opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-19 10:51:34 +08:00
Code Issues Packages Projects Releases Wiki Activity
72,536 Commits 72 Branches 243 Tags
ea9e2fb2f2749760c19ca9e21f06ab021dbafd7c
Commit Graph
72536 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Marius van den Beek ea9e2fb2f2 Merge pull request #17497 from mvdbeek/provide_working_url_for_to_every_request 
[23.2] Provide working routes.url_for every ASGI request
 2024-02-20 15:43:55 +01:00
Marius van den BeekandNicola Soranzo e9c91076f8 Cut out intermediate environ variable 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2024-02-20 15:43:20 +01:00
John Davis 877b5f6f2c Merge pull request #17499 from martenson/clean-magres 
[23.2] Add magres datatype
 2024-02-20 08:41:29 -05:00
mvdbeek bba92a84ad Add type annotation for fix_url_for 
I have no clue why this doesn't fail type checking since we don't have
a hint for app.legacy_mapper, but ok.
 2024-02-20 10:01:30 +01:00
Marius van den BeekandNicola Soranzo 322326e6e2 Drop unnecessary string substitution 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2024-02-20 10:01:30 +01:00
mvdbeek f4bc7f7b46 Provide working routes.url_for every ASGI request 2024-02-20 10:01:30 +01:00
Martin Cech 65dcd585bb re-add expanded related datatypes definitions 2024-02-19 11:47:31 -08:00
Martin Cech d5587ceef0 remove duplicated datatype entry 2024-02-19 11:42:24 -08:00
Nalin Gupta 319f9ef768 Added urls for datatype descriptions 2024-02-19 11:41:14 -08:00
Nalin Gupta 50e6656f0b Added description tags to datatypes 
Added description (and sometimes description_url) tags for
param, castep, den_fmt, call, cif and magres datatypes
 2024-02-19 11:40:47 -08:00
Nalin Gupta 75a66821b6 Improved linting, Fixed PBC not showing for EXTXYZ 
Also removed set_peek() method from extxyz due to functionality
being present in AtomicStructFile abstract class.
 2024-02-19 11:40:16 -08:00
Nalin Gupta 0e16e39e80 Changed parent of AtomicStructFile 
Earlier parent class was Text but was changed to GenericMol file for
XYZ and Extended XYZ files
 2024-02-19 11:40:16 -08:00
Nalin Gupta bf89543b3b Moved ASE metadata parsing to abstract class 
Transfered the metadata parsing using the ASE IO library to an abstract
class "AtomicStructFile"
 2024-02-19 11:40:16 -08:00
Nalin Gupta ded1e99336 Small fix made to magres metadata output 2024-02-19 11:40:16 -08:00
Nalin Gupta b27bd519c6 Added capability to show metadata for magres file 2024-02-19 11:40:15 -08:00
Patrick Austin f3f9e6c279 Fix CI linting, tests for Magres datatype #26 2024-02-19 11:40:13 -08:00
Nalin Gupta e765fe21b3 Adding sniffer for magres datatype 2024-02-19 11:39:48 -08:00
Marius van den Beek a7afcc9e29 Merge pull request #17491 from jdavcs/23.2_fix_merge 
[23.2] Fix merge
 2024-02-19 10:40:11 +01:00
John Davis e0baa03327 Delete file added during forward merge of 23.1 2024-02-18 15:39:32 -05:00
John Davis b83b8bbd58 Merge branch 'release_23.1' into release_23.2 2024-02-18 15:31:25 -05:00
John Davis 3308279e87 Merge branch 'release_23.0' into release_23.1 2024-02-18 15:22:08 -05:00
Marius van den Beek 29f7a29345 Merge pull request #17481 from mvdbeek/succes_typo_fix 
[23.2] Fix succces typo
 2024-02-16 15:25:25 +01:00
Marius van den Beek c5632e53c2 Merge pull request #17480 from bernt-matthias/topic/del-print 
[23.2] Remove two print statements
 2024-02-15 19:50:28 +01:00
Matthias Bernt 80c7cc22b0 remove two print statements 
that I likely forgot the remove
 2024-02-15 18:35:29 +01:00
mvdbeek e781140ff1 Fix succces typo 2024-02-15 18:34:44 +01:00
Marius van den Beek 44487a50ee Merge pull request #17474 from mvdbeek/fix_failed_metadata_state 
[23.2] Set metadata states on dataset association, not dataset
 2024-02-15 16:39:13 +01:00
Marius van den Beek 3cfe20c1df Merge pull request #17477 from davelopez/23.2_backport_#17466 
[23.2] Fix auto-select of file name in upload (Backport of #17466)
 2024-02-15 12:34:43 +01:00
mvdbeek 513ca7494d Drop overly complicated state setter logic 
I doubt anyone instinctively know when to use `._state`, `.state`,
`.raw_set_dataset_state` or `.set_dataset_state` and I think that was
part of what led to this bug.
 2024-02-15 11:28:37 +01:00
hujambo-dunia 4c9c809b1d Fix for a regression change; Auto-select/highlight file name text in input field for usability; change was lost when not carried over to newer code platform from https://github.com/galaxyproject/galaxy/blob/release_23.1/client/src/mvc/upload/default/default-row.js#L139 2024-02-15 10:18:00 +01:00
mvdbeek 6d0212518b Set metadata states on dataset association, not dataset 2024-02-14 19:09:16 +01:00
Marius van den Beek 51c5705a5c Merge pull request #17471 from mvdbeek/merge_forward_conflict 
Merge release_23.1 into release_23.2
 2024-02-14 16:48:31 +01:00
mvdbeek ccb3e9021c Merge branch 'release_23.1' into release_23.2 2024-02-14 15:31:26 +01:00
Marius van den Beek ed7c257d56 Merge pull request #17406 from ahmedhamidawan/create_saveas_workflow_with_errors_bug 
[23.2] Fix creating new erronous workflow can produce multiple empty workflows
 2024-02-13 18:14:29 +01:00
Nicola Soranzo f4229aad0a Merge pull request #17440 from mvdbeek/fix_it_templating 
[23.2] Build param dict before creating entrypoint
 2024-02-13 16:41:44 +00:00
Marius van den Beek 91d9d494ae Merge pull request #17459 from mvdbeek/backport_public_hdca_check 
[23.1] Only check access permissions in `/api/{history_dataset_collection_id}/contents/{dataset_collection_id}`
 2024-02-13 17:19:03 +01:00
Ahmed Awan d18003e661 add api test for hdcas in public histories being accessible 2024-02-13 15:01:58 +01:00
Ahmed Awan 4eab971489 remove check_ownership from dataset_collections.contents 
... since this api only needs to `check_accessible` as it is not modifying a collection
 2024-02-13 15:01:56 +01:00
Ahmed Awan 8c3d967ad3 fix published history collections are empty on expand 
Only check ownership in `__get_history_collection_instance` if:
`collection_instance.history.published` = False
 2024-02-13 15:00:39 +01:00
mvdbeek 9eebb60647 Sandwich IT entry point creating after param_dict building and env var creation 2024-02-13 14:57:12 +01:00
Marius van den Beek c94ec0d46f Merge pull request #17456 from davelopez/23.1_fix_bulk_operation_menu_bis 
[23.1] Fix history bulk operations menu (part 2)
 2024-02-13 11:32:21 +01:00
davelopez b7b5c05afd Increase readability 2024-02-12 17:20:36 +01:00
davelopez 811f8cf8fd Fix bulk menu conditions 2024-02-12 17:06:58 +01:00
davelopez 79fee2a7d4 Add more test conditions for bulk menu 2024-02-12 17:06:20 +01:00
davelopez f130a3edf8 Refactor test to reduce selector duplication 2024-02-12 11:17:31 +01:00
mvdbeek 3aa84429e0 Build param dict before creating entrypoint 
Fixes https://github.com/galaxyproject/galaxy/issues/17438.
 2024-02-10 12:15:12 +01:00
mvdbeek 880977943e Add templating to test IT 2024-02-10 12:15:12 +01:00
Marius van den Beek d4836758ae Merge pull request #17448 from ahmedhamidawan/23.0_datasetStore_saveDatasets_fix 
[23.0] Fix `datasetStore.saveDatasets` bug
 2024-02-10 11:40:40 +01:00
Marius van den Beek 9d0a2009a0 Merge pull request #17445 from nuwang/make_extra_props_more_defensive 
More defensive access of extra props in filesources
 2024-02-10 11:38:53 +01:00
Ahmed Awan 948c0134f6 [23.0] Fix datasetStore.saveDatasets bug 
When we update the datasets in the `datasetStore`, we can sometimes set multiple properties to undefined.
This happens because a dataset in the store fetched from `/api/datasets/${id}` has a keys mismatch from a dataset coming from `/api/histories/${historyId}/contents` in `watchHistory`, where the latter has lesser keys.
To address this, I replaced 'localItem' with 'item' in the loop that updates the keys, ensuring the correct properties are retained during the store update.
 2024-02-09 14:59:56 -06:00
John Davis 8884dfa86c Merge branch 'release_23.1' into release_23.2 2024-02-09 13:41:34 -05:00