
.. to_doc

19.05
===============================

.. announce_start

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

* Implement the ability to favorite tools.
  `Pull Request 7209`_
* Add data dialog option to tool form data selector.
  `Pull Request 7553`_, `Pull Request 7460`_
* Many workflow editor connection fixes and enhancements making
  them more correct, accessible, and transparent
  (with huge thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7466`_, `Pull Request 7435`_, `Pull Request 7972`_,
  `Pull Request 7979`_, `Pull Request 7642`_, `Pull Request 7989`_,
  `Pull Request 7254`_
* Add a Galaxy IE for cellxgene.
  `Pull Request 7268`_
* Implement expression tools and non-data tool outputs
  (with thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7556`_, `Pull Request 7796`_, `Pull Request 7797`_,
  `Pull Request 7944`_
* Add Galaxy cloud runner support
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 7226`_
* More robust task messaging
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7548`_
* Allow implicit conversion for input collection parameters
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7683`_
* Allow import of "Format 2" workflows by default.
  `Pull Request 7659`_
* Decompose Galaxy into Python libraries in-tree.
  `Pull Request 7524`_
* Rewrite and generalize History import and export - dozens of fixes, support for collections,
  Python library support, etc..
  `Pull Request 7367`_, `Pull Request 7214`_, `Pull Request 7366`_,
  `Pull Request 7369`_, `Pull Request 7370`_, `Pull Request 7358`_,
  `Pull Request 7505`_, `Pull Request 7507`_, `Pull Request 7363`_,
  `Pull Request 7193`_, `Pull Request 7192`_, `Pull Request 7537`_,
  `Pull Request 7540`_, `Pull Request 7684`_, `Pull Request 7704`_
* User facing release notes
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 7527`_
* Implement dataset source and hash tracking.
  `Pull Request 7487`_, `Pull Request 4659`_, `Pull Request 7549`_
* Custos integration for AuthNZ
  (thanks to `@machristie <https://github.com/machristie>`__).
  `Pull Request 7195`_
* Flush out API support for AuthNZ and CloudAuthz
  `Pull Request 7598`_, `Pull Request 7609`_,
  `Pull Request 7592`_, `Pull Request 7597`_,
  `Pull Request 7639`_
* Update to PSA 3.1 and support login with Globus identity.
  `Pull Request 7463`_
* Swap from 'slug.js' to 'slugify.js' - saving 10 MB in client bundles.
  `Pull Request 7538`_
* Update all client dependencies - including to Backbone 1.4, Bootstrap 4.2, Vue 2.6.
  `Pull Request 7544`_, `Pull Request 7637`_
* Allow admins to import dynamic JSON-based tools.
  `Pull Request 7545`_
* Implement environment modules mapping files
  (thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
  `Pull Request 7398`_
* Allow tool testing of multiple files within a zip output
  (thanks to `@thermokarst <https://github.com/thermokarst>`__).
  `Pull Request 7400`_
* Add datatype converters between tabular and CSV.
  `Pull Request 7246`_
* Add Azure and GCP support for ObjectStore Cloud backend.
  `Pull Request 7272`_
* Add a validator that ensure metadata value is on a range.
  (thanks to `@fmareuil <https://github.com/fmareuil>`__).
  `Pull Request 7288`_
* Fix post job actions for "Database Operation" tools, implement ``change_datatype``
  for collection output
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7480`_
* Implement and enforce ESLint linting of the entire client code base.
  `Pull Request 7202`_, `Pull Request 7860`_
* Multiple enhancements to the LSF cli-plugin job runner - support
  out of memory handling, project specification, and Spectrum LSF.
  (thanks to `@pcm32 <https://github.com/pcm32>`__ and
  `@selten <https://github.com/selten>`__).
  `Pull Request 6866`_, `Pull Request 7581`_, `Pull Request 7486`_
* Drop support for Python 3.4 and officially support Python 3.5 or greater.
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7291`_
* Batch bulk hide and delete operations when multiple selected.
  `Pull Request 5495`_
* Implement client initialization pipeline.
  `Pull Request 7117`_
* Allow storing objects in the object store by UUID.
  `Pull Request 7154`_, `Pull Request 7650`_
* Replace login and registration mako templates with VueJS components.
  `Pull Request 6621`_, `Pull Request 7047`_, `Pull Request 7329`_,
  `Pull Request 7442`_, `Pull Request 7756`_, `Pull Request 7347`_
* Track messages generated tool stdio tags in the database instead of just appending them
  to tool standard error. Structured UI in reporting also.
  (with help from `@bernt-matthias <https://github.com/bernt-matthias>`__)
  `Pull Request 7095`_
* Track job script stdout and stderr separately from the tool's stdout and stderr in the database.
  `Pull Request 7095`_
* Support loading/using tools that are not in the install database
  (with help from `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7316`_, `Pull Request 8021`_
* Git providers error reporting plugins
  (thanks to `@selten <https://github.com/selten>`__).
  `Pull Request 7485`_
* Rename ``_future_expose_api`` to ``expose_api`` and ``expose_api`` to ``legacy_expose_api``
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7743`_
* Add ``mtx`` datatype
  (thanks to `@bebatut <https://github.com/bebatut>`__ and
  `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7569`_, `Pull Request 7702`_, `Pull Request 7717`_
* Add ``geojson`` datatype
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 7773`_
* Add shapefile (``shp``) datatype
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 7819`_
* Add ``imgt.json`` datatype for IMGT immune system libraries
  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
  `Pull Request 7587`_
* Add microarrays data types ``gpr`` and ``gal``
  (thanks to `@bensellak <https://github.com/bensellak>`__).
  `Pull Request 7457`_
* Add ``spaln`` database type
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 7718`_
* Redefine ``cel`` datatype
  (thanks to `@bensellak <https://github.com/bensellak>`__).
  `Pull Request 7514`_
* Run most tests formerly ran on Travis on CircleCI
  (with help from `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7424`_, `Pull Request 7573`_, `Pull Request 7451`_,
  `Pull Request 7207`_, `Pull Request 7539`_, `Pull Request 7574`_
* Toolshed API enhancements.
  `Pull Request 6652`_
* Kubernetes job runner integration test and enhancements
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 6958`_
* Implement sniffing of datatypes for library datasets.
  `Pull Request 7379`_
* Rewrite tool output metadata collection - now portable and more correct, tested,
  and documented.
  `Pull Request 7470`_, `Pull Request 7459`_, `Pull Request 7156`_
  `Pull Request 7483`_, `Pull Request 7158`_, `Pull Request 7213`_,
  `Pull Request 7694`_, `Pull Request 7596`_, `Pull Request 7186`_,
  `Pull Request 7471`_
* Add ``python`` to ``Count1`` tool requirements
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7185`_
* Fixes and enhancements for the grouping1 tool - including not removing empty cells
  at the begin/start of lines
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__ and
  `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7205`_, `Pull Request 7844`_
* Workflow editor accessibility fixes.
  `Pull Request 7750`_
* Python dependency updates and documentation fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7215`_, `Pull Request 7247`_, `Pull Request 7285`_,
  `Pull Request 7740`_
* Remove requirement pin on specific Sphinx version
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7365`_
* Drop conditional pygmentz requirement (autoinstalled as necessary), minor
  formatting in conditional-reqs
  `Pull Request 7219`_
* Fix spacing between checkbox and buttons in history sharing view.
  `Pull Request 7222`_
* Use regular font-size and styling in uploader.
  `Pull Request 7232`_
* Remove underline from history datasets.
  `Pull Request 7235`_
* Add headless testing option for Selenium tests.
  `Pull Request 7287`_
* Build tool XML schema docs using ``sphinx_markdown_tables``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7313`_
* Refactor dataset controller to reuse input validation checks between get/set.
  `Pull Request 7322`_
* Add web server documentation notes about ``Range`` support
  (thanks to `@pvanheus <https://github.com/pvanheus>`__ and
  `@nsoranzo <https://github.com/nsoranzo>`_).
  `Pull Request 7323`_, `Pull Request 7334`_
* Fall back to binary comparison if BAM conversion fails during tool tests
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 7342`_
* Update ``area`` issue/PR labels
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7344`_
* Remove deprecated ``collect_outputs_from`` configuration option.
  `Pull Request 7144`_
* Remove ``ToolsController._rerun_tool()`` API method
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7345`_
* Refactor ``item_attrs.py`` for reuse without mixin inheritance.
  `Pull Request 7346`_
* Add ``--force_path_paste`` argument to tool test verify script.
  `Pull Request 7356`_
* Separate client node version requirement into individual dotfile for reuse.
  `Pull Request 7357`_
* Improve tool testing for counting datasets in paired collections
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 7359`_
* Do not default to ``DEV_WHEELS=1`` if no ``git`` is found
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 7371`_
* Restore gray scale difference between panel vs portlet background color for
  contrast.
  `Pull Request 7387`_
* Specify exceptions more precisely in user API controller.
  `Pull Request 7397`_
* Automatically set ``cookie_path`` using ``url_for()``.
  `Pull Request 7404`_
* Allow configuration location of user preferences extra configuration
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 7428`_
* Add hover styling to target tool in tool panel
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 7437`_
* Update Docker testing image
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7439`_, `Pull Request 7187`_
* Remove unused code
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7445`_
* Note `cannot import name _remove_dead_weakref` error and solution
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 7461`_
* Add option to pass in individual globs to client unit test watcher
  `Pull Request 7477`_
* Update of tours overview according to `#5860
  <https://github.com/galaxyproject/galaxy/issues/5860>`__
  (thanks to `@selten <https://github.com/selten>`__).
  `Pull Request 7478`_
* Add new metadata and data table tool validators
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 7500`_
* Updated documentation in ``admin/scaling.md`` for Systemd
  (thanks to `@ooobik <https://github.com/ooobik>`__).
  `Pull Request 7515`_
* Replace backbone tagging views with VueJs components.
  `Pull Request 7516`_
* Eliminate import dependency of datatypes on galaxy.web (``url_for``).
  `Pull Request 7521`_
* Static plugin staging as a part of client build instead of startup.
  `Pull Request 7532`_
* Implement dockerized variant of ``update.sh`` for project Python dependencies.
  `Pull Request 7546`_
* Refactor XSD output elements to share common output attributes.
  `Pull Request 7555`_
* Improve linking between job conf handler assignment and documentation
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 7558`_
* Refactor ``galaxy.web.security`` into ``galaxy.security.idencoding``.
  `Pull Request 7560`_
* Move the 'create new history' out of the history context menu
  `Pull Request 7565`_, `Pull Request 7606`_
* Improve workflow cog menu user interface.
  `Pull Request 7594`_, `Pull Request 7858`_
* Make ``galaxy.model.dataset_collections`` more usable outside manager context.
  `Pull Request 7595`_
* Webpack bundle overhaul and initial dynamic loading.
  `Pull Request 7605`_
* Don't un-hide mapped-over outputs when job fails
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7630`_
* Continue gracefully in set_meta if unable to count number of dataset lines.
  `Pull Request 7641`_
* Implement functional dict-ifiable tool outputs and error detection.
  `Pull Request 7651`_
* Refactor ``IntegrationTestCase`` to allow integration test functions.
  `Pull Request 7657`_
* Drop .pyc files before attempting to migrate
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7677`_
* Add docs to OIDC backends configuration file.
  `Pull Request 7691`_
* Update ``CITATION`` to latest Galaxy update paper
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7698`_
* Update pull request procedures to exempt notes, changelogs, and
  packages from mandatory review.
  `Pull Request 7706`_
* Update procedures to relax the vote requirement for fixing bugs in releases
  `Pull Request 7707`_
* Improve error message if GFF file is missing attribute col
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7708`_
* Add hostname to task message queues
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7712`_
* OIDC login buttons based on configuration
  (thanks to `@machristie <https://github.com/machristie>`__).
  `Pull Request 7720`_
* Enable the selection of library datasets in the tool form
  `Pull Request 7746`_
* Replace ``enable_beta_export_format2_default`` with
  ``default_workflow_export_format``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7748`_
* Report a couple common errors in dataset/job report.
  `Pull Request 7755`_
* Add singularity to valid types, allow customization of test history name
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7760`_
* Update parameter_input type when changing parameter type
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7780`_
* Don't clean up jobs when running tests if `$GALAXY_TEST_NO_CLEANUP` is set
  `Pull Request 7798`_
* Add option to wait for the database to become available
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 7827`_
* Remove recursion from ``expand_nested_tokens()``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7834`_
* Allow composite upload if all non-optional files are selected
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7872`_
* Cleanup integration test configuration code.
  `Pull Request 7874`_
* Add "Reset" button to composite upload interface
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7875`_
* Add local namespaced resolver to default container resolvers
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7896`_
* Use node-watch instead of fs.watch to watch for db changes
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7967`_
* Remove reset handler from ruler input element.
  `Pull Request 6321`_
* Declutter the history 'cog' menu.
  `Pull Request 6437`_
* Remove deprecated OpenID features.
  `Pull Request 7028`_, `Pull Request 7395`_
* Restores OpenID post authentication protocols.
  `Pull Request 7676`_
* Replace custom UI colors with equivalent theme colors, consolidate color
  handling.
  `Pull Request 7203`_
* Modernize library toolbar client code.
  `Pull Request 7234`_
* Large refactoring of model migrations
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7621`_, `Pull Request 7248`_,
  `Pull Request 7737`_, `Pull Request 7695`_
* Implement a general purpose tagging component in the Galaxy client code.
  `Pull Request 7270`_
* Define doctype method on XMLParser target
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7303`_
* Refactor ``galaxy.util.handlers`` -> ``galaxy.web.stack.handlers``.
  `Pull Request 7339`_
* Move ``create_history_template`` out of ``galaxy.util``.
  `Pull Request 7522`_
* Refactor ``galaxy.web.form_builder`` into ``galaxy.util.form_builder``.
  `Pull Request 7529`_
* Drop unused install keyword and load TS workflows with utf-8 encoding
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7423`_
* Remove biostar integrations.
  (with help from `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7443`_, `Pull Request 7510`_
* Refactor TagManager (back) to TagHandler.
  `Pull Request 7530`_
* Refactor ``output_collect.py`` toward a database session-less modality.
  `Pull Request 7541`_
* Drop D3 from publicly provided libs
  `Pull Request 7542`_
* Fix dependency cycle between ``galaxy.security`` and ``galaxy.model``.
  `Pull Request 7554`_
* Refactor ``galaxy.dataset_collections`` into ``galaxy.model.dataset_collections``.
  `Pull Request 7588`_
* Toastr debowerization and refactoring.
  `Pull Request 7640`_
* Tweak ``popup-menu.js`` error handling.
  `Pull Request 7643`_
* Update Conda version that new Galaxies will install
  `Pull Request 8048`_

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

* Explicitly specify system user under which Kubernetes jobs should run.
  `Pull Request 8103`_
* Ensure Kubernetes job querries filter the same namespace as defined in the
  job destination.
  `Pull Request 8092`_
* Fix client styleguide asset handling.
  `Pull Request 7664`_
* Handle subworkflows in view workflow mako
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7276`_
* Fix removing tags from a dataset previously only the first tag could be removed
  (thanks to `@gtrack <https://github.com/gtrack>`__).
  `Pull Request 7674`_, `Pull Request 7680`_
* Fix displaying and editing SelectTagParameters in workflow editor
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7534`_
* Fix workflow output rectification.
  `Pull Request 7101`_
* Interactive Environment Fixes
  `Pull Request 7917`_
* Make job script actually return tool exit code
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 7147`_
* Fix client galaxy object instance access in visualizations.
  `Pull Request 7198`_
* Assorted component bugfixes.
  `Pull Request 7200`_
* Update IE proxy dependencies.
  `Pull Request 7208`_
* Cleanup code for univa job runner
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 7210`_
* Verify and update .venv's node version.
  `Pull Request 7220`_
* Update ``use_interactive`` default in docs
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7221`_
* Fix hotdata method access.
  `Pull Request 7256`_
* Fix saving imported subworkflows
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7262`_
* Fix "occured" typo everywhere
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7266`_
* Fix flakey history import metadata test
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7279`_
* Do not skip the client build in dockerized selenium tests
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7280`_
* Fixes for the cluster documentation
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7281`_
* Fix ``ObjectNotFound`` exception when exporting an history
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 7286`_
* Do not remove tools from other installed revisions when uninstalling TS
  repo
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7300`_
* Remove unused keyword in resend email helper.
  `Pull Request 7315`_
* Fix popupmenu creation.
  `Pull Request 7318`_
* Fix trackster toolbox filter for logged-in users
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7319`_
* Remove overlapping tooltip from dropdown button in library toolbar.
  `Pull Request 7321`_
* UI fixes for libraries.
  `Pull Request 7337`_
* Fix ``test_import_metadata_regeneration`` API test
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7340`_
* Possible fix for fasta file never getting filesize
  (thanks to `@Slugger70 <https://github.com/Slugger70>`__).
  `Pull Request 7374`_
* Fix upload button style.
  `Pull Request 7381`_
* Fix link doc syntax
  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
  `Pull Request 7388`_
* Update application documentation
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7391`_
* Fix pie chart and portlet height in flexboxes.
  `Pull Request 7396`_
* Fix ``LocalShellRunner``
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7438`_
* Use a lock on cleanup, expire_tool and cache_tool
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7446`_
* Fix loading workflows with steps without default label
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7448`_
* Remove broken configuration option tool_submission_burst
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7449`_
* Restore ``get_filename`` to ``galaxy.tools.verify:verify()``
  `Pull Request 7452`_
* Fix documentation for statsd and uwsgi
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 7453`_
* Fix hidden parameter use in workflows
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7458`_
* Fix syntax of XSD tool schema.
  `Pull Request 7462`_
* Fix workflow building typo
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7472`_
* Correct ``virtualenv`` download with no ``wget``/``curl``
  (thanks to `@hmenager <https://github.com/hmenager>`__).
  `Pull Request 7476`_
* Use a relative ``output.publicPath`` to avoid 404 errors when serving with a url
  prefix
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 7481`_
* Restrict loading of JSON files on the server via the workflow API to Galaxy
  admins
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7499`_
* Fix warning message formatting in sharing controller
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7504`_
* Make sure ``temp_output_dir`` path is absolute
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7517`_
* Create directory before copying file there
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 7519`_
* Fix routing when serving Galaxy at a prefix.
  `Pull Request 7523`_
* Small object store fixes.
  `Pull Request 7536`_
* Fix entering workflow parameter in workflow run form
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7543`_
* Extend reload test case logging
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7547`_
* Correct db-self handler assignment method
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 7561`_
* Fix database config doctests when env vars are in use for dburi
  `Pull Request 7562`_
* Fix help warnings style.
  `Pull Request 7566`_
* Fix to run ``bootstrap_history.py`` inside Galaxy's virtualenv
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7584`_
* Update cloud imports to adhere with cloudbridge interface changes.
  `Pull Request 7586`_
* Fix RStudio GIE
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 7590`_, `Pull Request 7925`_
* Fix styleguide.
  `Pull Request 7602`_
* Fix history options menu href navigation
  `Pull Request 7612`_
* Minor cli and metadata fixes
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7614`_
* Improve string escaping and changeset validation on toolshed.
  `Pull Request 7616`_
* Delay workflow step execution for discovered & mapped-over input
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7633`_
* Fix float to int casting
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7634`_
* Adjust ``test_run_with_numeric_input_connection`` to extra line
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7645`_
* Fix incorrect LDDAs being used as collection members.
  `Pull Request 7646`_
* Fix GenomeSpace tools.
  `Pull Request 7647`_, `Pull Request 7697`_
* Bugfix for input selection with tag representation in ``ui-select-default``.
  `Pull Request 7658`_
* Drop now unused import endpoint from workflow controller.
  `Pull Request 7660`_
* Fix for ``trans.redirect`` not setting cookies/headers.
  `Pull Request 7663`_
* Fix shutdown for Pulsar MQ Runner.
  `Pull Request 7667`_
* Fix "Run workflow" jumps when clicking
  (thanks to `@gtrack <https://github.com/gtrack>`__).
  `Pull Request 7675`_
* Detect errors using exit code for sort tool
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7679`_
* Fix ``format_source`` for implicit conversion inputs and ``fasta.gz`` upload
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7682`_
* Plugin static staging fix.
  `Pull Request 7689`_
* Fix side panel styling, adjust appearance in reports.
  `Pull Request 7690`_
* Patch for metadata setting of minimal BIOM1 files
  (thanks to `@bebatut <https://github.com/bebatut>`__).
  `Pull Request 7696`_
* Only check for exit code on actual sort command
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7699`_
* Update ``pytest-posgresql`` to 1.4.0, which removes a hard dependency on
  ``psycopg2``
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7703`_
* Fix runner param validation in the DRMAA runner.
  `Pull Request 7709`_
* Restrict workflow invocation index to current user
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7711`_
* Copy ``tools_by_id`` before collecting dependency status
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7713`_
* Fix uWSGI startup with separate ini file under Python 3
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7716`_
* Fix (re)starting Galaxy using paste, ``GALAXY_RUN_ALL=1`` and ``--wait``
  under macOS
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7722`_
* Fix check on links in ``CompressedFile.safemembers()``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7723`_
* Unpause dependent jobs when resuming jobs
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7724`_
* Commented-out cloudbridge requirement for the cloud/send tool.
  `Pull Request 7727`_
* Fix comments
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7738`_
* Upgrade to latest Pulsar release for various remote job running fixes.
  `Pull Request 7744`_, `Pull Request 7865`_
* Fix automatic user registration.
  `Pull Request 7749`_
* Sanitize HTML in messages using ``galaxy.util.sanitize_html``.
  `Pull Request 7751`_
* Fix Kubernetes integration tests for Docker on Mac.
  `Pull Request 7754`_
* Fix BootstrapVue component specification in Citations.
  `Pull Request 7778`_
* Symlink two more images that are accessed via non-webpack'd applications.
  `Pull Request 7779`_
* Make ``url_get`` return unicode
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7782`_
* Disable flexible spreading of radio buttons by default.
  `Pull Request 7788`_
* Fix default value handling of color parameter.
  `Pull Request 7475`_
* Fix various Python deprecations
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7800`_
* Return HTTP 400 for `GET /api/datasets/nonexistent_id`
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7806`_
* Encode email messages using UTF-8
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7812`_
* Fix nested macro/token expansion on Python 3
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7823`_
* Possible fix for WSGI process issue `#7758
  <https://github.com/galaxyproject/galaxy/issues/7758>`__
  (thanks to `@tmcgowan <https://github.com/tmcgowan>`__).
  `Pull Request 7824`_
* Fix ``InputValueWrapper`` gt/ge/lt/le comparisons
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7826`_
* Fix trackster issue with constraining (``overflow:non-visible``) containers.
  `Pull Request 7845`_
* Improve upload accessibility.
  `Pull Request 7848`_
* Adjust appearance of user creation form in admin panel.
  `Pull Request 7851`_
* Use just the env name when checking ``CONDA_DEFAULT_ENV``
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7853`_
* Fix workflow extraction for jobs whose JobToDatasetOutputAssociation
  references a discovered dataset
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7855`_
* Fix flag for library dataset option in data selector.
  `Pull Request 7859`_
* Fix bug preventing handler runner plugin handling.
  `Pull Request 7870`_
* Fix click targeting for quota usage details
  `Pull Request 7877`_
* Allow typing e in float param field.
  `Pull Request 7880`_
* Update Cheetah dependency, fixes ``AssertionError``
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7887`_
* Fix application of history default permissions to anonymous histories
  carried over upon login.
  `Pull Request 7904`_
* Fix multi-history copying of collections.
  `Pull Request 7906`_
* Remove GFF headers during conversion and test fix
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 7916`_
* Fix community tags showing JSON file.
  `Pull Request 7923`_
* Fix upload of gzipped VCF files
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7933`_
* Fix documentation building
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 7934`_
* Listen to history changes in tool form until job has been submitted.
  `Pull Request 7943`_
* Fixed wrong example for ``amqp_ack_republish_time`` in
  ``job_conf.xml.sample_advanced``
  (thanks to `@AndreasSko <https://github.com/AndreasSko>`__).
  `Pull Request 7983`_
* Backport various upload encoding fixes from `#7995 <https://github.com/galaxyproject/galaxy/issues/7995>`__
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 8000`_, `Pull Request 8004`_
* Disable create user button while request is being processed
  `Pull Request 8029`_
* Fix multipanel history search
  `Pull Request 8085`_

.. include:: 19.05_prs.rst

