.. 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 `__). `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 `__). `Pull Request 7556`_, `Pull Request 7796`_, `Pull Request 7797`_, `Pull Request 7944`_ * Add Galaxy cloud runner support (thanks to `@nuwang `__). `Pull Request 7226`_ * More robust task messaging (thanks to `@mvdbeek `__). `Pull Request 7548`_ * Allow implicit conversion for input collection parameters (thanks to `@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 `__). `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 `__). `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 `__). `Pull Request 7398`_ * Allow tool testing of multiple files within a zip output (thanks to `@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 `__). `Pull Request 7288`_ * Fix post job actions for "Database Operation" tools, implement ``change_datatype`` for collection output (thanks to `@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 `__ and `@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 `__). `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 `__) `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 `__). `Pull Request 7316`_, `Pull Request 8021`_ * Git providers error reporting plugins (thanks to `@selten `__). `Pull Request 7485`_ * Rename ``_future_expose_api`` to ``expose_api`` and ``expose_api`` to ``legacy_expose_api`` (thanks to `@mvdbeek `__). `Pull Request 7743`_ * Add ``mtx`` datatype (thanks to `@bebatut `__ and `@nsoranzo `__). `Pull Request 7569`_, `Pull Request 7702`_, `Pull Request 7717`_ * Add ``geojson`` datatype (thanks to `@bgruening `__). `Pull Request 7773`_ * Add shapefile (``shp``) datatype (thanks to `@bgruening `__). `Pull Request 7819`_ * Add ``imgt.json`` datatype for IMGT immune system libraries (thanks to `@jj-umn `__). `Pull Request 7587`_ * Add microarrays data types ``gpr`` and ``gal`` (thanks to `@bensellak `__). `Pull Request 7457`_ * Add ``spaln`` database type (thanks to `@pvanheus `__). `Pull Request 7718`_ * Redefine ``cel`` datatype (thanks to `@bensellak `__). `Pull Request 7514`_ * Run most tests formerly ran on Travis on CircleCI (with help from `@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 `__). `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 `__). `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 `__ and `@mvdbeek `__). `Pull Request 7205`_, `Pull Request 7844`_ * Workflow editor accessibility fixes. `Pull Request 7750`_ * Python dependency updates and documentation fixes (thanks to `@nsoranzo `__). `Pull Request 7215`_, `Pull Request 7247`_, `Pull Request 7285`_, `Pull Request 7740`_ * Remove requirement pin on specific Sphinx version (thanks to `@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 `__). `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 `__ and `@nsoranzo `_). `Pull Request 7323`_, `Pull Request 7334`_ * Fall back to binary comparison if BAM conversion fails during tool tests (thanks to `@bernt-matthias `__). `Pull Request 7342`_ * Update ``area`` issue/PR labels (thanks to `@nsoranzo `__). `Pull Request 7344`_ * Remove deprecated ``collect_outputs_from`` configuration option. `Pull Request 7144`_ * Remove ``ToolsController._rerun_tool()`` API method (thanks to `@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 `__). `Pull Request 7359`_ * Do not default to ``DEV_WHEELS=1`` if no ``git`` is found (thanks to `@ic4f `__). `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 `__). `Pull Request 7428`_ * Add hover styling to target tool in tool panel (thanks to `@hexylena `__). `Pull Request 7437`_ * Update Docker testing image (thanks to `@mvdbeek `__). `Pull Request 7439`_, `Pull Request 7187`_ * Remove unused code (thanks to `@nsoranzo `__). `Pull Request 7445`_ * Note `cannot import name _remove_dead_weakref` error and solution (thanks to `@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 `__ (thanks to `@selten `__). `Pull Request 7478`_ * Add new metadata and data table tool validators (thanks to `@bernt-matthias `__). `Pull Request 7500`_ * Updated documentation in ``admin/scaling.md`` for Systemd (thanks to `@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 `__). `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 `__). `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 `__). `Pull Request 7677`_ * Add docs to OIDC backends configuration file. `Pull Request 7691`_ * Update ``CITATION`` to latest Galaxy update paper (thanks to `@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 `__). `Pull Request 7708`_ * Add hostname to task message queues (thanks to `@mvdbeek `__). `Pull Request 7712`_ * OIDC login buttons based on configuration (thanks to `@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 `__). `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 `__). `Pull Request 7760`_ * Update parameter_input type when changing parameter type (thanks to `@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 `@ic4f `__). `Pull Request 7827`_ * Remove recursion from ``expand_nested_tokens()`` (thanks to `@nsoranzo `__). `Pull Request 7834`_ * Allow composite upload if all non-optional files are selected (thanks to `@mvdbeek `__). `Pull Request 7872`_ * Cleanup integration test configuration code. `Pull Request 7874`_ * Add "Reset" button to composite upload interface (thanks to `@mvdbeek `__). `Pull Request 7875`_ * Add local namespaced resolver to default container resolvers (thanks to `@mvdbeek `__). `Pull Request 7896`_ * Use node-watch instead of fs.watch to watch for db changes (thanks to `@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 `__). `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 `__). `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 `__). `Pull Request 7423`_ * Remove biostar integrations. (with help from `@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 `__). `Pull Request 7276`_ * Fix removing tags from a dataset previously only the first tag could be removed (thanks to `@gtrack `__). `Pull Request 7674`_, `Pull Request 7680`_ * Fix displaying and editing SelectTagParameters in workflow editor (thanks to `@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 `__). `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 `__). `Pull Request 7210`_ * Verify and update .venv's node version. `Pull Request 7220`_ * Update ``use_interactive`` default in docs (thanks to `@nsoranzo `__). `Pull Request 7221`_ * Fix hotdata method access. `Pull Request 7256`_ * Fix saving imported subworkflows (thanks to `@mvdbeek `__). `Pull Request 7262`_ * Fix "occured" typo everywhere (thanks to `@nsoranzo `__). `Pull Request 7266`_ * Fix flakey history import metadata test (thanks to `@mvdbeek `__). `Pull Request 7279`_ * Do not skip the client build in dockerized selenium tests (thanks to `@nsoranzo `__). `Pull Request 7280`_ * Fixes for the cluster documentation (thanks to `@nsoranzo `__). `Pull Request 7281`_ * Fix ``ObjectNotFound`` exception when exporting an history (thanks to `@abretaud `__). `Pull Request 7286`_ * Do not remove tools from other installed revisions when uninstalling TS repo (thanks to `@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 `__). `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 `__). `Pull Request 7340`_ * Possible fix for fasta file never getting filesize (thanks to `@Slugger70 `__). `Pull Request 7374`_ * Fix upload button style. `Pull Request 7381`_ * Fix link doc syntax (thanks to `@galaxyproject `__). `Pull Request 7388`_ * Update application documentation (thanks to `@nsoranzo `__). `Pull Request 7391`_ * Fix pie chart and portlet height in flexboxes. `Pull Request 7396`_ * Fix ``LocalShellRunner`` (thanks to `@mvdbeek `__). `Pull Request 7438`_ * Use a lock on cleanup, expire_tool and cache_tool (thanks to `@mvdbeek `__). `Pull Request 7446`_ * Fix loading workflows with steps without default label (thanks to `@mvdbeek `__). `Pull Request 7448`_ * Remove broken configuration option tool_submission_burst (thanks to `@mvdbeek `__). `Pull Request 7449`_ * Restore ``get_filename`` to ``galaxy.tools.verify:verify()`` `Pull Request 7452`_ * Fix documentation for statsd and uwsgi (thanks to `@abretaud `__). `Pull Request 7453`_ * Fix hidden parameter use in workflows (thanks to `@mvdbeek `__). `Pull Request 7458`_ * Fix syntax of XSD tool schema. `Pull Request 7462`_ * Fix workflow building typo (thanks to `@mvdbeek `__). `Pull Request 7472`_ * Correct ``virtualenv`` download with no ``wget``/``curl`` (thanks to `@hmenager `__). `Pull Request 7476`_ * Use a relative ``output.publicPath`` to avoid 404 errors when serving with a url prefix (thanks to `@abretaud `__). `Pull Request 7481`_ * Restrict loading of JSON files on the server via the workflow API to Galaxy admins (thanks to `@nsoranzo `__). `Pull Request 7499`_ * Fix warning message formatting in sharing controller (thanks to `@mvdbeek `__). `Pull Request 7504`_ * Make sure ``temp_output_dir`` path is absolute (thanks to `@nsoranzo `__). `Pull Request 7517`_ * Create directory before copying file there (thanks to `@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 `__). `Pull Request 7543`_ * Extend reload test case logging (thanks to `@mvdbeek `__). `Pull Request 7547`_ * Correct db-self handler assignment method (thanks to `@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 `__). `Pull Request 7584`_ * Update cloud imports to adhere with cloudbridge interface changes. `Pull Request 7586`_ * Fix RStudio GIE (thanks to `@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 `__). `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 `__). `Pull Request 7633`_ * Fix float to int casting (thanks to `@mvdbeek `__). `Pull Request 7634`_ * Adjust ``test_run_with_numeric_input_connection`` to extra line (thanks to `@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 `__). `Pull Request 7675`_ * Detect errors using exit code for sort tool (thanks to `@mvdbeek `__). `Pull Request 7679`_ * Fix ``format_source`` for implicit conversion inputs and ``fasta.gz`` upload (thanks to `@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 `__). `Pull Request 7696`_ * Only check for exit code on actual sort command (thanks to `@mvdbeek `__). `Pull Request 7699`_ * Update ``pytest-posgresql`` to 1.4.0, which removes a hard dependency on ``psycopg2`` (thanks to `@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 `__). `Pull Request 7711`_ * Copy ``tools_by_id`` before collecting dependency status (thanks to `@mvdbeek `__). `Pull Request 7713`_ * Fix uWSGI startup with separate ini file under Python 3 (thanks to `@nsoranzo `__). `Pull Request 7716`_ * Fix (re)starting Galaxy using paste, ``GALAXY_RUN_ALL=1`` and ``--wait`` under macOS (thanks to `@nsoranzo `__). `Pull Request 7722`_ * Fix check on links in ``CompressedFile.safemembers()`` (thanks to `@nsoranzo `__). `Pull Request 7723`_ * Unpause dependent jobs when resuming jobs (thanks to `@mvdbeek `__). `Pull Request 7724`_ * Commented-out cloudbridge requirement for the cloud/send tool. `Pull Request 7727`_ * Fix comments (thanks to `@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 `__). `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 `__). `Pull Request 7800`_ * Return HTTP 400 for `GET /api/datasets/nonexistent_id` (thanks to `@nsoranzo `__). `Pull Request 7806`_ * Encode email messages using UTF-8 (thanks to `@nsoranzo `__). `Pull Request 7812`_ * Fix nested macro/token expansion on Python 3 (thanks to `@mvdbeek `__). `Pull Request 7823`_ * Possible fix for WSGI process issue `#7758 `__ (thanks to `@tmcgowan `__). `Pull Request 7824`_ * Fix ``InputValueWrapper`` gt/ge/lt/le comparisons (thanks to `@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 `__). `Pull Request 7853`_ * Fix workflow extraction for jobs whose JobToDatasetOutputAssociation references a discovered dataset (thanks to `@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 `__). `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 `__). `Pull Request 7916`_ * Fix community tags showing JSON file. `Pull Request 7923`_ * Fix upload of gzipped VCF files (thanks to `@nsoranzo `__). `Pull Request 7933`_ * Fix documentation building (thanks to `@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 `__). `Pull Request 7983`_ * Backport various upload encoding fixes from `#7995 `__ (thanks to `@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