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Author SHA1 Message Date
John Chilton 4bcd4fed01 Improved typing for tool shed structured app. 2023-04-08 16:34:06 -04:00
John Chilton 97294cc412 Cleanup method signature for display_installed_jobs_list_page. 2023-04-08 16:34:06 -04:00
John Chilton 747b291398 Some initial typing for shed's metadata_util. 2023-04-08 16:34:06 -04:00
John Chilton 6aeb297942 Remove unused code in search_util. 2023-04-08 16:34:06 -04:00
John Chilton 79fd5915c3 More typing for repository_util. 2023-04-08 16:34:05 -04:00
John Chilton 42a29e04c5 Schema for by categories... 2023-04-08 16:34:05 -04:00
Dannon dcc7c950bc Merge pull request #15908 from ElectronicBlueberry/advanced-tool-search-tweaks 
Advanced tool search result tweaks
 2023-04-07 17:15:02 -04:00
mvdbeek 474260f290 Merge branch 'release_23.0' into dev 2023-04-06 22:00:53 +02:00
Marius van den Beek cbced4620d Merge pull request #15909 from mvdbeek/fix_parallelism_hang_in_pulsar_tests 
[23.0] Fail linked job if task fails
 2023-04-06 21:18:54 +02:00
Marius van den Beek 851625cf8c Merge pull request #15902 from nsoranzo/merge_23.0_forward 
Merge 23.0 into dev
 2023-04-06 20:52:43 +02:00
mvdbeek eb1a2fffcb Fail linked job if task fails 2023-04-06 20:01:55 +02:00
Nate Coraor 9a283fc833 Merge pull request #15907 from mvdbeek/fix_stdout_stderr_puslar 
[23.0] Fix tool stdio on pulsar and implement job stdio
 2023-04-06 13:03:58 -04:00
Marius van den BeekandLaila Los 0804f0e63a Fix types in terminal tests 
Co-authored-by: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
 2023-04-06 18:47:14 +02:00
mvdbeek decc96638f Fix tool stdio on pulsar and implement job stdio 
Depends on https://github.com/galaxyproject/pulsar/pull/318
 2023-04-06 17:07:00 +02:00
David López 95156cb32e Merge pull request #15906 from dannon/admin-deny-route 
[23.0] Admin interface navguard
 2023-04-06 15:48:34 +02:00
Laila Los c91b5a93aa unify outline and top-bar color 
move spacing to table
 2023-04-06 15:26:49 +02:00
Laila Los 9c5c71d8ca align scroll to top button to the right 
reduce distance to edge, to not overlap with open buttons
 2023-04-06 15:13:53 +02:00
Laila Los 6e9a7d6c3f fix open button roundness 
reduce nesting
 2023-04-06 15:09:34 +02:00
Dannon Baker ae7049e52f Add router onError handling and simple component that doesn't require any context for presenting an error. 2023-04-05 22:35:20 -04:00
Dannon Baker 9481922089 Basic navigation guard for admin routes; todo: notification of some 
sort.
 2023-04-05 15:34:38 -04:00
Marius van den Beek 5464443d98 Merge pull request #15897 from davelopez/23.0_fix_public_histories_annotation_search 
[23.0] Fix history annotation filtering: make it case insensitive
 2023-04-05 15:05:28 +02:00
Nicola Soranzo d31a347547 Fix comparison-overlap mypy error 2023-04-05 13:54:05 +01:00
Dannon 6dd0fae7d4 Merge pull request #15900 from ElectronicBlueberry/dont-compile-tests 
Exclude tests from TypeScript compilation
 2023-04-05 08:36:11 -04:00
Nicola Soranzo c655360e4e Merge branch 'release_23.0' into dev 2023-04-05 12:39:43 +01:00
Nicola Soranzo 7452b2e319 Merge branch 'release_22.05' into release_23.0 2023-04-05 11:51:03 +01:00
Laila Los 680c322ceb exclude tests from compilation 2023-04-05 12:23:48 +02:00
Marius van den Beek f420a619e4 Merge pull request #15896 from bernt-matthias/merge/22.01_22.05 
[22.05] merge 22.01
 2023-04-05 10:29:56 +02:00
John Chilton 0698979061 Merge pull request #15894 from davelopez/23.0_fix_export_archive_extension 
[23.0] Fix short term storage archive export extension on download
 2023-04-04 13:04:36 -04:00
davelopez b6c4668776 Make annotation filtering case insensitive 2023-04-04 18:28:37 +02:00
davelopez 0a043971af Add unit test for model_store_storage_target 2023-04-04 17:31:32 +02:00
Matthias Bernt a99c137ed9 Merge branch 'release_22.01' into merge/22.01_22.05 2023-04-04 16:15:45 +02:00
Dannon 2acf21276a Merge pull request #15891 from ElectronicBlueberry/webhook-z-index 
[23.0] Fix tool bar on top of pop-ups
 2023-04-04 09:08:49 -04:00
Marius van den Beek f76d894fa9 Merge pull request #15893 from bernt-matthias/fix/cached_explicit_singularity_container_description 
[22.01] cached_explicit_singularity: needs to copy container description
 2023-04-04 14:35:04 +02:00
davelopez d5bc7fff8e Guess mime type for short term storage files 2023-04-04 14:18:17 +02:00
davelopez 8b715de141 Fix extension lost after cleaning filename 2023-04-04 14:15:20 +02:00
Matthias Bernt e81fc67d44 cached_explicit_singularity: copy container description 
otherwise `container_description.identifier = cache_path` (at the end of the function)
will modify the original (i.e. the tools) container description which influences
i.e. (may break) successive container resolutions.
 2023-04-04 12:09:36 +02:00
David López e11b56d92b Merge pull request #15892 from mvdbeek/fewer_pending_not_ok_operation_tools 
Allow pending inputs in some collection operation tools
 2023-04-04 09:43:01 +02:00
Dannon 18db85436a Merge pull request #15745 from ahmedhamidawan/history_filters_states 
Add StatesInfo component
 2023-04-03 14:46:34 -04:00
Dannon Baker 8e23b292d6 Reorder dataset states to reflect status and experience; this is reflected in the history item states help component 2023-04-03 11:37:59 -04:00
mvdbeek 314f135330 Allow pending inputs in some collection operation tools 
For those tools where it makes sense. We can't of course do this for
tools that filter outputs based on dataset size or dataset state,
or tools that make decisions based on extra datasets (e.g text files
with new identifiers).
 2023-04-03 17:36:50 +02:00
Nicola Soranzo bee3d2e7ac Merge branch 'release_22.05' into release_23.0 2023-04-03 16:31:48 +01:00
M Bernt 967f08b3b5 Merge pull request #15884 from bernt-matthias/fix/per-destination-container-resolver-file 
Enable per-destination ``container_resolver_config_file``
 2023-04-03 12:40:29 +02:00
Laila Los b855a818b4 increase webhook z-index 2023-04-03 12:24:27 +02:00
Marius van den Beek 42c9affa93 Merge pull request #15882 from davelopez/22.05_fix_ids_on_errors 
[22.05] Remove some IDs from error messages
 2023-04-03 10:35:26 +02:00
Matthias Bernt ac91975640 add test for loading a per destination container resolver config 
from a file (with global container config configured at the same time)
 2023-04-02 10:39:44 +02:00
Ahmed Awan c6a15b515b Remove failed, upload and empty from list of filterable dataset states 2023-04-01 21:31:06 -04:00
Martin Cech 905e89ff01 Merge pull request #15883 from mvdbeek/tags_in_collection_view 
[23.0] List tags in ``/api/dataset_collections/{hdca_id}/contents/{parent_id}``
 2023-03-31 19:03:02 -04:00
Matthias Bernt a8551c8f0c fix loading of per destination container_resolvers 
- per destination container_resolvers per `container_resolvers_config_file`
  did not work because `ContainerFinder` did not check if this key is set
  in the `destination_info` (but only `container_resolvers`)
  this is crucial for job configuration using XML
- per destination container_resolvers did not work if a global config
  was given with `container_resolvers` and per destination config
  used `container_resolvers_config_file`

and there was one f missing in an f-string
 2023-03-31 20:06:36 +02:00
mvdbeek 7f425d1140 List tags in /api/dataset_collections/{hdca_id}/contents/{parent_id} 
Fixes https://github.com/galaxyproject/galaxy/issues/15878.
I don't love it, but the endpoint is paginated, and if we want
to show tags in the summary view I think we have to do this.
 2023-03-31 17:41:37 +02:00
Marius van den Beek 7d9cbc72c4 Merge pull request #15841 from pauldg/fix_rocrate_metadata 
[23.0] Fix Invocation RO-Crate metadata
 2023-03-31 16:45:49 +02:00