.. to_doc

19.01
===============================

.. announce_start

Enhancements
-------------------------------

.. major_feature

* Adds Aequatus visualisation plugin
  (thanks to `@anilthanki <https://github.com/anilthanki>`__).
  `Pull Request 6484`_
* Integrate framework code for interfacing with cloud authorization providers.
  `Pull Request 5903`_
* Added support for chaining dynamic destinations
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 7006`_
* Upgrade web client building to use `webpack <https://webpack.js.org/>`__ 4
  `Pull Request 6917`_
* Vue.js rewrite of admin data manager user interface
  (thanks to `@scrathat <https://github.com/scrathat>`__).
  `Pull Request 6729`_
* Implement 'make all datasets private' functionality.
  `Pull Request 6952`_
* Add datatype sniff button to edit dataset attributes page
  (thanks to `@qiagu <https://github.com/qiagu>`__).
  `Pull Request 7018`_
* Overhaul handler assignment methods.
  `Pull Request 7129`_, `Pull Request 7091`_
* Add tool for sending dataset to the cloud.
  `Pull Request 6583`_
* Infrastructure/API Support for composite uploads/downloads.
  `Pull Request 6844`_
* Improvements to tool testing including allowing remote tests and tests without admin API keys.
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7160`_, `Pull Request 7167`_, `Pull Request 7199`_
* Add ISA-TAB datatype
  (thanks to `@phnmnl <https://github.com/phnmnl>`__).
  `Pull Request 5787`_
* Adding itp and mdp datatypes (for gromacs)
  (thanks to `@simonbray <https://github.com/simonbray>`__).
  `Pull Request 6812`_
* Add pqr datatype
  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
  `Pull Request 6816`_
* Add nmrML datatype
  (thanks to `@phnmnl <https://github.com/phnmnl>`__).
  `Pull Request 6903`_
* Add RMA6 datatype (MEGAN6 read-match archive)
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 6962`_
* Add fastg datatype
  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
  `Pull Request 6987`_
* Add datatype for Mash Sketch files.
  (thanks to `@dfornika <https://github.com/dfornika>`__).
  `Pull Request 7087`_
* Add JavaScript client library utility function to create history entries.
  `Pull Request 6693`_
* Give all model objects with an id a __repr__ that includes the id
  `Pull Request 6757`_
* Add styled loader vue component
  (thanks to `@inkuzmin <https://github.com/inkuzmin>`__).
  `Pull Request 7052`_
* Restore the ability to track jobs for a WF invocation step.
  `Pull Request 6559`_
* Improvements to the grouping tool
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 6577`_
* Trim whitespace from data manager conf paths
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 6682`_
* Track workflow step input definitions in our model.
  `Pull Request 6850`_, `Pull Request 7103`_
* Deprecate `size` attribute of `<param/>` and remove it from tools
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 6684`_
* Create container_resolvers_conf.xml.sample
  (thanks to `@pcm32 <https://github.com/pcm32>`__).
  `Pull Request 6700`_
* Update to latest galaxy-lib.
  `Pull Request 6709`_
* Updates to OIDC backends default configuration.
  `Pull Request 6727`_
* Small local testing improvements
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 6738`_
* Add backrefs to mapped objects pointing at `Dataset`.
  `Pull Request 6754`_
* Fixes for the upload row template.
  `Pull Request 6758`_
* Disable file name text field after upload.
  `Pull Request 6762`_
* Remove empty log messages.
  `Pull Request 6763`_
* Release issue scaffold tweaks.
  `Pull Request 6778`_
* Warn job runner plugin writers not to emulate `condor.py`.
  `Pull Request 6783`_
* Add `PB` and `EB` to `util.size_to_bytes`
  `Pull Request 6786`_
* Add a `pgcleanup.py` action to purge HDAs of purged histories.
  `Pull Request 6801`_
* Various `pgcleanup.py` enhancements.
  `Pull Request 6736`_, `Pull Request 6877`_
* Fix typos on "reserve_memory" / "reserve_cpu"
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 6817`_
* Add more detail about container tags
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 6818`_
* Add docs about running jobs in containers
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 6820`_
* Remove `trans` from OIDC-related types.
  `Pull Request 6826`_
* Clarify code used in output <filter> tags
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 6827`_
* Convert `user_is_admin` and `user_can_do_run_as` to properties.
  `Pull Request 6835`_
* Don't create jobs for inactive users.
  `Pull Request 6837`_
* Replace deprecated `assertEquals()` method
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 6841`_
* Improvements to GIE docs
  (thanks to `@thobalose <https://github.com/thobalose>`__).
  `Pull Request 6846`_
* Indicate language in client docs to enable syntax highlighting..
  `Pull Request 6848`_
* Fix panel header margins in history and tool panel
  `Pull Request 6854`_
* Small fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 6861`_
* Datatype upload integration test and fixes
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 6869`_
* Use small button for editable text fields in history annotation
  `Pull Request 6878`_
* Improve Kubernetes job error handling
  (thanks to `@ilveroluca <https://github.com/ilveroluca>`__).
  `Pull Request 6886`_
* Fixes and updates to the Neo4j GIE
  (thanks to `@thobalose <https://github.com/thobalose>`__).
  `Pull Request 6897`_
* Allow ``remove_value`` filter on data tables
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 6914`_
* Update all dependencies
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 6921`_
* Be more precise with the job runner worker thread join timeout and improve
  documentation.
  `Pull Request 6924`_
* Selenium test enhancements and fixes.
  `Pull Request 6927`_, `Pull Request 6982`_
* Small testing tweaks from the CWL branch.
  `Pull Request 6929`_
* Tests need to count data sets and collections
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 6931`_
* Eliminate some mutable defaults in `populators.py`.
  `Pull Request 6933`_
* Default shed tool installation to `database/shed_tools`.
  `Pull Request 6937`_
* Add option to strip url prefix from pair names to collection builder
  (thanks to `@shiltemann <https://github.com/shiltemann>`__).
  `Pull Request 6943`_
* Small API workflow test improvements.
  `Pull Request 6954`_
* Switch from PhantomJS to Chrome Headless for unit tests.
  `Pull Request 6959`_
* Added a metadata element to the biom1 datatype
  (thanks to `@Slugger70 <https://github.com/Slugger70>`__).
  `Pull Request 6972`_
* Update locale.js
  (thanks to `@istevenshen <https://github.com/istevenshen>`__).
  `Pull Request 6974`_
* Use `virtualenv` when `conda` is on `PATH`
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 6975`_
* Improvements to exit code and regex parsing
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 6977`_
* Optimize images with optipng
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 6980`_
* Fix tool XSD to list tags as attribute of `TestCollection`
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 6983`_
* Use ``detect_errors="exit_code"`` in ``__SET_METADATA__`` tool
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 6989`_
* Don't mount external `/tmp` for tests.
  `Pull Request 6990`_
* Upgrade nodeenv's nodejs to 10.13.0 LTS.
  `Pull Request 6991`_
* Fix broken links on Job Configuration page.
  `Pull Request 6992`_
* Allow rules module override and refactor submodule imports
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 6993`_
* Fix JSON loading permission problem with run-as-real-user DRMAA job runner
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 6995`_
* CLI plugin for `LSF <https://en.wikipedia.org/wiki/Platform_LSF>`__
  (thanks to `@pcm32 <https://github.com/pcm32>`__), `Pull Request 7007`_
  `Pull Request 6788`_
* A new UNIVA extension to the DRMAA job runner
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 7004`_, `Pull Request 7161`_
* DRMAA fix to soft catch of external runner fails
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 6997`_
* Replace global Galaxy references with galaxy singleton accessor/setter.
  `Pull Request 7005`_
* Workflow test case - test marking inputs as outputs.
  `Pull Request 7016`_
* Expose published workflows through API
  (thanks to `@frederikcoppens <https://github.com/frederikcoppens>`__).
  `Pull Request 7020`_
* Pass a ``JobWrapper`` instead of a ``Job`` to ``stop_job()`` methods
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7023`_
* Fix `element_identifier` access
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7031`_
* Avoid replacing data-referenced input values with default values
  `Pull Request 7043`_
* Update error parsing docs
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 7049`_
* Add resubmit handlers on Pulsar connection failures
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 7053`_
* Add new "Help" item to the help menu.
  `Pull Request 7054`_
* Eliminate dependency on make for automatic client build.
  `Pull Request 7060`_
* Remove legacy job handling hacks.
  `Pull Request 7082`_
* De-couple objectstore abstraction from XML.
  `Pull Request 7085`_
* Localize version strings to the working directory w/predictable path.
  `Pull Request 7086`_
* Replace display applications mako with vue component
  `Pull Request 7097`_
* Run singularity in silent mode
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7104`_
* Eliminate unused code block in `output_collect`.
  `Pull Request 7109`_
* Add `to_dict()` to ObjectStores.
  `Pull Request 7110`_
* Enable tagging and annotation of jobs regardless of state.
  `Pull Request 7115`_
* Remove unused `__collected_datasets__` from tool hook dict.
  `Pull Request 7123`_
* Add a Vue.js component to display tool errors in the admin panel.
  `Pull Request 7124`_
* Update help text in `filter_from_file` tool.
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 7127`_
* Remove unneeded session flushes and adds when discovering outputs.
  `Pull Request 7134`_
* Drop tools without installable dependencies
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7136`_
* Small de-duplication cleanups to `galaxy.jobs`
  `Pull Request 7155`_
* Improve tool form client to add error listener for input elements.
  `Pull Request 7183`_, `Pull Request 7229`_
* Stop tool migrations checking by default (was broken in some cases).
  `Pull Request 7275`_
* Replace `trans` with `session` and `request` in PSA Storage.
  `Pull Request 6838`_
* Share ssh key generation across tests
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 6865`_
* Specify `POST` and `GET` actions for cloudauthz API actions.
  `Pull Request 6876`_
* Prevent sanitized history names being saved in database.
  `Pull Request 6898`_
* Rework language in cloud data fetch tool from "Upload" to "Get"
  `Pull Request 6899`_
* Refactor collection mapping workflows toward independence from tools.
  `Pull Request 6911`_
* Normalized jQuery bundle.
  `Pull Request 6970`_
* Replaced jStorage with store.
  `Pull Request 6994`_
* Remove ``sudo: false`` from .travis.yml, it will stop being supported soon
  `Pull Request 7035`_
* Fixes state-change animations causing 'block' display.
  `Pull Request 7122`_


Fixes
-------------------------------

.. major_bug


.. bug

* Fixes to allow config schema to validate
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 5919`_
* Patch `update.sh` to address dependency update issues on a macOS.
  `Pull Request 6694`_
* Fix wrong version being returned if requested version doesn't exist
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 6702`_
* Small mixed fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 6722`_
* Prevent errors when a library dataset has been purged from disk
  (thanks to `@dpryan79 <https://github.com/dpryan79>`__).
  `Pull Request 6784`_
* Fix apply rules bug in filter first/last N rows.
  (thanks to `@shiltemann <https://github.com/shiltemann>`__).
  `Pull Request 6814`_
* Updated volume kwds.
  (thanks to `@thobalose <https://github.com/thobalose>`__).
  `Pull Request 6840`_
* Remove some model objects added in `#5013
  <https://github.com/galaxyproject/galaxy/issues/5013>`__ but unused before
  the PR was merged, and fix a model object typo
  `Pull Request 6843`_
* Revert selective metadata flushing - breaks multiple uploads/outputs.
  `Pull Request 6858`_
* prevent double sanitizing history name when renaming
  (thanks to `@almahmoud <https://github.com/almahmoud>`__).
  `Pull Request 6871`_
* Fix rule editor element alignment.
  `Pull Request 6874`_
* Fix styleguide; change permissions on jstree.scss.
  `Pull Request 6879`_
* Fix username filtering for published workflows
  (thanks to `@almahmoud <https://github.com/almahmoud>`__).
  `Pull Request 6882`_
* Align toolshed makos used in the admin panel, fix slider height.
  `Pull Request 6883`_
* Improve resilience on handling sharing attributes.
  `Pull Request 6884`_
* Update Bug Reports docs to use YAML syntax
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 6909`_
* Fix ``expr: non-integer argument`` error when running ``make``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 6913`_
* Do not log exception info twice
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 6916`_
* Fix typos in ``scripts/bootstrap_history.py``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 6941`_
* Make BAM index only available for coordinate sorted BAM files
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 6946`_
* Use recently introduced overflow utility instead of overwriting card
  defaults
  `Pull Request 6948`_
* Fix sniffing of readname sorted BAM files
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 6950`_
* Fix for workflow parameter collection in workflows view.
  `Pull Request 6955`_
* Topic/empty data table
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 6957`_
* Allow deferring 'to_ext' extension to the server
  `Pull Request 6960`_
* Allow upload for ``rdata.sce`` format
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 6963`_
* Fix traceback when starting under Python3 with ``galaxy.ini``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 6978`_
* Fix charts entrypoint for compatibility with newer chunk changes.
  `Pull Request 6984`_
* reclaim ownership for failed jobs
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 6996`_
* Change join two dataset output format to tabular
  (thanks to `@qiagu <https://github.com/qiagu>`__).
  `Pull Request 6998`_
* Fixes for Python 3.7
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7008`_
* Fix PID file handling for gunicorn
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7013`_
* Fix display_in_tool_panel status for shared workflows
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7014`_
* Use solid background for text field autocomplete options
  `Pull Request 7027`_
* Follow-up on `#6850 <https://github.com/galaxyproject/galaxy/issues/6850>`__
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7029`_
* Fix error when building images
  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
  `Pull Request 7036`_
* Fix ``involucro_auto_init`` default value
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7038`_
* Fix resubmission on tool error detection.
  `Pull Request 7040`_
* GRT: Rip out all parameters, round file sizes
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 7041`_
* Pass through ``--daemon`` option to gunicorn
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7042`_
* Escape dataset names in job submission success message
  `Pull Request 7062`_
* Update ``galaxy.yml.sample`` and ``galaxy_options.rst``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7064`_
* Fix link to requirements.txt.
  `Pull Request 7065`_
* Improved parsing of sizes (bytes)
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 7067`_
* Downgrade bdbag - 1.5.0 requires python:>=2.7.9
  `Pull Request 7070`_, `Pull Request 7079`_
* Fix process key
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7071`_
* Fix welcome on redirect from facebook auth
  `Pull Request 7074`_
* Fix set_peek method for copied datasets
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7078`_
* Fix toolshed repository error display
  (thanks to `@jvanbraekel <https://github.com/jvanbraekel>`__).
  `Pull Request 7080`_
* Fix via refactor set_metadata so more output metadata pruned properly.
  `Pull Request 7084`_
* Replace `credentials` with `authz_id`
  `Pull Request 7088`_
* TravisCI configuration workaround for problems with boto configuration.
  `Pull Request 7092`_
* Fix ``size_to_bytes`` for some float values
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7096`_
* Client readme updates.
  `Pull Request 7102`_
* Don't write outputs to object store twice.
  `Pull Request 7111`_
* Fix `make client-watch` extra error message.
  `Pull Request 7113`_
* Properly escape history names in scratchbook titles.
  `Pull Request 7114`_
* Fix activation of ``_galaxy_`` conda env
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7116`_
* Increase timeout on flakey unit test.
  `Pull Request 7120`_
* Fixes and tests for collecting extra files for discovered datasets.
  `Pull Request 7131`_
* Address CORS issue in toolshed iframe handlers.
  `Pull Request 7135`_
* Use regular js-event handling instead of jquery for uploader
  `Pull Request 7145`_
* Fixes toolshed and reports styling that was previously applied at the…
  `Pull Request 7146`_
* Correct code error in 'build job runner' tutorial.
  `Pull Request 7148`_
* Added store library to exported libs in bundleEntries.
  `Pull Request 7149`_
* Fixes for library support of YAML/dictified tools.
  `Pull Request 7152`_, `Pull Request 7153`_
* Fix for authnz managers
  (thanks to `@machristie <https://github.com/machristie>`__).
  `Pull Request 7166`_
* Misc fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7168`_
* Fix process_key test and deal with unordered repeat elements
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7169`_
* Fix test_test_data_download
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7171`_
* Document ``message_box_class`` option
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7174`_
* Prevent XSS on toolshed when browsing repo changeset
  `Pull Request 7180`_
* Fix HDA accessibility check in Page's renderForSave name fetching
  `Pull Request 7181`_
* Fix for workflow parameter test case.
  `Pull Request 7188`_
* Fixes for library dataset permission API.
  `Pull Request 7190`_
* Properly document handler assignment method configuration and fix logging
  configuration docs.
  `Pull Request 7191`_
* Re-enable script staging.
  `Pull Request 7196`_
* Fix error in view_tool_metadata
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7201`_
* Data library: fix tag_using_filenames not properly converted to bool
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 7204`_
* Fixes to event handling re-enabling multi-history panel drag and drop functionality.
  `Pull Request 7218`_
* Fix displaying tool help images on python 3
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7228`_
* Fix data_source tools on python 3
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7236`_
* Interval datatype fixes
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7237`_
* `strip()` text when parsing xml
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7252`_
* Fix install operation in `installed_repository_grid`
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7253`_
* Update sqlalchemy-migrate requirement to 0.12.0
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7265`_
* Fix `_.escape` typo in toolshed group detail view.
  `Pull Request 7267`_
* Fix installing tools via tool_id
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7277`_
* Remove errant space in `intermine_simple_display.loc.sample`.
  `Pull Request 7298`_

.. include:: 19.01_prs.rst