[ARVADOS] created: 1.1.3
Git user
git at public.curoverse.com
Thu Feb 8 16:38:30 EST 2018
at a8ab699692f6ab37efdceb89e2343d82d9452128 (tag)
tagging f7d7147e97751d5a4514443a3dd6a264786c883e (commit)
replaces 1.1.2
tagged by Fernando Monserrat
on Thu Feb 8 18:37:29 2018 -0300
Release 1.1.3
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat at veritasgenetics.com>
Fernando Monserrat (3):
#12850 add tag as input for docker tag
#12850 trim whitespaces for lint
refs #12850 Merge branch '12850-docker-tag-version'
Fuad Muhic (86):
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com> Init commit
Improved HTTP request filtering and response error handling.
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Implemented collection_create, collection_delete and collection_update
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Added a new collection class. Added a method to retrieve list of files
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Refactored most of the code.
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Credentials fix.
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Created in-memory representation of collection file structure.
Added ability to extract Subcollection from collection content tree.
Updated README and did some minor fixes to Arvados.R and Collection.R
Added ability to read file from a collection and made minor fixes to
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Moved all classes from RefClass OOP model to R6 and made improvements
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Removed debug logs.
Implemented feature to get size of ArvadosFile or Subcollection
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Added ability to write to a collection file.
Refactored collection tree into separate file.
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Added feature to create new file in a particular collection.
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Added feature to delete file from a collection.
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Made Subcollection and ArvadosFile more flexible.
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Added feature to move File-like object inside collection.
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Added function to work with projects.
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Updated README file
Users are no longer able to delete root folder.
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Added a fix to project create and project update.
Fixed some bugs and improved error handling.
Merge branch '11876-r-sdk' of git.curoverse.com:arvados into 11876-r-sdk
Made updating groups and collections less verbose.
Methods listCollections and listProjects now work properly
Collections getFileContent method renamed to getFileListing.
Split Collectin's add method to add and create methods.
Added code to notify user when API is unable to locate webDAV server.
Added methods listAllCollections and listAllProjects.
Collection classes no longer use each others private state.
Merge branch '11876-r-sdk' of git.curoverse.com:arvados into 11876-r-sdk
Added support for unit testing.
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Added a few unit test for Arvados class
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Added more unit tests to Arvados class
collection$get("file") and collection$get("./file") now return the same file
Reworked functionality for removing content from collection.
Added unit tests for CollectionTree class
Added two utility functions and created unit test for them.
Added unit tests for Subcollection class
Merge branch '11876-r-sdk' of git.curoverse.com:arvados into 11876-r-sdk
Added unit test for ArvadosFile and Collection classes
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Added unit tests for RESTService class
Added unit tests for RESTService and HttpParser classes
Updated README to reflect current project state
Factored out HttpRequest and HttpParser classes from Arvados class to
Added additional unit tests to Arvados class
Fixed ArvadosFile/Subcollection move bug and improved http query
Removed plus sign hack from HttpRequests createFiltersQuery method
Added unit tests for HttpRequest class.
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
ArvadosFile's connection method now returns curl connection instead of
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
getFileListing now returns sorted list
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Updated test to reflect changes to getFileListing method
Updated unit test name to reflect changes made to getFileListing method
Implemented custom print functions for all public classes
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Added error checking code to Collection and Subcollection classes
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Reworkder HttpRequest class to use RETRY functionality
Arvados class now accepts additional parameter which specifies max
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Fix 5 failing tests
Joshua C. Randall (1):
fix bwa-mem.cwl docker repo
Lucas Di Pentima (54):
12479: New tag editor for structured vocabulary. There are pending
12479: Get remote vocabulary definition, use a fallback is it doesn't exist.
12479: Assign default vocabulary on model instantiation
12479: Passing UUID & controller name data from data-mount-mithril element
12479: Add Selectize via npm package
12479: Refactoring to simplify the code.
12479: Remove tag button working.
12479: Properties saving working. Remove tag button styling.
12479: WIP making the save objject show the save state
12479: Replacing isDirty flag with dirty stream
12479: Save button changes state when having changes to save and after
12479: When requesting the collection, only ask the api server for the
Merge branch 'master' into 12479-wb-structured-vocabulary
12479: Add placeholder messages on selectize boxes. Filter keys/values
12479: Avoid saving tags with name and/or value being empty string.
12479: Syntax error fixed.
12479: Old tag editor files removal. Tests commented out.
12479: Removed tags related code on wb, not needed with the new
12479: Removed commented out test
12479: Renamed 'overridable' property to 'strict'. Both toplevel
12749: Several fixes and enhancements:
12479: Removed table border. Fixed indentation.
12479: Selectize tweaks to enhance usability. Removed all table
12479: Allow the user to edit the currently accepted value on a
12479: Merge branch 'master' into 12479-wb-structured-vocabulary
12479: UX enhancements:
12479: Removed plugin. Fixed onFocus() behavior on strict listings.
12479: Replaced selectize widget with awesomplete to solve some
12479: Re-added 'key' to the tag key div, because the lack of it
12479: Avoid tags tab reloading after saving.
12479: Merge branch '12479-wb-structured-vocabulary' of git.curoverse.com:arvados into 12479-wb-structured-vocabulary
12479: Merge branch '12479-wb-structured-vocabulary' of git.curoverse.com:arvados into 12479-wb-structured-vocabulary
12479: Accept tags with empty values
12479: Updated example vocabulary. Attempt to show all the items
12479: Clear vocabulary.json cache every 5 minutes.
Merge branch '12479-wb-structured-vocabulary'
11454: (WIP) Login to remote clusters using federated identity.
11454: Conditional login to remote API servers.
12758: Query the API server for group memberships using a
Merge branch '12758-federated-id-group-sync'
Merge branch 'master' into 11454-wb-federated-search
11454: Cache the local session token's uuid after being requested from the API.
11454: Do federated logins by requesting the current user object
11454: Show a link to the remote workbench on the sessions page.
11454: Removed unnecessary call on migrateNonFederatedSessions()
12268: Update the libcloud dependency to our forked version 2.2.2.dev4
Merge branch '12268-libcloud-2-3-0'
11454: Add the salted token on search result links from federated
11454: On /search & /sessions page, check if the current user is
11454: When adding a uuid prefix on the add session box, append
11454: Remotes listed on remoteHosts show "enable/disable" action button
Merge branch '11454-wb-federated-search'
11454: Syntax errors fixes.
Merge branch '11454-fix-syntax-errors'
Peter Amstutz (55):
11876: Add stub directory for R SDK.
12870: Don't send invalidation for inodes still referenced by kernel
12870: Fix test
12913: Apply secondaryFiles to inputs to RunInSingleContainer
12913: Add integration test for fix
Merge branch '12913-secondary-mounts' refs #12913
12921: Fix outputTTL to apply to RunInSingleContainer
Merge branch '12921-run-in-single-hints' closes #12921
12940: Use runit directly instead of runsvinit
12940: Fix bundler issues
12940: Fix fallback when overlay2 isn't available for docker-in-docker
Merge branch '12940-arvbox-runit' closes #12940
11876: Fix bug using Arvados$new with no parameters
11876: Add ArvadosFile$connection and $flush
12934: Bump cwltool and schema salad
12934: Sort glob results
12934: crunch-run creates .keep file in empty directories
12934: Fix version reporting
12934: Add .keep via manifest manipulation instead of creating real files
12934: Remove debug log
12934: Fix unit tests.
12934: Fix gofmt
12934: Rewrite file paths in pack instead of using "overrides"
12934: Bump cwltool version for packing fix.
Merge branch '12934-cwl-conformance' refs #12934
12990: Add update lock to shared directory update.
12990: Re-query project roots in order to get full record
Merge branch '12990-fuse-shared' refs #12990
Fix missing files needed by arvados-tests.sh refs #12935
Refactor arvbox Go setup and use govendor. refs #12935
12764: Writable file/directory support wip
12764: arvados-cwl-runner support
12764: Fixes
12764: Pass one cwl test
12764: Support empty anonymous directories by creating a .keep placeholder.
12764: Update documentation.
12764: Support 'dockerOutputDirectory' for containers to get to 100% conformance.
12764: Tweak docs
12764: Improve error handling around staging writable files
12764: bump cwltool version for conformance fixes
12764: gofmt fix
12764: Handle empty directories. Fix test.
12764: gofmt fix
Merge branch '12764-writable-file' refs #12764
12934: Tweak output of directories to pass conformance tests
Merge branch '12934-cwl-dir-output' refs #12934
Fix sdk/cwl unit test refs #12934
Writable staged files/dirs need to be 0777 to match outdir mode. refs #12764
12764: crunch-run temporary directories have common parent
12764: Remove CleanupTempDir. Better name for parent temp.
12764: Explicitly set desired permissions on copied files/dirs
12764: Set mode on copied single files. Fix tests.
Merge branch '12764-secure-tmp-parent' refs #12764
11876: Add sdk/R to run-tests.sh
Merge branch '11876-r-sdk' refs #11876
Tom Clegg (73):
12844: Refuse to unreference a directory by moving it into itself.
Merge branch 'patch-2' of https://github.com/jrandall/arvados
Merge branch '12844-webdav-move-into-self'
Fix copyright header, and copyright header checker exit code.
Note DCO requirement.
12755: Revert ce0a973 for python33 packages.
12755: Resume packaging arvados-docker-cleaner for centos7.
Merge branch '12755-python3-centos7'
12876: arvados-client get [-format=yaml] uuid
12876: Util to accept subcommand after initial args.
12876: More compatibility with "arv get".
12876: Fix up error/usage messages.
12876: Simplify legacy option parsing.
12876: Pass commands through to ruby/python programs.
Drop superfluous "node-info" prefix in node-info.txt log file.
12702: Add /arvados/v1/users/{uuid}/update_uuid API.
12702: Add API docs for users#update_uuid.
Merge branch '12870-fuse-binds-invalidate'
12876: Merge branch 'master' into 12876-arvados-client
12876: List subcommands like "arvados-client keep get" in main usage.
12876: Recover from more symlink confusion.
12876: Call attention to missing python and ruby dependencies.
12720: Invoke StartLimitInterval three different ways.
Merge branch '12720-systemd-compat'
12908: Mention SelectType=select/cons_res in slurm config advice.
Merge branch '12908-slurm-cons-res'
Update govendor bundle.
12702: Disallow updating sys/anon UUIDs. Test updating current user.
Merge branch '12876-arvados-client'
12876: Update govendor bundle.
Merge branch '12702-migrate-user'
Fix duplicated auth_uuid in container test fixtures.
Update go dependencies. Add check for missing dependencies.
Update tests to reflect gomux change.
Merge branch 'govendor'
12933: Include node properties in crunch2 logs.
12933: Log node info in node.json, similar to container.json.
12933: Merge branch 'master' into 12933-log-node-properties
12933: Add missing params arg, remove outdated comment.
Merge branch '12933-log-node-properties'
12705: Add "change account owner" and "merge remote account" pages.
Merge branch '12705-user-migrate-docs'
12705: Update authorized user when refreshing token cache.
12705: Note 5 minute cache effect during user migration.
12479: Use onupdate + stable vnode keys, let focus handle itself.
12479: Open autocomplete when focusing an empty field.
12479: Fix per-tag strict mode.
12479: Set dirty flag on change even when clearing input.
Merge branch '12705-token-cache'
Fix wrong cluster label on search page when authenticated remotely.
12891: Remove superfluous ThinDockerClientProxy wrapper.
12891: Refactor slurm commands.
12891: Don't use SIGKILL when telling crunch-run to cancel.
12891: Don't give up after trying once to stop the docker container.
12891: Fix use of magic string.
12891: Avoid flapping finalState after cancel.
12891: Use docker "rm -f" instead of "stop" to cancel container.
12891: Simplify "arv-mount exits before container ends" detection.
12891: Fix some test races.
12891: Don't wait for WaitContainer to receive loggingDone.
Merge branch '12891-log-on-cancel'
12746: Log host cgroup stats to hoststat.txt.
12746: Don't stop hoststat until after capturing output.
Merge branch '12746-crunch2-hoststat'
13011: Fix 411 error when writing empty block to Azure storage.
Merge branch '13011-empty-block-error-411'
12902: Leave child CR "cancelled" (not "on hold") when parent exits.
12902: Update state=Final when cancelling a container request.
12902: Label CRs "Cancelled" if finalized with incomplete container.
12902: Fix crash on null container_request name.
12902: Say "created at" instead of "started at" for a queued ctr.
12902: Offer Cancel button for "on hold" containers.
Merge branch '12902-queued-to-cancelled'
Tom Morris (2):
Update docs in README
Bump version to 0.0.2
Ward Vandewege (5):
Prepare for packaging.
Fix typo
Expand the README a bit, fix some syntax errors, add instructions for
Dependency update.
Add systemd unit file for arvados-health.
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