add reference to the ticket regarding the bash upgrade
Merge branch '15612-update-centos7-to-bash-4' refs #15612
15648: update to rh-python36
15648: update documentation adding upgrade to rh-python36
Add support for Debian 10 (aka 'Buster') to Makefile
Add support for Debian 10 (aka 'Buster') to Makefile
Merge branch '15839-add-debian-buster-packages'
Krzysztof Majewski (9):
NumberFormatException fix
NumberFormatException fix
NumberFormatException fix
Merge branch 'master' of https://github.com/MajewskiKrzysztof/arvados
Merge branch 'master' of https://github.com/MajewskiKrzysztof/arvados
Merge branch 'master' of https://github.com/MajewskiKrzysztof/arvados
Get project by uuid.
Fix file token error
Add missing EXISTS filter.
Lucas Di Pentima (408):
14012: Early cached manifest validation by doing HEAD req on first block.
Merge branch 'master' into 14012-arvput-check-cache
14012: Do HEAD request on the oldest non-expired signature for cache validation
14012: Rephrases error message.
14012: Fix test
14012: Split cache file name generation for readability
14012: Enhance test coverage on _cached_manifest_valid() method
13006: Test exposing the bug
13006: Changes is_a filter to use a substring query to support remote UUIDs.
13006: Adds expression index on links.[tail|head]_uuid
Merge branch '14012-arvput-check-cache'
13006: Fail when using is_a filter on uuid attr and prefix_uuid doesn't match.
13006: Uses 'is_a' filter again because it's being fixed on the API server.
Merge branch '13006-api-is_a-filter' into 13006-sync-groups-is_a-filter
Merge branch '13006-api-is_a-filter'
Merge branch '13006-sync-groups-is_a-filter'
14640: Upgrades API to rails 4.2.11
14640: Upgrades WB rails to 4.2.11
Merge branch '14640-api-wb-activejob-upgrade'
14539: Persists empty directories by adding a '\056' empty file.
14539: Tests that '\056' cannot be used as a file or directory name.
14539: Fixes fuse tests.
14539: Escape backslash & space chars on file/dir names, with tests.
14482: Enhance code readability
14482: Don't list empty dir placeholder files on collections listings.
14482: Handle escaped chars on manifest validation.
14482: Fix Manifest::files_count()
Merge branch 'master' into 14539-pysdk-empty-dir
14538: Update comment.
14539: Encode \t & \n chars on file/dir names on collection's manifest.
Merge branch 'master' into 14482-rubysdk-empty-dir
14482: Adds failing test about partially unescaped file tokens.
14482: Allow unescaped " " on stream and file token regexes (WIP)
14539: Fixes literal backslash escaping.
14539: Fixes and simplifies the escape() function. Updates test.
14539: Removes pointless code comment.
14539: Simplifies a bit further the regexp replacement on escape() function.
Merge branch '14539-pysdk-empty-dir'
14482: Manifest validation including 8-bit escaped chars; with tests.
14482: Stricter token regexes.
Merge branch '14482-rubysdk-empty-dir'
14770: Fixes parameter on acr call.
14718: Issue salted token when passing 'remote' param to login.
14718: Changes the way remote param is packed into return_to.
14718: Validates remote cluster id parameter on login endpoint & callback.
14718: Updates controller test to support josh_id's return_to new format.
Merge branch '14718-api-login-salted-token'
14738: Fixes the double-slash usage on requests to prevent 301 from controller
14738: Enhances code readability when concatenating strings.
14738: Replaces double with single quotes for code style.
Merge branch '14738-tag-editor-fix-es5'
Merge branch '14770-wb-acr-bad-param'
13937: Export stats as prometheus metrics. (WIP)
13937: Refactors approach to pass volume metrics as curried vecs (WIP)
13937: Moves statsTicker metrics init to its own func.
13937: Adds facility for drivers to register their own counters.
14860: Exposes the bug with a new test.
14860: Fixes bug by assigning the signed manifest text to the snapshot being saved.
Merge branch '14860-fix-collection-versioning'
Merge branch 'master' into 13937-keepstore-prometheus
13937: Simplified volume specific metric handling (WIP)
14804: Exposes the bug with a test.
14804: Returns 503 status (instead of 404) on GET when a volume does the same.
14794: Adds Workbench2 menu item.
14804: Adds test scenario comment
Merge branch '14804-keepstore-transient-backend-errors'
14794: Adds configuration to point to workbench2 URL explicitly
14794: Adds test
14794: Adds workbench2 url to workbench's config on arvbox
14794: Validates workbench2_url config at startup.
14794: Moved config validator to lib/ so that it can be testable.
Merge branch '14794-link-wb1-to-wb2'
14884: Adds unicode-named file upload test.
13937: Don't try to update stats if they aren't initialized (useful for tests)
13937: Fixes file naming inconsistency between storage drivers.
13937: Adds counters to S3 driver.
13937: Adds counters to azure driver.
14916: Adds upgrading note with script example for collection checking.
14916: Rephrases upgrade notes. Enhances example script with success message.
Merge branch '14916-rubysdk-upgrade-note'
Merge branch 'master' into 13937-keepstore-prometheus
13937: Simplifies arg passing on Start() funcs
13937: Fixes metrics naming
13937: Simplifies volume counter stats assignments. Fixes test.
13937: Adds tests for operation & I/O counters.
13593: Adds 'async' parameter to groups create & update calls for perms updates.
13593: Updates API documentation.
13937: Removes unnecessary data passing on tests.
13593: Changes default async permission update interval. Clears cache.
13593: Cleans up old experimental code.
13937: Removes the 'any' operation type for a better way of testing driver labels
13593: Moves & enhances group creation with async=true test.
Merge branch '13937-keepstore-prometheus'
Merge branch '13593-async-perm-graph-update'
14966: Fixes test.
14966: Implements cleanup on test case teardown.
Merge branch '14966-api-test-hang-fix'
14873: Updates arvados & arvados-cli gems dependency on google-api-client.
14873: Removes protected_attributes gem dependency.
14873: Removes activerecord-deprecated_finders gem dependency.
Merge branch '14873-google-api-client-update'
14873: Rails 5 upgrade. Some tests still failing. (WIP)
14873: Replaces *_filter with *_action
14873: Fixes all deprecation notes on unit tests
14873: Adds missing copyright notices
14873: Fixes deprecation notes on functional tests.
14783: Fixes more deprecation warnings from functional tests.
14873: Adds new abstract class ApplicationRecord.
14873: Removes legacy setting as all controllers were migrated.
14873: Upgrades 'pg' gem & solves an issue related to a new internal table.
14873: Fixes deprecation warnings on integration tests.
14873: Fixes integration tests.
14873: Fixes parameter handling (WIP)
14873: Marks past migrations with version 4.2
14873: Skips indexes which 'columns' attribute isn't an Array.
14873: Gets rid of yet another deprecation warning.
14873: Adds headers to controller tests' requests.
Merge branch 'master' into 14873-api-rails5-upgrade
14873: Fixes unit tests.
14873: Removes debug data on fixture.
14873: Reverts previous fixture changes.
14873: Updates test for fix deprecation warning.
14873: Fixes nested params behavior on controller tests.
14873: Custom JSON attributes that default to [] or {} when nil.
14873: Fixes JSON custom types.
14873: Removes byebug debug call on test.
14873: Adds JSONB columns to discovery doc.
14873: Modifies failing tests for debugging purposes.
14873: Migrated functional tests to be integration tests.
14873: Changes perftest with benchmark because of unidentified errors.
14873: Fixes permission benchmark test
Merge branch 'master' into 14873-api-rails5-upgrade
14873: Adjusts latest API Server changes to be rails5 worthy.
14873: Fixes typo on schema file.
14873: Upgrades missing config settings.
14873: Updates dependency on our themes_for_rails fork.
14873: Fixes performance test.
Merge branch '14873-api-rails5-upgrade'
14988: Initial Gemfile update. Replaces EOLed sass gem.
14988: Updates assets server config.
14988: Updates *_filter callbacks to use the new *_action form.
14988: Allows units & functionals tests to run.
14988: File updates & additions from 'rake rails:update'
14988: Removes deprecated warning about mini_test. Adds byebug for tests.
15109: Adds admin doc section on how to manage the api server's log table.
15109: Adds missing doc file.
Merge branch '15109-logs-table-admin-docs'
14988: Uses wiselinks gem fork to fix some deprecation warnings.
14988: Fixes deprecation warnings on controller tests (WIP)
14988: Removes almost all pending deprecated warnings on functional tests.
14988: More deprecation warning fixes on functional tests.
Set up "test" environment before dropping the rails database.
Adjust the environment setting command to be consistent with other calls.
Merge branch 'rails5-schema-env-data'
14988: Refactors ArvadosBase class to not subclass ActiveRecord.
14988: Makes test runner defer the test failures summary.
Fixes API Server's test runner to print failures summary at the end of the run.
Merge branch 'api-tests-summary-fix'
15167: Adds mention about unlogged_attributes setting on Admin docs section.
Fixes test running call on API server to be able to run single test files.
15161: Re-adds API's config:check rake task (as a noop)
Merge branch '15161-config-check-rake-fix'
14988: Fixes functionals tests (WIP)
14988: Fixes unit test by adding 'x-python' type to the preview-allowed list.
14988: Fixes CSS syntax issue.
14988: Fixes CSS syntax error on Jobs controller tests.
14988: Adds missing create!() method to ArvadosBase.
14988: Fixes anonymous config & token usage issues on tests.
14988: Removes deprecation warning about rendering nothing.
14988: Disables wiselinks gem. Testing if it's really needed.
14988: Fixes exception raising when logging out.
14988: Fixes .dup method behavior on ArvadosBase.
14988: Adds empty subdir to test/ as it's required by rails.
14988: Fixes exception raising due to a change in rails5 behavior.
Merge branch 'master' into 14988-wb-rails5-upgrade
14988: Fixes merge conflict
Merge branch 'master' into 14988-wb-rails5-upgrade
14988: Fixes assert_equal param ordering for proper error messages.
14988: Fixes pipeline instance controller's param handling.
14988: Upgrades bootstrap-sass to deal with CVE-2019-8331.
14988: Fixes bootstrap import issue
Merge branch '15167-unlogged-attrs-api-docs'
15227: Adds test exposing bug.
Syncs up generated config.
15227: More tests to expose the bug.
15227: Fixes type checking on json attributes.
14988: Fixes destroyed? method to return false on new records.
14988: Restores debug message when accessing non-loaded attributes.
Merge branch '15227-apiserver-properties-bugfix'
Merge branch '14988-wb-rails5-upgrade'
14946: Upgrades Gemfile.lock's bundler requirement on api server & worbench.
14946: Updates pattern matching because of newer git message changes.
14946: Reverts Gemfile.lock changes. Updates documentation.
14946: Updates Dockerfiles for building & testing packages.
15258: Adds /lib to the eager_load paths.
15258: Removes /lib from eager load paths because of failing integration tests.
15258: Explicitly require libs instead of relying on autoloading.
Merge branch '15258-wb-report-issue-bugfix'
Merge branch 'master' into 14946-ruby-2.5
15725: Adds test exposing 2 issues when trashing collections with versioning
15275: Saves snapshot as system user instead of assigning a signed manifest to it
15275: Avoids running manage_versioning when not needed.
15275: Moves comment to its proper place.
15275: Adds another test exposing the jsonb changed field bug.
15275: Don't create snapshot when trashing collection.
15275: Don't create snapshots whenever is_trashed is true.
15275: Simplifies method code.
Merge branch '15275-collection-delete-bugfix'. Refs #15275
15275: Re-adds the test exposing this branch's particular bug.
Merge branch 'master' into 15275-attribute-dirtyness-bugfix
15275: Checks for jsonb types changes by comparing deserialized values.
15275: Adds test for different jsonb properties comparisons cases.
Merge branch '15275-attribute-dirtyness-bugfix'
14946: Fixes 'gem install' invocation.
14946: Adds Gemfile.lock file on login-sync.
14946: Updates SSO's install documentation so it doesn't ask for ruby 2.5
Merge branch 'master' into 14946-ruby-2.5
14946: Fixes warnings related to uninitialized instance variables, and others.
14946: Fixes Fixnum deprecation warning.
14946: Removes shadowed Collection.uuid method as it isn't being used.
14930: Adds --trash-at & --trash-after arguments to arv-put (WIP)
14930: Moves the trash_at compute logic into its own method.
14930: Assumes timezone-less provided trash datetimes as local.
14930: Removes unused variable assignments on tests.
14930: Fixes utc offset calculation when naive datetime provided & adds tests.
14930: Adds trash_at syncing when updating a collection with '--trash-after N'
14874: Adds Collections.DefaultProperties to arvados config.
15306: Adds integration tests with query string & form encoded params.
15306: Don't check for empty responses now that we use a filter.
15306: Adds testing on collections#show that expose the bug.
15306: Removes trailing slash on test.
15306: Adds more test cases confirming the issue is encoding independent.
15306: Fixes the bug.
15306: Adds similar test to groups, exposing the same issue as collections.
15306: Fixes issue on groups controller.
15306: Don't interpret include_trash="false" as include_trash=true.
15306: Fixes tests to POST form & json encoded params.
15306: Adds include_trash param definition to container requests.
15306: Moves include_trash param declaration to the controller.
15306: Adds warning log message when parameter isn't boolean.
Merge branch '15306-api-nonjson-params'
Merge branch 'master' into 14874-protected-collection-properties
14930: Assumes end-of-day datetime when --trash-at YYYY-MM-DD only.
14930: Adds expiration notice in local time at the end of the run.
14874: Adds default properties behaviors at collection creation.
14874: Adds protected properties check for collection updates.
Merge branch 'master' into 14946-ruby-2.5
Merge branch '14946-ruby-2.5'
14930: Don't ignore DST settings.
Merge branch 'master' into 14930-arvput-trash-at
Merge branch 'master' into 14874-protected-collection-properties
14874: Fixes 'the the' typos on documentation & code comments.
15350: Fixes unnecessary api client instantiations on examples.
15350: Adds PySDK recipe to get a container request's state.
15350: Simplifies recipe code.
Merge branch '15350-pysdk-cookbook-recipe'
Merge branch '14930-arvput-trash-at'
Merge branch 'master' into 14874-protected-collection-properties
14874: Adds admin documentation, grouping it with collection versioning.
14874: Fixes issue with keys being loaded as symbols from application.yml
14874: Shows errors when trying to update properties on wb1 tag editor.
14874: Adds protected properties error handling to wb's tag editor.
14874: Renames DefaultProperties to ManagedProperties. Fixes documentation.
14874: Adds admin script examples on documentation.
14874: Simplifies example scripts and expands documentation.
Merge branch 'master' into 14874-protected-collection-properties
Merge branch '14874-protected-collection-properties'
14874: Adds Collections.ManagedProperties to Go SDK.
14874: Capitalizes managed properties keys, updates documentation.
14874: Fixed missing config sync.
Merge branch '14874-post-merge-fixes'
15209: Makes python components packages ask for current PySDK version.
Merge branch 'master' into 15209-python-arv-deps-pinned
15209: Fixes pysdk dependency strings on pam, fuse & nodemanager.
Merge branch '15209-python-arv-deps-pinned'
Fixes test runner execution so that it can run individual tests on rails 5
Merge branch 'wb-test-runner-fixes'
Unify string quotation on python example scripts on doc site.
15318: Updates test to expect X-Request-Id value on error messages.
15318: Adds X-Request-Id value to every error response. Fixes test.
15318: Updates tests.
15318: Updates go components' tests to consider the req-ids.
Merge branch '15318-ReqIds-on-api-errors'
15219: Logs exceptions with backtraces as part of the JSON log.
15219: Tests for exception backtraces being included on the json log.
Merge branch 'master' into 15319-api-useful-stacktraces
15319: Adds troubleshooting documentation to the Admin section.
15319: Fixes example log path and links troubleshooting page from install page.
Merge branch '15319-api-useful-stacktraces'
Pins mithril version to fix CI pipeline.
15496: Sets default attribute to 'x' instead of nil on check_box_tag.
Merge branch '15496-wb1-group-membership-admin'
14716: Keep-web config params as part of the cluster config.
14716: Splits WebDAVCache config into its own struct to be assignable.
14716: Adds legacy keep-web config loading.
14716: Migrates to new config.
14716: Fixes tests (WIP)
14716: Updates run_test_server script to run keep-web without deprecated flags.
14716: Sets anonymous user token using the new way on tests.
14716: Testing workbench integration test fix.
14716: Removes old usage message.
14716: Adds legacy config test.
14716: Updates documentation, add test check.
14716: Adds upgrade notes for keep-web.
14716: Analyzing integration test fix failure
Merge branch 'master' into 14716-webdav-cluster-config
14716: Updates arvbox scripts
14716: wb integration tests (wip)
14716: Migrates NodeProfiles to Services on arvbox.
14716: Fixes wb integration test.
14716: Sets empty anonymous token on failing wb integration tests.
14716: Fixes install documentation.
14716: Removes duplicated key from a past merge.
14716: Fixes yaml lib being used.
14716: Fixes on config loading.
14716: Removes test config loading func that short-circuited load mechanism.
14716: Moves keep-web legacy config loading test to lib/config.
14716: Fixes config type init function naming.
Merge branch 'master' into 14716-webdav-cluster-config
14716: Removes legacy config file existance check.
Merge branch '14716-webdav-cluster-config'
14716: Fixes install documentation.
14716: Rearranges sections: install, configure, run keep-web.
10998: Adds Collections.WebDAVCache.MaxBlockEntries config knob.
10998: Adds test to confirm that keepclient's block cache is set up.
10998: Sets up keepclient's block cache at handler's initialization.
14716: Fixes on documentation.
Merge branch '14716-doc-fixes'
Merge branch '10998-keepweb-block-cache-size'
15605: Updates vendor.json to use the latest goamz version.
Merge branch '15605-goamz-update'
15499: Make reuse tests fail to expose the bug.
15429: Changes full text searching on wb1 utilizing new trigram indexes.
15429: Removes unused to_tsquery()
15429: Renames ilike_filters function & file. Fixes comments, tidies up code.
15429: Escapes the underscore char so it can be used as a literal.
Merge branch '15429-wb1-use-trigram-search'
15716: Don't include modules on .rake files
15716: Fix tests by importing CurrentApiClient module on missing places
15716: Merge branch 'master' into 15716-api-keepservice-list-fix
Merge branch '15716-api-keepservice-list-fix'
15497: Fixes tests to confirm that runner containers don't get reused.
15497: Don't reuse runner containers.
15497: Adds issue # to comment.
Merge branch '15497-reuse-fix'
15642: Adds tests exposing the bug.
15642: Fixes legacy config loading for keep-web.
15642: Fixes legacy config loading for arv-git-httpd.
Merge branch '15642-cluster-config-fix'
15067: Adds vocabulary format documentation on the Admin section.
15067: Corrects vocabulary format documentation.
15067: Adds additional grammar corrections to wb2's documentation.
15067: Fixes formatting.
Merge branch '15067-wb2-vocabulary-doc'
15849: Adds vocabulary migration example script.
15849: Fixes file paths on wb2's arvbox config.
15849: Errors out when a duplicated label is detected on the vocabulary.
15849: Moves script to the documentation, includes it on the admin section.
15849: Moves script to 'tools/' subdir, with some fixes.
15849: Adds symlink to script from doc's includes subdir.
15849: Removes default value setting to required argument.
15849: Adds a message for dry-run mode when nothing should be migrated.
Merge branch '15849-vocab-migration-example'
Merge branch 'MajewskiKrzysztof-exists-filter'
Merge branch 'file-token-error' of git://github.com/MajewskiKrzysztof/arvados into MajewskiKrzysztof-file-token-error
Merge branch 'MajewskiKrzysztof-file-token-error'
Pins signet gem version on arvados-login-sync to keep ruby 2.3 compatibility.
15944: Fixes published ports list when running arvbox on public mode.
15944: Merge branch 'master' into 15944-arvbox-publicdev-fix
15944: Takes arvbox container's default gw IP as internal client.
Merge branch '15944-arvbox-publicdev-fix'
Merge branch '15902-slow-query'
Adds information about the new vocabulary format on the release notes.
16141: Exposes the bug.
16141: Adds missing collection fields to GoSDK.
16141: Fixes Collection type on Go SDK. Adjusts test.
16141: Expands test for other object types.
16141: Fixes GoSDK's User type.
16141: Adds better message on test in failing situations.
16141: Fixes test to use the 1st keep_service's uuid the test server returns.
16141: Fixes GoSDK's Collection type.
16141: Updates the test to use a different, more complete collection fixture.
16141: Fixes User type, adjusts fixture to make the test pass.
Merge branch '16141-gosdk-missing-fields'
16144: Adds tests exposing the bug.
16144: Fixes the bug.
16144: Adds more checks and simplifies nested conditionals.
16169: Adds test exposing the requirement propagation bug.
16266: Adds tests exposing potential XSS vulnerability on escape_javascript()
16266: Applies monkeypatch to fix CVE-2020-5267 on workbench1.
16263: Assigns nil to select attributes when receiving empty values.
16263: Adds nullify behavior to users's batch_update endpoint.
16263: Don't cache modified_by_*_uuid fields when using LoginCluster.
16263: Makes gofmt happy.
16263: Adds test exposing a bug on filter unmarshalling.
16263: Bool filter bug fix.
16263: Adds test exposing a bug when using 'limit' with the max int64 value.
16263: Adds unit test case confirming 'limit' bug.
16263: Decodes JSON numbers as strings instead of float64.
16263: Pulls from official git repo when running federation tests.
16313: Updates minimum requestd ram on docker containers from 4 to 16 MB.
16435: Allows 2 or 3 fields per record on the CSV file.
16435: Adds support for different permission levels: read, write & manage.
16435: Avoids creating duplicated group->user links.
16435: Adds & updates tests.
16435: Updates the documentation.
16341: Upgrades rack on API & Workbench.
16492: Upgrades websocket-extensions gem to fix a security alert.
Nico Cesar (1):
Typo in one of the parameters
Peter Amstutz (671):
14574: Ensure output callbacks take workflow lock
Merge branch '14574-expression-fix' refs #14574
14593: Fix a-c-r when running on the "jobs" API
14593: Add note about broken crunch1 to upgrade docs.
14593: Fix typo.
Merge branch '14593-acr-crunch1' refs #14593
14476: When creating a Runner, check input is valid before submitting
14476: Fix RunnerTemplate
14476: Add test that submitting with missing parameters correctly gets error.
14495: Add dispatchcloud.EstimateScratchSpace()
14476: Remove redundant falsey check
Merge branch '14476-cwl-missing-input' refs #14476
14594: Update to latest cwltool
Merge branch '14594-update-cwltool' refs #14594
14495: Add warnings when estimateDockerImageSize gets bad input
Merge branch '14495-crunch-docker-space' refs #14495
14595: Add leave_modified_at_alone
14595: Fix comment.
Merge branch '14595-leave-modified-at' refs #14595
Set DBName correctly for arvbox demo, hopefully fix ci.commonwl.org
Update README and community doc page. refs #14617
Update cwltool refs #14510
14327: Don't create new collection if source has expected secondaryFiles
Fix test_with_arvbox.sh to use https://versions.arvados.org no issue #
14327: Add comments
Merge branch '14327-cwl-unnecessary-collections' refs #14327
14660: Add workbench2 to arvbox. Improve SSL support in arvbox.
14660: Proxy keep-web for https. Install root cert inside the container.
14660: Enable workbench2 to connect to development server via websockets.
14660: make "sv restart" work for workbench2, prevent fail loop
Merge branch '14660-arvbox-workbench2' refs #14660
Configure UTF-8 locale inside arvbox, no issue #
arvbox uses 'down: ready' as ready condition no issue #
13964: Azure provider WIP
13964: Can successfully create a VM, list existing VMs
13964: Full lifecycle for NICs/VHDs/VMs
13964: Return Arvados instance type
13964: Detect and report rate limit and quota exceeded errors
13964: Don't panic running tests on stubs
13964: VM names are namespaced. Can set/get tags.
13964: InstanceTags type
13964: SSH access WIP
13964: Tweak test
13964: Set and check node-token WIP
13964: ssh key verification wip
13964: ssh key checking
13964: Trim space
13964: Fix string pointer capture
13964: Forget the node token once the key fingerprint is known
13964: Fail on missing node-token tag
14324: Azure driver WIP
14324: Azure driver for crunch-dispatch-cloud
14324: Remove context from interface, use Stop() instead
14324: Use logrus in Azure driver. Fix Sirupsen->sirupsen in imports
14324: Fix tests
Fix arvbox demo for workbench2 no issue #
14324: Fix API throttling header fallbacks. Add gocheck_test
14324: Embed test public key instead of reading from file
Merge branch '14324-cdc-azure' refs #14324
13306: Fix 12213-keepref test
arvbox certificates can have DNS in subjectAltName
13306: test_with_arvbox.sh can test either python2 or python3
13306: select between "conformance" and "integration" in test_with_arvbox.sh
13306: test_with_arvbox can select api
13306: fix crunchv1 bug
arvbox support for python3 refs #13306
14725: Don't give a cluster_id when updating container request record
14826: API server looks in CA cert path that works on CentOS
14725: Fix tests.
Merge branch '14725-wes' refs #14725
14826: Fix copy and paste error
Merge branch '14826-cert-path' refs #14826
11561: Add lock_count to containers, cancel container on unlock exceeded
Merge branch '11561-limit-container-locks' refs #11561
14291: EC2 driver WIP
14291: Working on instance creation
14291: Add github.com/aws/aws-sdk-go to vendor
14291: Add individual packages in github.com/aws/aws-sdk-go to vendor
14291: Still trying to nail down aws go sdk vendor
14291: Vendoring
14291: Support EBS attached storage and preemptible instances
14291: Change instance type to a supported one, add SetTags test
14291: Fix tag prefix typo
14291: minimal stub so that tests don't panic when run without live config
14291: Adjust ExtraScratch (int) to AttachScratch (bool)
14844: Azure fixes
Merge branch '14844-cdc-azure-fixes' closes #14844
14870: Ruby SDK fix for copying collection into root of an empty collection
Merge branch '14870-ruby-sdk-cp-r' refs #14870
14870: Saving previous retry logs into collection WIP
14870: Update Arvados Ruby SDK gem dependency for bugfix
14870: Copy previous container logs to "container uuid" subdir
14870: Add tests
14870: Fix another test
14291: Tweak symbol naming
14870: Remove \x01 from edge cases
14291: Introduce "AddedScratch" and "IncludedScratch" to InstanceType
14870: Adjust edge case some more, a file named '\' isn't legal either
14870: Oops need to fix edge case assertion, too
14291: Add missing packages to vendor
14291: Add more missing packages to vendor
14291: Add more missing packages to vendor
14291: Another update to vendor.json
14291: Try again with vendor.json
14291: Report errors from ImportKeyPair
Merge branch '14870-retry-logs' refs #14870
14291: Tweak Scratch/AddedScratch/IncludedScratch behavior
14291: Add EbsVolumeType, also test fixes
14291: Generate key fingerprints that work with AWS. Filter out terminated instances
14291: Exclude both "shutting-down" and "terminated" instances.
14880: Fix argument parsing issues
Add test script. Add licensing information
Tweak test script no issue #
14291: EbsVolumeType → EBSVolumeType
Merge branch '14291-cdc-aws' refs #14291
14880: Fix help message typo.
Merge branch '14880-keepdocker-argparse' refs #14880
Add 'sdk/java-v2/' from commit '55f103e336ca9fb8bf1720d2ef4ee8dd4e221118'
14669: Add java v2 SDK to run-tests
14670: Add java sdk v2 to docs
14670: Tweak install instructions
Arvbox updates, no issue #
Fix a-c-r printing logs on error refs #14870
14322: Convert uuids on input to portable data hashes
14322: Propagate collection UUID to container mount
14322: Tests for edge cases
14322: CollectionFsAccess accepts UUIDs
14322: Tweak documentation to mention uuid keep URI form
14322: Fix tests
14322: Update workbench to use new collectionUUID
14322: Tweak workbench support from manual testing
14322: Add additional example input files
14322: Update comment on bwa-mem-input-mixed.yml
14322: Workbench links collection uuids in workflow inputs
14322: Add missing test files
14322: Fix noisy unicode logging error in tests, add comments
14322: Tweak JSON_KEEP_LOCATOR_REGEXP and comment
Merge branch '14322-cwl-uuid-input' refs #14322
Move back arvbox version of nodejs to fix composer compile issue
arvbox nginx redirects http to https
Merge branch 'master' into 14669-java-sdk-v2
Merge branch '14669-java-sdk-v2' into 14670-new-java-sdk-docs
test mode creates certificate so that setting up SSO can succeed
run prepare.py in fed tests in docker container refs #15040
prepare.py in fed tests uses default python refs #15040
Fix assigning APIHost in NewClientFromConfig refs #15045
15050: Limit number of containers that crunch-dispatch-local runs at a time
15050: Need to make sure to raise the semaphore when we're done
15050: After waking up, check if the container was cancelled
Merge branch '15050-limit-cdl-containers' closes #15050
Update arvbox docs to describe how to install root cert
Merge branch 'arvbox-cert-docs' no issue #
Pin networkx because 2.2 is the last version to support Python 2.7 and 3.4
Run check-exist.py in Docker container refs #15040
check-exist uses default python (oops) refs #15040
13996: Config migration WIP
13996: Migrating defaults to new config structure
13996: Updating API server to use new config object WIP
13996: More config updates
13996: Migrate majority of defaults to config.defaults.yml
13996: Parsing durations wip
13996: More config migrations, refactor some code into config_loader.rb
13996: Migrate tests to new config
13996: Fixing test WIP
13996: Unit tests pass
13996: Don't force check for GitInternalDir, breaks tests
13996: Explicitly get string representation of URLs
13996: Fix discovery document remoteHosts
13996: Add rake config:diff
13996: Update comments
13996: Adjust config:dump to dump active config
13996: Refactor, create ConfigLoader class
13996: Can now use database info from config.yml
13996: Fix tests.
13996: Re-add symlink config.default.yml
13996: Fix legacy_jobs_api check
13996: Move configuration load earlier, before database setup
13996: Copy config into OrderedOptions for nicer access
13996: Update tests for cleaner config access
13996: Don't override name of test db if one was provided in database.yml
13996: Update rest of code for cleaner config access
13996: Tweak rake tasks
13996: Documentation for config migration
13996: Enable ERB for application.yml and database.yml
13996: Improve docs a bit
Merge branch 'master' into 14670-new-java-sdk-docs
Add gradle to arvbox, refs #14670
Update arvbox documentation for devenv config, no issue #
14670: Fix jdk and gradle links
Merge branch '13996-new-api-config' refs #13996
14670: Fix run-tests. Skip failing test.
14670: Ignore failing test
14670: Skip test (fixed)
Set secrets.secret_key_base refs #13996
Merge, don't replace RemoteClusters refs #13996
14670: Add an example page
15119: Fixes for Workbench1.ExternalURL and Controller.ExternalURL
Merge branch '15119-api-config-fixes'
14670: Update documentation with example gradle file
Handle unrecognized uuid_prefix of remote host refs #13996
Merge branch '14670-new-java-sdk-docs' refs #14670
Add gradle.properties with empty ossrhUsername/Password refs #14670
15164: Add locking between container completion and reuse
15112: Script to re-run containers
15112: Don't submit anything, just produce a csv file with results
15112: Rename since it doesn't rerun anything
15112: log root user. log progress.
Merge branch '15164-cr-finalize-lock' closes #15164
Fix mistake setting container_count_max from wrong config parameter
15028: Update cwltool/schema-salad deps, fix tests
15028: Fixing 1.0 conformance tests
15028: Fix reporting logs on container requests
15028: Instead of suppressing update, reload old version for submit
15028: Set the correct loading context to reload tools
15028: Bump cwltool
15028: Fix discover secondaryFiles after internal v1.1 update
15028: Propagate --enable-dev and handle blank node ids
15028: Bump cwltool
15028: Support optional secondaryFiles
15028: Handling secondaryFiles on record fields
15028: More conformance fixes
15028: Fix set_secondary with union types
15028: Fix timelimit, set_secondaryfiles
15028: Support WorkReuse
Merge branch '15112-rerun-containers' refs #15112
arvbox crunch-run and certificate fixes
Pin pykka < 2 for nodemanager no issue #
15061: Correctly filter out "*" from RemoteClusters
15061: API support for linking local account to remote user
15061: Implement admin variant of user merge by uuid
15061: Add missing file
15061: add federation-migrate script
15061: Move federation migrate script into sdk
15061: Add documentation for using arv-federation-migrate
Merge branch '15061-fed-login' refs #15061
Migrate arvbox api application.yml settings to config.yml
Add workbench2Url to discovery document refs #15064
15061: Check well-connectedness. Fix typos.
15061: Add warning about clusters that are not in tokens file.
15061: Code cleanup, improve validity checking & error handling
Merge branch '15061-fed-migrate' refs #15061
Add user email and cancel button to federated user redirect page
Update the note about supported Python versions for Arv SDK.
15241: Fix input bare collection as directory
Merge branch '15241-collection-input' refs #15241
Fix cwl tests refs #15241
Increase client_max_body_size in arvbox to support file uploads.
arvbox use lowercase keys for database connection params refs #15273
15028: Bump cwltool to accept v1.1
15028: Bump schema salad version. Use containers API preferentially.
Fix reporting logs on container requests refs #15028
15028: Fix tests
15028: Fix test on python3. Add conformance-v1.1 to run_in_arvbox suites.
15028: 'conformance' changed to 'conformance-v1.0'
15028: Move 'conformance' default to v1.0 fallback
15028: Fix bashism
15028: Update to latest cwltool.
Merge branch '15028-cwl-v1.1' refs #15028
15311: Remove stringify-symbol behavior on database load
Merge branch '15311-api-no-colons' refs #15311
arvbox certificates should be valid for 1 year not 30 days. no issue #
15028: Bump cwltool version for bugfix.
15028: Make sure tests use a version that supports CWL v1.1
15028: Fix test
Merge branch '15028-fix-tests' refs #15028
Test setUp sets cwltool global names set used to ensure unique names
15332: Updated federation demo to do something a little more interesting.
Merge branch '15332-fed-demo' refs #15332
15087: Display pending/running containers and queue delay.
15087: Make container status a separate panel
15295: Needs locks_count
15368: Add note about debian dependencies for installing from pip
15368: Change doc references from "arv keep put/get" to "arv-put/get"
15368: Don't require git to install arvados-python-client
Merge branch '15368-python-deps' closes #15368
15087: Fix tests.
15087: Add links to the oldest/longest running container
"arvbox run test" is --interactive if not run with any other arguments.
Merge branch '15087-wb-queued-containers' closes #15087
15295: Fix updating and checking lock_count when updating state
15295: Check that keep references are well formed
15295: Make "lock by different token" a PermissionDeniedError
15295: Fix test
15296: Shutdown cancels processes unless running inside a container
Merge branch '15295-keep-ref-check' closes #15295
Merge branch '15296-cwl-cancel-procs' closes #15296
14812: Config migration WIP
14812: Finish first pass migrating config items
14812: First pass migrating tests.
14812: Fix test
14812: Passing unit and functional tests
14812: Fixing up integration tests
14812: Get defaults and config from arvados-server
14812: Migrate UserProfileFormFields
14812: Tweak install order because API server depends on arvados-server
Tweak arvbox build order, API server depends on arvados-server
14812: Fix lib/config tests
14812: Migrate previously missed config items
14812: Remove commented debug line
14812: Move TrustAllContent to Collections
14812: Fix email defaults
14812: Tweak config export
15358: Add encoding option to CollectionFsAccess.open() and use in fetch_text()
14812: Fix a couple more tests
14812: We can't log the error, might as well make it fatal.
14812: Sync config defaults (off by one line)
14812: Improve error reporting
14812: Remove obsolete defaults from development section
Merge branch '15358-fetch-text-encoding' closes #15358
14812: Delete legacy load_config.rb
"arvbox clone" doesn't clone data, just dependencies. no issue #
14812: Add documentation about migrating Workbench config.
14812: Update API install documentation for new config as well.
14812: Add note about config migration to upgrading notes
14812: Documentation fixes
Merge branch '14812-wb1-new-config' refs #14812
Arvbox won't create application.yml if arvados_config.rb exists.
15421: Document "includes" parameter to group contents endpoint
15421: Elaborate a little more on what include= is useful for
Fix arvbox demo build. Add Services.Controller to config.yml
15421: Improve wording
arvbox rotates its TLS certificates when they expire
Merge branch '15421-include-param-doc' closes #15421
arvbox update go version, refactor creating cluster config.
Fix testing on master
Don't set ARVADOS_CONFIG if it isn't there.
Fix _dbconfig
Merge branch '14713-fix-master' refs #14713
15422: Collection provenance/used_by supports traversing containers
15422: Provenance for collections handles containers
15422: provenance and used_by endpoints traverse containers
15422: Add provenance and used_by to collection API doc
15422: Restored collection provenance for jobs
15422: highlight output/log/mount/container_image
15028: Add upgrade notes about going from CWL v1.0 to v1.1
Merge branch '15422-collections-prov-doc' refs #15422
Fix arvbox no issue #
15028: Reorganize CWL documentation some more
15028: Add link to extensions page
Merge branch '15028-cwl11-doc-update' refs #15028
Fix test
14713: Migrate old crunch-dispatch-slurm config to new config
14713: Fix handling default/missing keys, can't load default file
14717: Migrate websockets to new config
14717: Fix fallback behavior for component config vs main config
14717: Rename WebsocketKeepaliveTimeout to SendTimeout and add a comment
14717: Fix ws tests
14717: Remove LegacyComponentConfig behavior
14717: Refactor run_test_server.py and run_test.sh to use config.yml
14717: Delete obsolete functions from run_test_server.py
14717: Fixups since tests now use config.yml
14717: More test fixes. Configure correct websockets address.
14717: Make sure tests use git http and keep-web URLs from config.yml
15467: Explicitly configure for IPv4
Arvbox config doesn't need to set SupportedDockerImageFormats
arvbox creates /var/lib/arvados/run_tests/config.yml
14717: Make CONFIGSRC mandatory for run-tests.sh
14717: Put setup_config back into install_env, with comments
15467: List to map changes (WIP)
15467: Migrate lists to hashes
15467: check that array config items must end in 'List'
15467: Introduce "StringSet"
15467: Test to check that reflection works as intended
15467: Better CONFIGSRC check, always write config.yml in start_services
15467: Test case where it ends in 'List' but isn't one
Merge branch '15467-config-fixups'
15467: Services only load their own legacy config files
15356: Update Composer install doc
15356: arvbox writes API_HOST to composer.yml
Merge branch '15356-composer-config' refs #15356
Merge branch '15467-legacy-config' refs #15467
ec2 SecurityGroupIDs should be a StringSet refs #15467
Fix DisabledAPIs in schema controller, keys are symbols, refs #15467
run-tests ensure that ARVADOS_CONFIG is set, refs #15467
Fix discovery doc dockerImageFormats, refs #15467
15467: Updating ws docs wip
15467: Update install docs for crunch-dispatch-slurm
15467: Adding KeepServices WIP
15467: Added tests for KeepServices
15467: Formatting fixes
15467: Replace KeepServices with SbatchEnvironmentVariables
15467: Fix config.default.yml for SbatchEnvironmentVariables
15467: Add note about units for byte sizes, reorganize config a bit
run-tests.sh fixups refs #15356
15467: Fix SbatchEnvironmentVariables documentation typo
Merge branch 'run-tests-fix' refs #15467
Move generation of config values into arvbox cluster_config.sh
Merge branch '15467-update-install-docs' refs #15467
15181: Remove jobs API support from arvados-cwl-runner
15181: Reduce memory request, in case that was causing test failures
15181: Remove some more jobs API references
15181: Tweak a few more integration tests to request fewer resources
Merge branch '15181-remove-acr-jobs-support' refs #15181
15133: Delete crunch_scripts, start clearing out API server
15133: API tests passing
15133: Delete crunch-job & arv-run-pipeline-instance
15133: Move removing jobs API code+tests
15133: Delete legacy crunch v1 docs
15133: More test updates. Remove arv-run.
15133: Fix more tests
15133: Delete crunchrunner
15133: Remove 'commits' table, move functions to CommitsHelper
15133: Remove more referencesto arv-run and arv-run-pipeline-instance
15133: Delete crunch v1 from arvbox
15133: Add read-only jobs API to release notes
15133: Disallow creating/updating jobs API records in model
15133: Remove 'arv run' and 'arv pipeline' from arvados-client
15133: Remove some more failing workbench tests for job/pipeline
15133: Fix migration
15133: Can't edit pipeline descriptions any more.
15133: Re-add a stub crunch-dispatch.rb to make upgrade smoother
Merge branch '15133-remove-jobs-api' refs #15133
15361: handling imports wip
arvbox add InternalURLs for services, nginx proxy for keepproxy.
Delete crunch-dispatch.rb stub as requested by ops refs #15133
Fix arvbox keepproxy ExternalURL no issue #
15361: Add tests for --create-workflow bugfixes
15361: Skip unecessary checklinks
15558: Support login to user account by email address
15558: Tweak logic
15529: Support for LoginCluster and RemoteTokenRefresh
15529: Redirect to LoginCluster
15529: Add some checks to login method
15529: Add test
15529: Prevent local login when LoginCluster is set
15558: Add tests for user lookup by alternate email
15583: Set with_count('none') on wb page notification tests
15583: Add with_count('none') more places
15558: email address must refer to unique user account
Merge branch 'master' into 15558-alternate-email-addresses
15558: Enforce uniqueness on identity_url
15361: Update cwltool/schema salad versions
15558: Fix duplicate identity_url in test fixtures
15529: LoginCluster uses ApiClientAuthorization.remote_host
15558: Only set identity_url when creating new user record
15361: Add missing test files
Merge branch '15529-federated-user-accounts' refs #15529
15558: Fix tests
Merge branch '15361-acr-create-workflow' refs #15361
Merge branch 'master' into 15558-alternate-email-addresses
Merge branch '15558-alternate-email-addresses' refs #15558
Add CurrentApiClient to User fix login failure refs #15558
15499: Create additional unmodified log collection on finalize!
Merge branch '15499-container-reuse-fix' refs #15499
15499: Only create additional log collection when container is Complete
Merge branch '15499-container-reuse-fix' refs #15499
15531: Add exported config to discovery document
15531: Federation migrate script wip
Fix Composer login, use https, refs #15356
Use arvados-fork for composer no issue #
arvbox needs to pull branch to ensure latest no issue #
15531: Implement merge with redirect_to_new_user=false
15531: Working on properly migrating usernames
15531: Fix remote token validate to use RemoteHosts.*.Insecure
15531: Test federation migrate script WIP
15531: Fed migrate script passes test cases
15531: Adjust redirect_to_new_user to intended behavior
15531: Add README
15531: Adjust behavior redirecting remote user to a local one, add test
Merge branch 'master' into 15531-logincluster-migrate
15531: Bump API server revision in discovery doc for feature test
15531: Refactor federation-migrate
15531: Update arv-federation-migrate documentation for LoginCluster
15640: Adjust memory requirements
arvbox pin yarn to 1.17.3 no issue #
Merge branch '15640-cwl-test-mem' refs #15640
15654: Update nokogiri
15654: Update rubyzip gem
Merge branch '15654-wb-gem-update' refs #15654
15684: Fix arvados-api-server and arvados-workbench packaging
Merge branch '15684-package-deps' refs #15684
15640: RunInSingleContainer needs minimum of 128 MiB RAM
Merge branch '15640-cwl-min-ram' refs #15640
15531: Documentation updates
arvbox update config.yml when config override is updated refs #15531
15531: Fixing up test framework
Merge branch 'master' into 15531-logincluster-migrate
15531: Moved federation section in admin guide
15531: Fix file ownership after git pull as root
15694: Catch exception from get_current_container in runtime_status_update
15694: Add test
15424: Add WelcomePageHTML to config, with default text
15531: Don't activate new user if old user is not active
Merge branch '15531-logincluster-migrate' refs #15531
15694: Improve test comments/assertions
15424: Tweak default WelcomePageHTML
Merge branch '15694-cwl-hang' closes #15694
Merge branch '15424-wb2-welcome-page' refs #15424
15717: If there are several InternalURLs for the same host, try them all
Merge branch '15717-svc-select-port' refs #15717
Merge branch 'MajewskiKrzysztof/master' refs #15740
13936: Add default InactivePageHTML text
Merge branch '13936-inactive-user-text' refs #13936
15660: Update documentation about using preemptible instances with c-d-c
15660: Clarify config.yml
15660: Harmonize preemptible / spot instance terms
Merge branch '15660-aws-spot-doc' refs #15660
Fixes for ARVBOX_PUBLISH_IP to use a custom hostname
Arvbox sets SystemRootToken
15803: Disallow setting is_active=false direct, use unsetup
15803: Improve error message
15803: Adjust workbench1 user panel to promote setup/unsetup buttons
15803: Fix user admin page tests
15803: Remove the 'email' can_login permission created for new users
15803: Tweak text on user admin page
15577: Documentation updates WIP
15577: Add user_agreements API page
15577: Add a way to skip SDK building to streamline doc writing
15577: Overhaul user and group management documentation
15577: Fix "user agreements" => "user_agreements" for consistency
Merge branch 'MajewskiKrzysztof/get-project-by-uuid' no issue #
Merge branch 'evgeny-sabirov/evgeny-sabirov/sdk/java-v2/optimize-ok-http-resource-usage'
15828: Configured workbench is a "trusted client" by default
Merge branch '15828-trust-wb' refs #15828
15107: arvbox uses "go mod download" instead of "go get ..."
15577: Edits based on feedback
Merge branch 'master' into 15577-ownership-transfer
Merge branch 'master' into 15577-ownership-transfer
15577: Rename some files, symlink old names
15107: Tweak test for Users.PreferDomainForUsername
Merge branch 'master' into 15803-unsetup
15577: Tweak user state update diagram and text formatting
Merge branch '15577-ownership-transfer' refs #15577
Fix arvbox "go get" for arvados-server no issue #
Refactor arvbox federation test scripts, no issue #
Don't set AnonymousUserToken in arvbox
Activate new users created on the login cluster by federation-migrate
15795: Accept SystemRootToken from configuration
Merge branch 'master' into 15803-unsetup
15803: Add test that inactive user is not activated on remote.
Merge branch '15803-unsetup' refs #15803
Merge branch '15795-sys-root-token' refs #15795
15572: First pass on new prereqs/planning page
15572: Start describing config file
15572: API server and controller install docs
15572: Ongoing install guide refresh/refactor
15572: Add nginx install page
15572: List nginx under external dependencies
15572: Documentation WIP
arvbox uses "go install" instead of "go get" no issue #
Fix support links
Remove biostars link
Update gitter link to arvados/community
Add Curii Corporation to AUTHORS
15572: Updated install docs for keep components, login/SSO
15572: Update workbench, composer, websocket, git, shell install docs
Merge branch 'master' into 15572-new-install-docs
15572: Updating dispatcher install
15572: Fix up left nav rendering highlighting
15572: Epic documentation commit
15572: Make notes on cloud/slurm dispatcher install to set up VM / compute nodes.
15572: Add hypothes.is annotations to docs
15572: Passes link checking
15572: Add missing file
15572: Documentation tweaks from experience installing dev cluster
15572: Install doc updates for workbench, ws, dispatcher
15572: Update gitolite install instructions
15572: WebDAV ExternalURL expected to have trailing slash
15572: Reorganize and update version migration documentation
15572: Make note that secret inputs must be submitted on command line
15572: More information about setting up Azure credentials
15572: GitSSH should have leading ssh://
15933: Declare 'uuid' param on users/setup method discovery doc
15933: Remove unused openid_prefix from users/setup tests
Merge branch '15933-setup-uuid-param' refs #15933
15572: Add notes about keep-web and compute node image configuration
15572: Fix Services.Workbench1 typo
15572: Fix healthcheck doc to refer to Services instead NodeProfiles
15572: add note that mount tmp device_type is not implemented
Merge branch 'master' into 15572-new-install-docs
15572: Add note about user visibility
Merge branch '15572-new-install-docs' refs #15572
Update default config with go generate refs #15572
15965: Decode as UTF-8 to avoid "not ASCII" error on Python 2
Merge branch '15965-docker-metadata-decode' refs #15965
Update comments/help text about config for crunch-dispatch-slurm and websockets
16006: Add cloud install worksheets
16006: Add checklist for SLURM install
Merge branch '16006-install-worksheet' refs #16006
Gemspec sets GIT_DIR and GIT_WORK_TREE to ensure correct gem version
Clean up Gemfile & Gemfile.lock
Update workbench and login-sync Gemfile.Lock
Fix glob typo to arvados.gemspec
Update docker repo, pin bundler to workaround bug
Update git commit pin for arvados gem
Update git commit pin for arvados gem (workbench this time)
Update python packages to use version_at_commit script
Fix assertVersionOutput to handle 'pre' versions
version-at-commit.sh uses '.dev' instead of '.pre'
Fix assertVersionOutput to handle '.dev' versions
Doc updates for install Ruby and Python SDKs and utilities
Restore behavior to choose version from latest of python sdk or cwl
Adjust default for LogSecondsBetweenEvents from 1s to 5s
LogSecondsBetweenEvents should be a duration
Add "copy files from a collection to a new collection" to cookbook
16046: Replace slash with space for "repo/image" collection name
Merge branch '16046-keepdocker-slash' closes #16046
"last supported version" should be release version not git commit
Support OS packaging of Ruby/bunder, with note in install docs
Arvbox uses OS package for Ruby instead of building from source
Support OS packaging of Ruby/bunder (fix login-sync)
Pin signet <= 0.11 to support Ruby 2.3
FUSE also needs version from latest(sdk, fuse)
Allow user 'setup' to succeed even if email notification fails
Fix test refs #16051
Improve the version assignment script to handle more cases
16072: Default image is runner image version, not latest
Merge branch '16072-acr-default-image' closes #16072
Restore bootstrap.min.js refs #16081
Fix setting workflow label field from record name fixes #16083
Use updated run_upload_packages
Add a bit more discussion about DNS on compute node images closes #16085
Add python3 build of arvados-cwl-runner
arvados/jobs image uses python3 for arvados-cwl-runner
Update text to refer to Arvados 2.0
Pin bundler to version compatible with all Rubies we support
Workbench1 package depends on graphviz
Update more documentation for new config file, add 'group favorites'
Workbench 2 isn't really beta if we're telling people to use it.
16108: Change wb1 'favorites' to filter on user_uuid instead of tail_uuid
16108: Use zzzzz- in examples
Merge branch '16108-favorites' refs #16108
16111: Add SSHHelpPageHTML so admin can provide custom instructions
Merge branch '16111-ssh-help' closes #16111
Add a note to the install section
16136: Prioritize 'Function' over 'Value' and ignore null
Merge branch '16136-original-owner' closes #16136
Improve readability of upgrade notes
Add note that some services require a minimal config.yml to start.
16139: Fix secondaryFile errors when running --submit --no-wait
16139: Add test
Annotate notify uses localStorage instead of sessionStorage
Merge branch '16139-cwl-secondaryfiles-fix'
Set upper version of setuptools for Python 2 support
Set upper version of setuptools for Python 2 in Centos7 container
Pin virtualenv<20
Merge branch '16144-nil-checks' refs #16144
Tweak upgrade notes
16202: Add Workbench.SSHHelpHostSuffix
16177: Use correct config item Collections.TrustAllContent
16177: Fix tests, test server config now has TrustAllContent: false
16169: Monkey patch load_tool.resolve_and_validate_document to fix bug
Nodemanager and crunchstat-summary sync with pysdk version
Ruby gems respect ARVADOS_BUILDING_VERSION
Remove Gemfile.lock from login-sync
16138: whitelist fields for arv-copy
16138: Remove additional pipelines related code
16138: Remove additional/code references to copying pipelines
16263: Add local_user_list flag to bypass LoginCluster behavior
16263: Add local_user_list to boolParams
16263: Add omitempty to GetOptions
16263: Fix omitempty placement
16263: UserMerge shouldn't be federated
16263: Generalize "local_user_list" flag to "no_federation"
16263: local_user_list -> no_federation in boolParams
16263: Add no_federation to user update
16263: Rename no_federation -> bypass_federation
16263: Missed rename
16263: Fix only_admin_can_bypass_federation
16263: Fix no_federation -> bypass_federation in boolParms
16263: Add bypass_federation test
16263: Tweak federation tests, use CWL 1.1
16263: User migration test also checks federated user behavior
16263: Add test for BypassFederation
Pin jssha to 2.4.2
Bump mithril for advisory https://www.npmjs.com/advisories/1094
Pin version of launchy gem while we still support Ruby 2.3
Pin version of launchy gem while we still support Ruby 2.3
16419: Use CAINFO instead of CAPATH
16366: "InternalURLs" and "AccessViaHosts" are consistent in install
16339: Fix $schemas rewriting bug
Pjotr Prins (2):
util.py: python-api https certificate openssl override as is used in GNU Guix
keep.py: python-api https certificate align pycurl with httplib2 certificate finder
Tom Clegg (766):
14360: Initial version of dispatch-cloud.
14360: Fix tests.
14360: Add explicit Start method to dispatcher.
14360: Update readme.
14360: Clarify sync loop timing.
14360: Close SSH connections when no longer needed.
14360: Use consts for tag keys.
14360: Split up long run func.
14360: Cut excess time.Now() calls.
14360: Just notify once per sync.
14360: Move shutdown-if-broken check to its own func.
14360: Move monitoring API test from lame driver to stub driver.
14360: Update busy/lastUUID/running together. Clarify race comment.
14360: Rename keeplocal -> dontupdate, add explanation.
14360: Rename View to InstanceView.
14360: Add missing mutex lock.
14360: Improve comments.
14360: Log level debug->warning for unexpected condition.
14360: Cancel containers asynchronously in Sync cleanup.
14360: Encapsulate scheduler object.
14360: Fix mismatched flag name, -nodetach -> -detached.
14360: Ensure signals don't pass to child in startup race.
14360: Remove redundant wkr.booted flag.
14360: Remove redundant wp.unallocated field.
14360: Fail Create calls fast during quota quarantine.
14360: Move slurm-only code to crunch-dispatch-slurm.
14360: Fix concurrent map access in tests.
14360: Add "idle" state.
14360: Note race in docs, fix flaky test.
14360: Move single-worker Pool methods to worker type.
14360: Don't block scheduling while locking containers.
14360: Fix false negative in test suite.
14360: Retry shutdown after configured timeout.
14360: Move lockfiles from /var/run to /var/lock.
14360: Merge branch 'master'
14538: Use concurrent writers to sync a directory.
14538: Use concurrent writers to sync multiple streams.
14538: Move cancel-on-first-error logic to contextGroup.
14538: Use concurrent writers to flush chunks while writing.
14538: Check write concurrency limit.
14538: Merge branch 'master' into 14538-async-write
14538: Fix test.
14538: Remove redundant condition.
14538: Reduce max writeahead to 1.
14538: Split inline func from sync() into commitBlock().
14538: Fix racy tests.
11419: Support text modes in Collection.open().
14360: Use nonblocking mode when checking for stale lock.
14360: Fix container UUID missing in proc info file.
14360: Notify pool on worker shutdown.
14360: Merge branch 'master' into 14360-dispatch-cloud
14360: Rename Workers -> CountWorkers.
14360: Disable management APIs if config has no ManagementToken.
14360: Rename -detached -> -no-detach.
14360: Add missing argument to -kill flag.
14360: Kill containers whose priority drops to 0 while running.
14360: Merge branch 'master' into 14360-dispatch-cloud
11419: Merge branch 'master' into 11419-text-mode
14538: Merge branch 'master' into 14538-async-write
Merge branch '14538-async-write'
Merge branch '11419-text-mode'
14360: Fix race between per-container lock and garbage collection.
14596: Use sbatch --no-requeue to avoid bogus container re-runs.
Merge branch '14596-no-requeue'
14596: crunch-run: don't do anything unless container is Locked.
Merge branch '14596-check-container-locked'
11419: Read JSON files in binary mode.
14360: Comment TestDispatchToStubDriver.
14360: Fix log spam on normal race condition.
14360: Locking comment.
14360: Comment stubServer.
14360: Avoid overreporting instances during Create/List race.
14360: Clean up stub driver.
14360: Shutdown between tests to eliminate leaking logs.
Merge branch 'master' into 14360-dispatch-cloud
14360: Remove log spam.
14360: Call ChooseType just once per container.
14360: Replace OnComplete/OnCancel with ExecuteContainer callback.
14360: Shutdown pool between tests to eliminate leaking logs.
14360: Debug log when acquiring lock.
14360: Fix panic in test when last container is run twice.
14360: Fix instance creation limiting.
14360: Fix test case.
14360: Test for errant Create calls after failure.
14360: Fix error log level on first probe after boot.
14360: Merge branch 'master' into 14360-dispatch-cloud
Merge branch '14360-dispatch-cloud'
14325: Propagate API env vars to crunch-run.
14325: Add worker state diagram.
14325: Add IdleBehavior to worker pool.
14325: Add management API endpoints for drain/hold/run behavior.
14325: More testing for hold/drain states.
14325: Configurable SSH target port for cloud VMs.
14325: Add total houly price metric.
14325: Test that ssh_executor obeys a negative VerifyHostKey result.
14325: Fix dropped request params when body not specified by caller.
14325: Test dispatch container queue against controller.
14325: Cancel containers with unsatisfiable runtime constraints.
14325: Use snake_case keys in management API responses.
14325: Include instance ID in log messages from stub VM.
14325: Shutdown unknown-state worker after boot timeout.
14325: Log when a worker's first probe succeeds.
14325: Move magic number to const.
14325: Obey EarliestRetry specified by cloud rate-limiting errors.
14325: Wake up scheduler when quota timeout expires.
14325: Don't shutdown busy VMs even if boot probe fails.
14325: Document Running() return value.
14325: Clean up unsafe concurrency in tests.
14325: Remove obsolete test stubs.
14325: Test resuming worker pool state after restart.
14325: Point to API details in interface doc comments.
14325: Build crunch-dispatch-cloud package.
14325: Don't count busy workers with state=Unknown as Unallocated.
14325: Change remaining LameInstanceSet uses to StubDriver.
14325: Clean up test suite logging.
14325: Fix test.
14325: Note assumption concurrent dispatchers share a VM size menu.
14325: Improve identifiers/comments.
14325: Rephrase confusing conditions and add comments.
14325: Merge branch 'master'
14325: Log stderr from last boot-probe when giving up on boot.
14806: Handle escaped chars when parsing docker image manifest.
14806: Fix test suite to work even if PERL5LIB is set.
14806: Merge branch 'master'
Merge branch '14806-crunch1-unescape-manifest'
14325: Merge branch 'master'
Merge branch '14325-dispatch-cloud'
14325: Rename crunch-dispatch-cloud → arvados-dispatch-cloud.
Merge branch '14325-dispatch-cloud'
14325: Fix PrivateKey config type.
14325: Start up immediately if there are no stale locks.
14828: Fix double-cancel of unsatisfiable container.
14845: Fix inconsistent timeout error message.
Merge branch '14828-fix-flaky-test'
14325: Start up immediately if there are no stale locks.
14807: Match systemd description to component name.
14807: Pass env vars on stdin instead of using SSH feature.
14807: When ProviderType is unspecified, default to Arvados type.
14807: Allow driver to specify SSH username.
14807: Pass SSH public key to driver.
14807: Accept .../instances/_/drain?instance_id=X.
14807: Fix SSH target address.
14807: Expose instance IP addresses in logs and management API.
14807: Log full instance ID.
14807: Always set node-token tag.
14807: Fix crunch-run --list output when /var/lock is a symlink.
14807: Include more detail in errors.
14807: Wait at least 1 second between retries on initial queue poll.
14807: Load API host/token directly from stdin without shell hack.
14807: Don't delete existing tags when updating.
14807: Move secret-tag host key verify mechanism out of Azure driver.
14807: Fix up azure log message.
14807: Split instance count/size/cost metrics by idle/hold status.
14807: Log when a container is added/removed from the queue.
14807: Use context to pass a suitable logger to all service commands.
14807: Cancel or requeue container when priority drops to zero.
14807: Log idle time in seconds instead of nanoseconds.
14807: Update API endpoints: instance_id is always a query param.
14807: Remove errant rm.
Merge branch '14845-fix-flaky-test'
14807: Send detached crunch-run logs to journal via systemd-cat.
14807: Fix admin permissions for containers.
14807: Fix logger type mismatch.
14807: Fix missing import.
14807: Merge branch 'master'
14807: Avoid doing concurrent update requests per container.
14807: Force test SSH server to listen on IPv4.
Merge branch '14807-dispatch-cloud-fixes'
14911: Fix initialization order.
Merge branch '14911-azure-panic'
14807: Start reporting metrics immediately.
Merge branch '14807-zero-metrics'
14920: Fix state==unknown during create/list race.
14920: Improve comment.
14920: Update metrics when worker state changes idle->running.
Merge branch '14920-unknown-booting-race'
14938: Fix unreliable test.
Merge branch '14938-unreliable-test'
Fix error message.
14947: run-tests: add --interactive, skip deps on --skip-install.
14977: Drop containers when the controller says they don't exist.
14977: Kill containers that don't exist according to controller.
14977: Don't try fixStaleLocks until worker pool state is loaded.
14977: Re-order statements for clarity.
Merge branch '14977-kill-if-not-in-queue'
14807: Fix unreliable test.
14807: Fail test if a container gets run twice.
14807: Escalate sigterm->sigkill->drain instance.
14807: Lengthen kill delays in stub driver to test term-kill-drain.
14807: Update tests to new worker/pool interface.
14947: Suggest "install deps" as first interactive command.
14807: Add comments to "error indicates success" code.
14807: Don't send SIGKILL to crunch-run processes.
14947: Install controller (cmd/arvados-server) for integration tests.
14947: Accept test suite options in interactive mode.
14947: Fix controller install in deps.
14947: Ignore --only / --skip args in interactive mode.
Merge branch '14947-run-tests-interactive'
14807: Tweak log message.
14807: Merge branch 'master'
Merge branch '14807-escalate-sigterm'
14807: Drain instances that crunch-run reports broken.
14807: Configurable rate limit for cloud provider API calls.
14807: Add "kill instance" management API.
14807: Report queue metrics.
14807: Give up if initial keep services list isn't loaded in 60s.
14807: Allow some fake nodes to remain unbroken.
Merge branch '14807-prod-blockers'
15007: Fix crash when Azure nic has IP config but no IP address.
Merge branch '15007-azure-panic'
14807: Load API host/token from cluster config if present.
14807: Refuse to create instance with AddedScratch>0.
14807: Pass token to service handlers explicitly, not via context.
14807: Fix go vet warnings about %s args.
14807: Add lib/service test.
14807: Move "fallback to ARVADOS_*" logic out to lib/service.
Merge branch '14807-prod-blockers'
Accept :py3 modifier for any Python suite in interactive mode.
run-tests.sh: don't prepopulate cmd if running in an emacs buffer.
14998: Report total_* (hierarchy) stats if available.
Merge branch '14998-hoststat-total'
15044: Override unusable nginx defaults. Test nginx startup success.
15044: Fix interactive command handling.
15044: Fix error messages.
15044: Always use the en_US.UTF-8 locale. Add sanity check.
15044: Test gofmt as a separate suite, instead of refusing to run Go tests.
15044: Listen on localhost instead of default dual-stack [::].
15044: Improve error reporting in test case.
15044: Fix workbench test args in interactive mode.
15044: Fix unnecessarily unsafe yaml load.
15044: Specify test database collation.
15044: Don't kill run-tests's keepproxy server in sdk/python tests.
15044: Fix sensitivity to group existence on the testing host.
Add another nil check to Azure driver.
14758: Fix panic on error reading request body.
Merge branch '14758-keepproxy-panic'
15044: Require newer mocha.
15044: Sanity-check test services when bringing them up.
Merge branch '15044-test-fixes'
Remove dependency on jq.
Give up if test services don't come up.
14796: Add arvados-dispatch-cloud (experimental) to install docs.
14796: Add Amazon EC2 configuration example.
14796: Tweak example boot probe command.
Merge branch '14796-dispatchcloud-install-docs'
Fix stale cached container state after successful Cancel.
Fix "failed" status leaking to subsequent attempt.
Fix "failed" status leaking to subsequent attempt.
15002: Fix container update permissions.
15002: Test invalid state changes, too.
Merge branch '15002-container-permissions'
15112: Report volumes without replicas as "none" in -dump output.
15112: Use FieldLogger interface so tests can use ctxlog.TestLogger.
15112: Fix mount IDs in test case.
15112: Test multiple volumes with same device IDs.
15112: Show #collections and class->#desired map in dump.
15112: Fix log check in test case.
15112: Error out right away on unusable manifest.
15112: Fix duplicate default.
15112: Stop processing collections on first error.
15112: Refuse to run if modified_at column has any nulls.
15112: Add test.
15112: Note rationale for non-obvious paging approach.
Merge branch '15112-dont-trash-needed-replica'
15112: Fill in missing modified_at values from before #14595.
Merge branch '15112-migration'
Update structure.sql for last migration.
15003: Generate config.DefaultYAML from source file.
15003: Load config over defaults.
15003: Add 'arvados-server dump-config' command.
15003: Use config lib for arvados-server.
15003: Move keys from RequestLimits to API section.
15003: Split out deprecated config stuff.
15003: Check DB conn in controller health check. Check test services.
15003: Add missed error checks.
15003: Error out if PostgreSQL connection map is ambiguous.
15003: Add config-check command.
15003: Update service names.
15003: Warn about unknown keys and bad value types.
15112: Add config option to save list of lost blocks to a file.
15112: Fix fd leak on error.
15112: Remove tempfile only if still locked (not renamed).
Merge branch '15112-save-lost-blocks-file'
14399: Retry Azure ListBlobs call after 503 errors.
14399: Don't insert error text in the middle of an index response.
Merge branch '14399-azure-list-retry'
15003: Merge branch 'master' into 15003-preprocess-config
15148: Include list of affected PDHs in LostBlocksFile.
Merge branch '15148-lost-collection-pdh'
15003: Merge branch 'master' into 15003-preprocess-config
Remove extra \n from log.Printf formats
Log if client hangs up while waiting for unix volume Serialize lock.
15003: Merge branch 'master' into 15003-preprocess-config
Merge branch '15003-preprocess-config'
15232: Fix type of Collections.BlobSigningTTL config key.
Merge branch '15232-blobttl-suffix'
15003: Fix warnings about site-specific keys.
15003: Temporarily disable config warnings.
Merge branch '15003-disable-config-warnings'
15003: Add dispatch-cloud configs to default/template file.
15273: Use lowercase keys for database connection params.
15273: Fix key-conflict test.
Merge branch '15273-db-conn-keys'
15003: Remove NodeProfiles section from cluster config.
15003: Use lib/cmd and lib/service packages for health service.
15003: Update dispatchcloud to new config struct.
15003: Update docs to new config struct.
15003: Merge branch 'master'
15003: Remove debug printf.
15003: Remove NodeProfiles section from integration test config.
15003: Port health aggregator from NodeProfiles to Services.
15003: Fix import cycle.
15003: Dedup fixture consts.
14878: Skip flock() when testing priority updater.
15003: Ignore SAMPLE entries in default config file.
14878: Add comment.
Merge branch '14878-priority-race'
Fix syntax for python3.
15003: Update doc comment on Map, and use it in lib/service.
15003: Merge branch 'master'
Merge branch '15003-new-config-struct'
14931: Support extra tags on resources created by dispatchcloud.
14931: Tag and filter instances by SetID, so driver doesn't need to.
14931: Add configurable prefix for built-in tags.
14931: Pass custom tags to cloud driver for shared resources.
15003: Format durations as "336h", not "336h0m0s".
14931: Change default tag prefix to "Arvados".
Merge branch '14931-custom-tags'
Merge branch '15003-duration-format'
15306: Adjust tests: check ?include_trash= and avoid paging.
15306: Avoid paging in query string tests, too.
15000: Export safe parts of cluster config at /arvados/v1/config.
15000: Ensure all config defaults are captured in config struct.
15000: Accept negative durations in config, fix crashing error log.
15000: Accept byte size suffixes (KB, KiB, ...) for numeric configs.
15000: Add Workbench configs.
Fix whitespace for gofmt 1.12.
15003: Load config from default location or -config arg, not stdin.
15000: Include bad value in error message.
Merge branch '15003-config-default-location'
15000: Remove example image ID.
15000: Move exported config threshold to "needed by clients".
15000: Update test.
15000: Recommend checking config publication errors during install.
Merge branch '15000-config-api'
15340: Add metrics for cloud ops/errors and instance disappearances.
15340: Skip metrics update when running tests with no registry.
Merge branch '15340-error-counters'
14287: Refactor controller to use strong types in API handlers.
14287: Dedup "UUIDs seen" list before diff in test.
14287: Fix accepting boolean params via query string.
14287: Fix accepting nil as filter operand.
14287: Accept rpc requests without tokens.
14287: Fix token in container test.
14287: Test timestamp precision is maintained by response munging.
14287: Propagate order param.
14287: Fix unparsed formatting directive.
14287: Fix PDHs and manifests in test fixtures.
14287: Fix PDH check to ignore additional hints.
14287: Fix accepting JSON-encoded params in request body.
14287: Ensure timestamps in responses have 9 digits of nanoseconds.
14287: Remove omitempty tags so zeroes/nulls appear in responses.
14287: Fix debug log level.
14287: Avoid converting integer params to float and back.
14287: Add "kind" key to controller responses.
14287: Remove zero/missing values when req uses select or count=none.
14287: Remove extra zeroes from items[] entries too.
14287: Propagate where param in list requests.
14287: Propagate etag in collection records in responses.
14287: Set controller log level=debug in tests if ARVADOS_DEBUG set.
14287: Test request formatting variations.
14287: Handle collection/.../provenance and .../used_by requests.
14287: Fill in resp.items[].kind even if no uuid/pdh is selected.
14287: Fix test fixture PDH.
14287: Propagate reader_tokens to Rails API.
14287: Accept order param as string or array.
14287: Change test fixture so PDH is really not readable by active.
14287: Don't send reader_tokens="[false]".
14287: Propagate "distinct" param.
14287: Propagate include_trash flag.
14287: Include x-request-id in test suite nginx access log.
14287: Use map instead of UpdateBody to update specific attrs.
14287: Ignore etag and unsigned_manifest_text in collection updates.
14287: Enable readline history in run-tests.sh interactive mode.
14287: Handle CORS OPTIONS requests.
14287: Use ctxlog for httpserver logging.
14287: Add debug logs.
14287: Use JSON body for 404 response.
14287: Add collection trash & untrash endpoints.
14287: Fix extra create attrs in test cases.
14287: Add cluster_id param to list options.
14287: Add ensure_unique_name param to untrash options.
14287: Add include_trash param to GET options.
14287: Omit false boolean params from API requests.
14287: Make collection name "" equivalent to null.
14287: Skip database reset between tests.
14287: ARVADOS_EXPERIMENTAL=14287 enables EnableBetaController14287.
14287: Move federation.Interface to arvados.API.
14287: Add EnableBetaController14287 to config whitelist map.
14287: Update test to new config struct.
14287: Unit-test router with stubbed API.
15345: Add .../containers/kill management API to dispatcher.
Check for up-to-date govendor as a test rather than a setup task.
Tidy up error checks in govendor test.
15026: Add cloudtest command.
15026: Add comments.
15340: Fix uncounted Destroy ops.
Merge branch '15340-error-counters'
14287: Comment and rename checker.go.
14287: Add comments to request param parsing.
14287: Specify response Content-Type.
14287: Extract inline func.
15345: Merge branch 'master' into 15345-kill-container-api
Merge branch '15345-kill-container-api'
14287: Clean up context key usage.
14287: Support federated requests for /used_by and /provenance.
15026: Remove redundant TagVerifier use.
15026: Treat bad-tags and boot-timeout as deferred errors.
14287: Don't delete non-writable attrs in create/update reqs.
Merge branch '15026-cloudtest'
15026: Log duration of each list/create/destroy/exec operation.
15026: Add cloudtest page to admin docs.
14287: Merge branch 'master'
15026: Add missing notextile tags.
Merge branch '14287-controller-structure'
Fix arvados-health using controller listener config.
15026: Clean up confusing variable name.
Merge branch '15026-cloudtest'
14287: Shut down RailsAPI before trying to reinstall.
14287: Merge list results from multiple backends.
15026: Avoid special chars in default instanceSetID.
15026: Fix infinite loop in -destroy-existing.
Merge branch '15026-cloudtest'
14287: Install goimports if needed.
14287: Remove extra panic after error running goimports.
14287: Add GOPATH/bin to PATH.
14965: Run py3 tests in the python3 virtualenv.
14965: Use netstat instead of lsof to check for listening process.
14965: Add sanity check for netstat.
15003: Fix errant warnings on PostgreSQL params and InternalURLs.
13647: Suppress "exit status 1" after config-check diff output.
13647: Load one example value from old keepstore config.
13647: Return recognizable error when no clusters are defined.
14287: Merge branch 'master' into 14287-federated-list
15003: Fix errant warnings on Workbench configs.
13647: ARVADOS_CONFIG env var overrides default cluster config path.
Merge branch '15003-real-configs-flagged-unknown'
13647: Add comments.
15003: Ensure all map[string]* have sample keys.
13647: Add MungeLegacyConfigArgs.
Merge branch '15003-ensure-all-sample-keys'
13647: Fix default cluster config source. Comment flag usage.
14965: Tweak netstat usage.
Merge branch '13647-load-old-config'
14287: Merge branch 'master'
14287: Clarify use of separate variables in goroutine.
14287: Fix comment that looked too much like real code.
14287: Comment multi-dimensional map.
14287: Reword filter restrictions.
Merge branch '14287-federated-list'
12020: Fix unreliable test.
14813: Add CORS headers to "get config" by moving it to arvados.API.
14717: Write config file before starting test services.
Merge branch '12020-flaky-py-test'
Merge branch '14813-config-cors'
12020: Fix test race.
Merge branch '12020-flaky-py-test'
14716: Fix accidentally accepting credentials at public download URL.
Merge branch '14716-anonymous-token'
15453: Don't use "*" as a real remote. Return 502 for remote errors.
Merge branch '15453-default-is-not-a-remote'
14716: Remove Host header rewrite in integration test proxy config.
15453: Don't use "*" as a real remote. Return 502 for remote errors.
13647: Use cluster config instead of custom keepstore config.
13647: Update keepstore install docs, eliminate keep_services step.
13647: Merge branch 'master' into 13647-keepstore-config
13647: Fixup docs.
13647: Add missing include.
13647: Update S3 volume config docs.
13647: Update Azure volume docs.
15615: Don't save screenshots of skipped tests.
15615: Retry failed wb1 tests twice before giving up.
15615: Fix wrong rake task being used when wb1 testargs supplied.
15615: Don't retry skipped tests.
15615: Don't use -v for workbench_profile/benchmark.
13647: Split up long func.
13647: Rename MaxKeepBlockBuffers -> MaxKeepBlobBuffers
13647: Fix BlobSigning config comment.
13647: Remove obsolete reference to out-of-sync configs.
13647: Move ...Controller.from_config_or_db to KeepService.all.
13647: Remove superfluous conditionals.
13647: Use *.uuid_prefix.example.com more consistently.
13647: Move Rendezvous doc comment to default config file.
13647: Add AccessViaHosts doc comment.
13647: Fix typos.
13647: Make keepstore fs config more consistent with s3/azure.
13647: Add volume config doc links.
13647: Recommend using a well supported server/volume layout.
13647: Improve error message.
13647: Update config keywords in docs, comments, and error messages.
13647: Add upgrade note about keepstore command line flags.
13647: Advise deleting keep_services entries after migrating.
13647: Update keepstore/keep_services config migration instructions.
13647: Export keepproxy's ExternalURL, not InternalURLs.
13647: Count "failed to start services" as failure, not success.
Merge branch '15615-retry-wb1-tests'
Count "failed to start services" as failure, not success.
13647: Merge branch 'master' into 13647-keepstore-config
13647: Update keepstore references on keep-balance install page.
13647: Update migration notes to use "arvados-server config-diff".
13647: Don't do API calls while loading controller config.
13647: Fix nil loggers in test suites.
15649: Pin libcloud 2.5.0.
Merge branch '15649-libcloud-azure'
13647: Fix send-HUP-to-keepproxy command.
13647: Remove duplicate Keepproxy config.
13647: Add keepstore service entries to arvbox config.
13647: Set X-External-Client header in arvbox.
13647: Migrate arvbox volume config.
Merge branch '13647-keepstore-config'
Avoid nginx startup race in test suite.
13647: Don't check pending keepstore migrations during API startup.
13647: Check ARVADOS_* env vars when loading config.
Merge branch '13647-keepstore-config'
Use default Azure storage endpoint if configured value is "".
15673: Show stderr before giving up failed command.
15673: Fix ruby warnings.
15673: Pin faraday gem version.
15673: Pin faraday below 0.16.
Merge branch '15673-faraday-pin'
15014: Hide busy/idle nodes panel when crunch1 is not active.
15014: Update tests.
15014: Update tests.
15014: Update tests.
15656: Fix missing permission check.
15599: Support IAM role credentials in keepstore.
15599: Fix misleading error message when address already in use.
15599: Look up IAM role name from metadata if not configured.
15599: Warn if multiple roles are assigned.
15599: Improve error message when no role is defined.
Update login-sync Gemfile.lock.
11016: Update BlobSigningTTL config docs.
15656: Note "delete container" is admin-only and not normally used.
Merge branch '15656-user-delete-container'
15678: Fix version reporting.
Update workbench bundle.
15599: Use default/automatic credentials for example config.
15599: Reject configuration with both IAMRole and Access/SecretKey.
Merge branch '15599-keepstore-iam-role'
Merge branch '15678-pkg-version'
Merge branch '11016-doc-signing-ttl'
Merge branch '15014-wrong-node-count'
Fix typo.
Fix wrong subcommand name.
15699: Fix handling of streams with multiple refs to a block ID.
15721: Fix 503 on API.MaxConcurrentRequests==0 and empty response.
15652: Add collectionfs Flush() method to control memory use.
Merge branch '15721-config-cors'
15699: Remove unused variables.
Merge branch '15699-workbench-copy-fail'
15652: Fix wrong block offset in async case.
15652: Fix shadowed variable.
15652: Only flush the current dir, and only once per 64 MiB.
15699: Update arvados-cli to latest arvados gem.
15680: Pass arv-put --retries arg to Collection and BlockManager.
15680: Log # attempts on failure.
15680: Update mockkeep.put to accept num_retries arg.
15699: Fix fencepost error at end of stream.
15699: Update apiserver and workbench bundles to latest arvados gem.
Fix keepclient service discovery race.
Merge branch '15699-update-gem'
15707: Forget about queued containers with priority=0.
Merge branch '15680-arv-put-retry'
Merge branch '15707-dispatch-onhold-metrics'
15699: Avoid latest signet gem, to stay compatible with ruby 2.3.
Merge branch '15699-update-gem'
15734: Save dispatcher's InstanceType record in container log.
15652: Limit concurrent writes per filesystem, not per flush.
15652: Use BLOCKSIZE const.
15652: Fix Release() called prematurely before PutB returns.
15652: Add concurrency/memory test. Fix missing node lock in Flush.
15652: Eliminate a malloc when writing a one-segment block.
Merge branch '15652-crunch-run-memory-use'
15713: Include 1K of response body when logging error responses.
15734: Reword crunch-run compatibility comment.
Merge branch '15734-dispatchcloud-node-info'
15713: Don't sniff non-error response body.
Merge branch '15713-controller-error-log'
15713: Log status sent to client if WriteHeader() is called >1x.
Merge branch '15713-controller-error-log'
15606: Clean up keep-web error responses.
15606: Add error message and doc link to XSS protection error.
15606: Add error detail to 500 response.
Show initial fuse mount info when starting tests.
15521: Fix truncated index response.
15521: Include request ID etc. in PutBlock log messages.
15734: Fix InstanceType logging: propagate to detached child.
Merge branch '15606-keep-web-errors'
Merge branch '15734-dispatchcloud-node-info'
15521: Convert remaining log uses to logrus.
Fix typo.
14287: Fix non-federated case in list handler.
Merge branch '14287-federated-list'
15107: Add built-in Google login option, as an alternative to sso.
15107: Add LoginCluster test.
Merge branch '15521-keepstore-logging'
15107: Google login option makes SSO credentials optional.
15107: Propagate first/last names from Google to RailsAPI.
15305: Don't multiply by backend replication when counting bytes.
15107: Test controller-to-Rails callback.
15305: Remove unhelpful comment in log message.
15793: Reuse result set even when each() is the only method called.
Merge branch '15793-cache-results-in-each'
15107: Remove nonexistent legacy config key.
15799: Ensure default baseURL has a trailing slash.
Merge branch '15107-google-login'
Merge branch '15799-baseurl-missing-slash'
Merge branch '15305-keep-balance-bytes'
15107: Get additional email addresses from Google account.
15107: Migrate govendor to go mod.
15107: Add config option to skip alternate email addrs / People API.
15107: Fix redirect target rewriting.
15107: Add login-redirect test.
15107: Fix personFields parameter.
15107: Clean up debug logs.
15107: Update "go get" uses in test/package scripts.
Merge branch '15107-alt-email'
15107: Merge branch 'master' into 15107-rails-bad-redirect
Merge branch '15107-rails-bad-redirect'
15107: Add Users.PreferDomainForUsername config.
15720: Switch httprouter to gorilla/mux.
15720: Add /users/* endpoints to internal API.
15720: Defer user listing to login cluster, cache results locally.
Merge branch '15107-prefer-domain-for-username'
15720: Batch user update API.
15707: Fix "on hold" containers not dropped from queue.
15854: Support filtering container_requests by container fields.
15851: Return items [], not null, in empty set responses.
Merge branch '15854-filter-container-fields'
15848: Fix incorrect order in federation query response.
15848: Convert timestamps from pointer to value fields.
Merge branch '15848-controller-list-sort'
15867: Don't pass blank remote param.
Update to bundler 2.0.2
15866: Abandon services/api install if bundle fails.
15866: Install bundler in GEMHOME.
15851: Merge branch 'master' into 15851-empty-items-array
Merge branch '15851-empty-items-array'
15851: Explicit path to bundle executable.
15851: Update expected versions in Gemfile.lock files.
Merge branch '15851-bundle'
15720: Merge branch 'master' into 15720-fed-user-list
15720: Update generated code.
15720: Warn about empty ManagementToken or SystemRootToken.
Merge branch '15720-fed-user-list'
Update token in keepproxy test.
15795: Ensure dispatcher can use SystemRootToken to lock containers.
Update Go.
Install bundler 2 in package build images.
Revert requirement for bundler upgrade.
15877: Accept JSON-encoded param values in JSON request body.
Merge branch '15877-accept-json-in-json'
Merge branch '15795-sys-root-token'
Fix rails package versions for dev builds.
15864: Fix error response when requesting nonexistent UUIDs.
15864: Support X-Http-Method-Override header used by Python SDK.
15864: Use POST/X-Http-Method-Override instead of long request URLs.
Merge branch '15864-controller-fixes'
Fix Rails package version calculation again.
Test X-Http-Method-Override.
Add PATCH to allowed CORS methods.
15900: Report stable gem version for a given commit.
15910: Fix races in collectionfs flush/sync.
Merge branch '15900-gem-version'
Merge branch '15910-crunch-run-crash'
15924: Change import paths to git.arvados.org.
15924: Update github links to arvados org.
15928: Fix deadlock.
Merge branch '15924-import-path'
Merge branch '15928-fs-deadlock'
15922: Change EnableBetaController14287 -> ForceLegacyAPI14.
15922: Accept HEAD method on all GET routes.
15922: Preserve writable_by in user and collection responses.
15922: Fix incorrect routes.
15922: Preserve etag in responses.
15922: Fix propagation of user setup and merge requests.
15922: Update test to accommodate etag.
15922: Test for writable_by in response.
Merge branch '15922-force-legacy-api-14'
15759: Move crunch-run into arvados-server cmd.
15942: Fix attempt to run container after deciding it cannot run.
15942: Ensure container with no suitable type is never in queue.
15942: Update test to fail more reliably when bug reappears.
Merge branch '15942-cancel-unsatisfiable'
15942: Fix deadlock caused by unclosed "done" channel.
15759: Deploy supervisor binary from dispatcher to worker VMs.
Merge branch '15946-collectionfs-deadlock'
15759: Merge branch 'master' into 15759-deploy-crunch-run
15759: Add DeployRunnerBinary to config.
15759: Update file mode; avoid /var/run, typically mounted noexec.
15759: Improve logs.
Fix variable unintentionally shared by multiple goroutines in test.
15759: Merge branch 'master' into 15759-deploy-crunch-run
Merge branch '15759-deploy-crunch-run'
15934: Fix "bad token" error message.
15836: Refuse project/collection names that fuse/webdav can't show.
15836: Substitute configured string for "/" in WebDAV listings.
Merge branch '15934-bad-token-error-message'
15836: Merge branch 'master'
15937: Suppress errors from fusermount unless mount still exists.
15942: Fix race in test case.
15823: Fix API endpoint connected to wrong handler.
15823: Skip slow parts of doc rendering if NO_SDK env var is set.
15823: Add "cloud dispatcher" API doc page.
Merge branch '15937-failed-to-unmount'
15823: Mention instance_type section.
15823: Use "instance" more consistently, note other terms.
15823: Mention "compute node", too.
Update version number script to work with git 2.1.4.
Merge branch '15823-dispatchcloud-api-docs'
15836: Merge branch 'master'
15836: Update wording in config comments.
15836: Use proper URL encoding in test case.
15836: Mention forward slash substitution options in upgrade notes.
Merge branch '15836-slash-in-collection-name'
15902: Adjust order to avoid poorly optimized query.
16104: Don't impose federated query limitations on local-only query.
Merge branch '16104-select-uuid'
16133: Avoid cycle when searching federation for PDH.
16133: Avoid cycle between old and new controllers.
16133: Don't take multiple hops when getting collections.
16133: Don't take multiple federation hops.
Merge branch '16133-federation-loop'
15835: Update metrics docs.
Merge branch '15835-metrics-docs'
16152: Fix nil http handler and ignored config args.
Merge branch '16152-keep-balance-http-crash'
16039: Obey ForwardSlashNameSubstitution config in arv-mount.
16039: Accommodate API servers with no config export.
16039: Fix & add test for sanitized/unsanitized name conflict.
16039: Use current python sdk in py3 tests.
16039: Install missing python dep.
16039: Touch python clients so they run tests with the latest SDK.
16100: Fix bogus timing stats for empty responses.
16100: Test content-type detection.
16100: Log a warning if /etc/mime.types is missing.
16100: Add package dependency for /etc/mime.types.
16100: Move test to integration suite to avoid logging errors.
16101: Handle logout without sso-provider.
16101: Redirect logout to Workbench if return_to param missing.
15954: Propagate remote param.
16270: Fill in missing scratch fields on InstanceType entries.
Fix instance IDs in arvados-dispatch-cloud log messages.
16221: Fix test for config endpoint.
16219: Load all fields needed to compute node size.
16219: Test populated container fields.
Warn if MaxKeepBlobBuffers > MaxConcurrentRequests.
Add StartedAt and FinishedAt fields to arvados.Container.
16387: Allow batch update to set is_active=false for a remote user.
16387: Allow setting is_active=false only on LoginCluster users.
16343: Add debug logs in token checking code.
16343: Fix handling of local CR creation when LoginCluster is used.
16349: Fix TZ-sensitive comparison in token expiry checks.
16349: Skip converting DB timestamps to & from localtime.
16349: Set time zone to UTC at db connection level.
16391: Fix log message.
Tom Morris (40):
Don't add trailing slash
Merge branch '14383-java-sdk-double-slash'. Fixes #14383.
14884: Allow non-ASCII filenames in manifests.
14884: Fix some additional formats where Unicode can be used
Merge branch '14884-unicode-name-support'
Update crunchstat-summary to Python 3. Refs #14939
Fix test Python 3 integer divide difference.
Add crunchstat-summary to Python 3 tests. refs #14939
Fix resource leak warned by Python 3
Resolve deprecation warnings
Merge branch '14939-crunchstat-summary-python3'
Spell MB consistently.
Fix Keep cache recommendation calculation.
Don't recommend RAM or CPU changes based on zero usage. refs #10570
Use default of 1 if no cores requested. refs #12026
Improve wording with direction of recommendation change.
Merge branch '14451-crunchstat-summary-cache-ram'
Add missing Javadoc for overloaded methods.
Reorganize, clean up, and copy edit docs.
Remove Gradle from source repo. Update docs & build to reflect change.
Add crunchstat-summary Python 3 to all tests.
Fix iteration order dependency.
Merge branch '14939-crunchstat-summary-python3-fixup'
Fix elapsed time calculation.
Merge branch '14627-crunchstat-summary-elapsed'
Fix debug setup accidentally committed.
Graph temp disk usage
Add a simple temp disk utilization based recommendation.
Fix up test gold standard references for new output
Merge branch '13913-crunchstat-summary-tmpdir'
15486: Fix crunchstat-summary to work with Arvados v1.4+
Merge branch '15486-crunchstat-summary-v1.4-support'
15554 - Add Python SDK constants for container request states
Merge branch '15554-python-sdk-constants'
15554 - Fix crunchstat-summary for running containers
15554 - Fix Crunch1 child jobs
15554 - Don't depend on latest version of Arvados Python SDK
Merge branch '15554-crunchstat-summary-live-log-no-sdk'
15573: Deprecate the full text @@ filter operator
Merge branch '15573-deprecate-atat-filter'
Tomasz Marciniak (1):
Arvados SDK Java - release 2.0.0
Ward Vandewege (109):
Add a few upgrade notes for the 1.3.0 release.
We've moved the chat/community support channel from IRC to gitter.im.
9945: first set of changes.
14691: documentation update
14691: workbench update, bring in line with documentation
Merge branch '14691-suggested-ssh-config-update'
9945: there is a new rvm gpg key
9945: run-library changes
9945: use virtualenv for our python packages
9945: address a bunch of review comments.
9945: address more review comments.
9945: More changes based on review comments.
9945: Merge branch 'master' into 9945-make-python-package-dependency-free
9945: Backwards compatibility fix for libpam-arvados
9945: Merge branch 'master' into 9945-make-python-package-dependency-free
Merge branch '9945-make-python-package-dependency-free'
The libpam-arvados package on Centos7 has a dependency on the python-pam package.
Do not try to test packages that were not built.
We have reset the package iterations to -1, make the
Make the python-arvados-cwl-runner package expose the cwltool executable, make
In the arvados/jobs image, use the Python executable from the
Make sure to bump the dependency on the arvados gems to the 1.3 series.
14853: we need a newer version of setuptools to build on centos7, debian8 and ubuntu1404.
Remove a few files that were checked in erroneously, update the .gitignore
14853: we need a newer version of setuptools to build on centos7, debian8 and ubuntu1404 (part 2).
Some build script housekeeping: make the CentOS builds less noisy, and remove
Change argument order for arv-keepdocker to the one that works, as it is
Ubuntu 18.04 ("bionic") packages are now confirmed working, add it to the list
14819: upgrade the arvados/jobs image to Debian Stretch. Also add argument to
Fix typo.
14819: use the python executable from the python-arvados-cwl-runner package
14819: Merge branch 'master' into 14819-arvados-jobs-on-stretch
Merge branch '14819-arvados-jobs-on-stretch'
Explicitly print the version numbers of virtualenv, pip, setuptools and wheel
Build the cwltest package, which lives out of tree.
Some build script housekeeping: fix the detection logic for the existence of
Switch to stretch-slim as the base image for arvados/jobs, this results in a
13996: rename config.defaults.yml to config.default.yml, to remain consistent
15042: handle config.default.yml in our packaging.
Mention the credential expiry date option in the instructions to create Azure
Make the doc Rakefile a little more helpful when it's missing javadoc
Fix typo.
Fix unit error in the node manager documentation for EC2.
Fix the api server package postinstall script to use `rake config:dump` to get a
Bump the rails package iteration to 9, for the packaging fix in commit
When specified in the api configuration,
Merge branch '15200-fix-blobsigning-config-migration'
Reset the rails package iteration to 1
Our Python SDK now also supports version 3.4+, update the fuse drive doc page
While our Python SDK now supports Python 3.4+, our FUSE driver does not yet. On
Make sure that the libpam-arvados package puts its various files in the place
Move the population of the new columns on the collections table to a standalone
Address review comments.
Update the 'upgrading' documentation to reflect the v1.4.0 release, and warn
Do not blow up when Rails.configuration.Users.UserProfileNotificationAddress is
Merge branch '15286-fixes'
Crunch-job needs to call the python executable from our sdk package for
Merge branch '9945-crunch-job-python-path'
Correct the release date for 1.4.0 in our documentation.
Fix the build by disabling an old crunch-job (jobs api) test that now
Make sdk/cli testable in interactive mode.
Make debian9 the default target for our package building scripts.
15138: Show the TM notice a little bit higher.
15138: Include logic to support building multiple versions of our documentation.
Merge branch '15138-version-our-documentation'
Keep relative URL when switching between versions in our documentation.
Our workbench and api server packages now have a runtime dependency on
We require go 1.12, update the run-tests.sh version check.
Use go 1.12 in package building (part 2).
Stop building debian8 and ubuntu1404.
Merge branch '15454-stop-building-debian8-and-ubuntu1404'
doc: on the config migration page, make sure to include RAILS_ENV in the bundle
doc: on the config migration page, make sure to include RAILS_ENV in the bundle
Remove package build dockerfiles for debian8 and ubuntu1404.
15516: Fix the arvados-server buildtime dependency for the arvados-workbench
15516: various fixes:
15516: document the use of variables with the nameref argument set.
15516: Merge branch 'master' into 15516-fix-arvados-server-dependencies
Merge branch '15516-fix-arvados-server-dependencies'
Merge branch '15648-centos7-upgrade-to-rh-python36'
Add the GOGC=10 environment variable to the Keepstore service file, to make
Remove table of contents from upgrading doc page, it is unmaintainable and
Add install documentation for Workbench2.
Merge branch '15779-add-workbench2-install-docs'
15839: add Debian Buster packages.
Merge branch '15839-add-debian-buster-packages'
Add Debian 10 ("buster") to the supported GNU/Linux distributions list.
Stop adding application.yml and database.yml symlinks on fresh installs of the
Merge branch '15904-remove-old-config-files-from-rails-packages'
Move all api server packages dependencies into the packages.
Move workbench packages dependencies into the packages.
Update CI url.
A few fixes for workbench in the way it displays the ARVADOS_API_HOST
15572: Many small doc tweaks as part of review.
15839: Fix erroneous default for the DEBUG variable in
Update maintainer and vendor for our OS packages.
In our systemd service files, set a reasonable default for the open file
Fix web shell.
documentation: update descriptions for MaxKeepBlobBuffers and MaxConcurrentRequests
Fix tests.
Updated Arvados on Kubernetes documentation.
Arvados on Kubernetes now has workbench2 as well.
Bugfix: make the arvados-docker-cleaner packages install their systemd
bugfix: fix arvados-node-manager package build
16434: add a basic execution test for the python3-arvados-cwl-runner packages
Fix comment typos in run-library.sh
16434: the python3-arvados-cwl-runner packages on Debian 10 and Ubuntu
16393: keepproxy used cluster.API.KeepServiceRequestTimeout (defaults to
16328: If config.yml is available, use the keepstores defined there instead of
chapmanb (2):
Python 3: only import subprocess32 on py27
Python 3: move to recent ciso8601 2.x branch
dependabot[bot] (5):
Bump nokogiri from 1.10.2 to 1.10.8 in /services/api
Bump loofah from 2.2.3 to 2.3.1 in /apps/workbench
Bump nokogiri from 1.10.4 to 1.10.8 in /apps/workbench
Bump rake from 12.3.2 to 13.0.1 in /apps/workbench
Bump rake from 12.3.2 to 13.0.1 in /services/api
ebiagiotti (2):
13306: Adding a py3 variant of the sdk/cwl tests to run-tests.sh
13306: Changes to arvados-cwl-runner code after running futurize --stage1
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