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Author SHA1 Message Date
Marius van den Beek e340737a3e Merge pull request #17037 from dannon/no-more-eventhub 
Remove eventHub custom module, swap to appropriate alternatives.
 2023-11-16 11:23:11 +01:00
Marius van den Beek 43c55730a3 Merge pull request #16795 from sveinugu/it_inject_entry_point_path 
Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf
 2023-11-16 09:25:33 +01:00
Dannon Baker d59c55420e Drop all eventHub usage. 2023-11-15 22:08:23 -05:00
Dannon Baker fc24d780f8 Swap ToolSection to watch vueuse eventbus 2023-11-15 22:08:23 -05:00
Dannon Baker 3bc2ac036f Swap HistoryEmpty to use veuuse's event bus 
Fix optional props in historyempty
 2023-11-15 22:08:23 -05:00
Dannon Baker 7bdf621a33 Swpa historyempty to comp+ts 2023-11-15 22:08:23 -05:00
Dannon Baker 090eefe042 Swap upload eventhub usage for simple store 2023-11-15 22:08:23 -05:00
Dannon Baker 4372e7f900 Swap UploadButton to composition+ts 2023-11-15 20:58:54 -05:00
Sveinung Gundersen 25065986e1 Added note on the removal of interactivetools_shorten_url 2023-11-15 19:05:22 +01:00
Sveinung Gundersen ed3b2885ec Revert removal of docs for default pools argument 2023-11-15 18:03:14 +01:00
Sveinung GundersenandMarius van den Beek 98f06670f9 Less secluded docker containers 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2023-11-15 17:35:39 +01:00
Sveinung Gundersen e9c43b9527 Lint fix 2023-11-15 13:57:22 +01:00
Sveinung Gundersen 499c1225d8 Cleanup/refactor of URL construction in InteractiveToolManager (as requested in https://github.com/galaxyproject/galaxy/pull/15147/files/906b309151a45b2c2f4fa8f7a64452518f2e8367#r1043548111) 2023-11-15 12:54:14 +01:00
Sveinung Gundersen 7ca529e92d Update gravity requirement to 1.0.4, waiting for required gravity + gx-it-proxy updates 2023-11-15 12:54:14 +01:00
Sveinung Gundersen 09a09d6964 Fixed linting, import sorting and unrelated mypy error (due to deprecated method) 2023-11-15 12:54:14 +01:00
Sveinung Gundersen d3c2838fcf Added note about lack of support for data_dir resolution of "interactivetools_map" config in gx-it-proxy and gravity 2023-11-15 12:54:14 +01:00
Sveinung Gundersen 54098bec47 Added simple job_conf.yml files for interactive tools, including config for Podman 2023-11-15 12:54:14 +01:00
Sveinung Gundersen 09020ed3f4 Removed info about default pools value as this is currently incorrect. Have also wasted time earlier due to this 2023-11-15 12:54:14 +01:00
Sveinung Gundersen da5a945bf1 Updated config sample files and interactive tools documentation 2023-11-15 12:54:14 +01:00
Sveinung Gundersen bf422d3474 Removed "interactivetools_shorten_url" 2023-11-15 12:54:14 +01:00
Sveinung Gundersen 73100de171 Shortened all interactive tool URLs incl encoded ids of entry points 2023-11-15 12:54:14 +01:00
Sveinung Gundersen b0e13e5149 Added "requires_path_in_url" and "requires_path_in_header" attributes to entry points for tools. Sendoff to gx-it-proxy. Cleanup 2023-11-15 12:54:14 +01:00
Sveinung Gundersen 51db30370c Using label instead of name to identify entrypoint 2023-11-15 12:54:14 +01:00
Sveinung Gundersen d6a5a6d05e Added 'label', 'requires_path_in_url' and 'requires_path_in_header' columns to 'interactivetool_entry_point' table and as attribute to entry points 2023-11-15 12:54:14 +01:00
Sveinung Gundersen 05f8de5d98 Updated JupyTool, Open Refine, Guacamole Desktop, and RStudio tools to potentially support path-based proxy 2023-11-15 12:48:39 +01:00
Sveinung Gundersen cf3fe8883b Initial implementation of entry_point_path inject 2023-11-15 12:48:39 +01:00
Martin Cech 6b3b35dcb2 Merge pull request #17021 from ahmedhamidawan/show_tool_panel_view_on_panel 
Show current tool panel view name on top of tool panel
 2023-11-15 03:13:06 +01:00
Ahmed Awan 4e24d565f7 add jest for ToolPanel to test changing views 2023-11-14 16:38:12 -06:00
Ahmed Awan c7670e8235 add view icon to ToolPanel header, add Favorites button back 2023-11-14 13:20:40 -06:00
Marius van den Beek 706e9776e5 Merge pull request #16252 from mvdbeek/delete_jobs_when_cancelling_invocation 
Delete non-terminal jobs and subworkflow invocations when cancelling invocation
 2023-11-14 19:11:30 +01:00
John Davis 4db3b94e6d Merge pull request #17020 from jdavcs/dev_sa20_job_index_query 
Upgrade job manager's index_query method to SA2.0
 2023-11-14 11:55:00 -05:00
John Davis 01e627fdd5 Move access permissions checks to service; add typing 2023-11-14 09:26:22 -05:00
mvdbeek 2a11420bc6 Prevent cancelled invocation resetting back to new or ready 2023-11-14 15:11:54 +01:00
mvdbeek 571c511dcd Use JobGrabber.get_grabbable_handler_assignment_method static method for consistency 2023-11-14 10:01:18 +01:00
mvdbeek 194f5ad5df Use sqlalchemy 2.0 query syntax 2023-11-14 09:59:39 +01:00
mvdbeek db9d5b5f8b Add new finished_states and move deleting to that 2023-11-14 09:48:31 +01:00
mvdbeek 6cde33f6e6 Apply Nicola's suggestions 2023-11-14 09:48:31 +01:00
Ahmed Awan 3e5233dc21 Show current tool panel view name on top of tool panel 
Remove button group, change whole header into a dropdown menu.
Fixes https://github.com/galaxyproject/galaxy/issues/16828
 2023-11-13 19:26:10 -06:00
John Davis a4df9223a0 Add assert to help mypy: search is guaranteed to be not null 2023-11-13 16:48:25 -05:00
John Davis 22934827ad Reorganize method for improved readability 
(I think factoring out these complex chunks of logic into local
functions makes it easier to follow the main query-building logic.)
 2023-11-13 16:14:57 -05:00
John Davis a0dd45ad00 Ensure UNION + ORDER BY works correctly in sqlite 2023-11-13 16:00:40 -05:00
John Davis 0ccfe05b4c Ensure the result of executing the select statement is models 
Calling union() on a statement creates a CompoundSelect object;
executing it will return tuples of column values, not models. To ensure
the method always returns models (regardless of whether the union is
called or not), we use aliased() to map the Job model to the
CompoundSelect.
 2023-11-13 15:21:04 -05:00
John Davis d253562fe2 Convert Query to Select 2023-11-13 13:42:27 -05:00
John Davis b1e4bdc389 Group local variables in one place 2023-11-13 13:29:33 -05:00
John Davis 0e6e176346 Use model class names in query-building w/o prefixes 2023-11-13 12:11:05 -05:00
John Davis 27eb8e2104 Rearrange to separate security logic from query-building 2023-11-13 11:44:26 -05:00
mvdbeek 6f1b60ae4c Fix class name logging 2023-11-13 15:45:28 +01:00
mvdbeek c1801363a7 Fix invocation cancel test 2023-11-13 15:45:28 +01:00
mvdbeek 2980c1ff77 Fix job state history 2023-11-13 15:45:28 +01:00
mvdbeek 2156432398 Refactor ItemGrabber into JobGrabber and InvocationGrabber 2023-11-13 15:45:28 +01:00