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36449 Commits
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
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 29f7a29345 Merge pull request #17481 from mvdbeek/succes_typo_fix 
[23.2] Fix succces typo
 2024-02-16 15:25:25 +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
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
mvdbeek 6d0212518b Set metadata states on dataset association, not dataset 2024-02-14 19:09:16 +01:00
mvdbeek ccb3e9021c Merge branch 'release_23.1' into release_23.2 2024-02-14 15:31:26 +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
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
mvdbeek 3aa84429e0 Build param dict before creating entrypoint 
Fixes https://github.com/galaxyproject/galaxy/issues/17438.
 2024-02-10 12:15:12 +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
John Davis 8884dfa86c Merge branch 'release_23.1' into release_23.2 2024-02-09 13:41:34 -05:00
John Davis 7bffadb651 Merge branch 'release_23.0' into release_23.1 2024-02-09 13:37:33 -05:00
Nuwan GoonasekeraandMarius van den Beek c7a5e4ff59 Code review suggestion 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2024-02-09 19:37:52 +05:30
nuwang bffb7a99c5 Use dataclass to initialize default values 2024-02-09 16:59:33 +05:30
nuwang ae982a2afb Add initializers to filesource options 2024-02-09 16:59:32 +05:30
John Davis c1f0aad0e1 Fix typo 2024-02-09 01:09:00 -05:00
Marius van den Beek e70ff43b75 Merge pull request #17439 from mvdbeek/backport_model_store_fixes 
[23.2] Backport model store fixes
 2024-02-08 15:41:04 +01:00
mvdbeek 2d702a7402 Merge branch 'release_23.1' into release_23.2 2024-02-08 12:22:32 +01:00
mvdbeek 0008b4d7cc Merge branch 'release_23.0' into release_23.1 2024-02-08 12:21:53 +01:00
Marius van den Beek 4c1c8e227f Merge pull request #17384 from ahmedhamidawan/fix_genome_build_filter_postgres 
[23.0] Fix History contents `genome_build` filter postgresql bug
 2024-02-08 12:20:32 +01:00
mvdbeek 327dfa0056 Merge branch 'release_23.1' into release_23.2 2024-02-08 11:08:15 +01:00
Marius van den Beek 62ee88db55 Merge pull request #17433 from davelopez/23.1_fix_bulk_operations_menu 
[23.1] Fix history bulk operations menu conditions
 2024-02-08 11:04:07 +01:00
John Chilton 87321dcffa Fix overlapping names in extra files for model stores. 2024-02-08 11:01:22 +01:00
John Chilton cf8e72ff98 Minimal test case demonstrating model stores break on implicit conversions. 2024-02-08 11:01:13 +01:00
Nicola Soranzo 5e14d03779 Merge branch 'release_23.1' into release_23.2 2024-02-07 22:50:08 +00:00
Nicola Soranzo 52933ed5fd Merge branch 'release_23.0' into release_23.1 2024-02-07 22:48:53 +00:00
davelopez f60f0ae6e3 Fix new edge case where all items might be already deleted 
This case was previously prevented at the UI level but should be considered here.
 2024-02-07 14:58:52 +01:00
Nicola Soranzo de8d4562b6 Add missing Werkzeug test requirement 
Used in `test/unit/util/test_get_url.py` since commit
69ebbb761a .

Pin Werkzeug in `lib/galaxy/dependencies/dev-requirements.txt`
to latest version compatible with pytest-httpserver 1.0.6 .

Fix unit test collection error on Python 3.11:
```
  File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.11/site-packages/pytest_httpserver/httpserver.py", line 26, in <module>
    from werkzeug.http import parse_authorization_header
ImportError: cannot import name 'parse_authorization_header' from 'werkzeug.http' (/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.11/site-packages/werkzeug/http.py)
```
 2024-02-07 05:44:42 +00:00
Nicola Soranzo 10ace7bd10 Update python-multipart to 0.0.7 
xref: https://github.com/tiangolo/fastapi/security/advisories/GHSA-qf9m-vfgh-m389
 2024-02-06 17:33:21 +00:00
davelopezandmvdbeek 7d27634879 Give webdav plugin a clean temp directory 
Co-authored-by: mvdbeek <m.vandenbeek@gmail.com>
 2024-01-31 11:25:46 +01:00
mvdbeek fbad571b13 Respect `upstream_gzip` config setting when streaming dataset collection archive 
Which means archives won't be compressed when this setting is activated.
This is about 20 times faster than the current default.
 2024-01-31 11:22:09 +01:00