Dannon Baker
7cc98038b0
make config-rebuild
2025-04-17 09:17:48 -04:00
Uwe Winter
f1f77564d2
Allow configuring the AI backend as long as it is OpenAI compatible.
2025-04-11 15:28:43 +10:00
Enis Afgan
c6e553be71
Update RStudio IT
2025-02-26 16:01:00 -05:00
davelopez
87d5773f2c
Add Zenodo file source template documentation
2025-02-19 10:36:33 +01:00
David López and José Manuel Domínguez
c896a28a95
Apply suggestions from code review
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Co-authored-by: José Manuel Domínguez <43052541+kysrpex@users.noreply.github.com >
2025-02-17 13:44:24 +01:00
davelopez
61f9ebf34f
Add InvenioRDM file source configuration documentation and templates
2025-02-17 13:44:19 +01:00
José Manuel Domínguez
2f4ac83cd5
Update eLabFTW file source template docs
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Include the template itself and a screenshot of the form generated by the template in the docs, just like it is done for the other templates.
2025-02-17 13:10:32 +01:00
Nicola Soranzo
2bf7c7e279
Merge branch 'release_24.2' into dev
2025-02-13 16:17:35 +00:00
David López
64d385f21e
Merge pull request #19493 from kysrpex/elabftw_file_source_template
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eLabFTW file source from file source templates
2025-02-13 17:08:48 +01:00
José Manuel Domínguez
e0e8dd2501
Set writable: true in file source template for eLabFTW
2025-02-13 15:33:56 +01:00
José Manuel Domínguez
1417037509
eLabFTW file source from file source templates
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Support user-defined file sources based on `eLabFTWFilesSource`. Add a file source template for eLabFTW and the required documentation.
2025-02-13 15:33:56 +01:00
Sanjay Srikakulam
e1e962ffe8
add rebuilt config files
2025-02-12 16:20:47 +01:00
Dannon Baker
1e0d76526c
Config rebuild for registration message update.
2025-02-12 07:55:59 -05:00
Sanjay Srikakulam
27d9ca67b2
Add config options and celery periodic task for failed jobs jwd cleanup task
2025-02-11 16:16:30 +01:00
mvdbeek
a14e006f65
Merge branch 'release_24.2' into dev
2025-02-06 19:30:16 +01:00
John Davis
54fc956cca
Add documentation on handling a deadlock error during db migration
2025-02-05 15:03:33 -05:00
John Davis
442ea85f17
Add canonincal_email_rules to galaxy + TS schemas
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Also, update description of email_ban_file config option.
2025-01-23 01:05:23 -05:00
John Davis
ad9f1bfb7d
Add email-ban-file config option
2025-01-16 16:50:44 -05:00
Nicola Soranzo
1b54c0bcd8
Calculate hash for new non-deferred datasets when finishing a job
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This is configurable with two new options:
- `calculate_dataset_hash`: in which cases Galaxy should calculate
a hash for a new dataset. Possible values: 'always', 'upload'
(the default), 'never'.
- `hash_function`. Possible values: 'md5', 'sha1', 'sha256', 'sha512'
Hashes are calculated via a Celery task, so currently only if
the 'enable_celery_tasks' option is set to true.
2024-11-21 15:55:14 +00:00
Dannon Baker
e858bf01a2
Make config-rebuild
2024-11-18 20:42:12 -05:00
Dannon Baker
944ac9c786
Make openai key configurable
2024-11-18 09:11:20 -05:00
Marius van den Beek
9b39ec7ef3
Merge pull request #18996 from martenson/schema-cond
2024-11-01 03:43:13 -04:00
Nicola Soranzo
93078d949a
Replace poetry with uv
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for lightning-fast Python dependency updates.
To update all dependencies (as done by the GitHub action):
$ make update-dependencies
To update only one package:
./lib/galaxy/dependencies/update.sh -p <PKG>
2024-10-31 10:22:52 +00:00
Nate Coraor
d622d2d8f1
Remove conda_auto_init default from schema as suggested
2024-10-28 14:50:01 -04:00
Nate Coraor
90caa402a5
Disable conda_auto_init default = true when not running from source
2024-10-24 10:05:41 -04:00
Martin Cech
c6ead00287
run make config-revuild
2024-10-15 12:03:25 +02:00
John Chilton
edc5bc2a8f
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
Sanjay Srikakulam
22863a1ccb
Add new config parameter for file sources temp dir and update the webdav file source
2024-10-10 10:44:40 +00:00
Sanjay Srikakulam
3d28b2b9c9
remove use_temp_files configuration parameter
2024-10-10 10:40:58 +00:00
Sanjay Srikakulam
1c9c33ee8d
lint fix
2024-10-10 10:40:58 +00:00
Sanjay Srikakulam
2ca28420fe
Add images of the webdav conf and template and update file source templates image
2024-10-10 10:40:58 +00:00
Sanjay Kumar Srikakulam
83eabbe054
lint fix
2024-10-10 10:40:58 +00:00
Sanjay Kumar Srikakulam
22791a8d43
Add WebDAV as user file source
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Adds WebDAV example template, configuration and updates the docs, and the file source model along with the client API schema
2024-10-10 10:40:58 +00:00
John Chilton
ab70b5be6a
Rebuild schema...
2024-10-05 17:23:26 -04:00
John Davis
d0d0838c51
Merge pull request #18481 from kysrpex/interactivetoolssqlalchemy
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Support high-availability setups for the interactive tools proxy
2024-09-04 18:04:53 -04:00
José Manuel Domínguez
9ee6636f4a
Rename interactivetools_map_sqlalchemy to interactivetoolsproxy_map
2024-09-03 14:17:12 +02:00
Nicola Soranzo
c778a2ae3f
Remove conda defaults channel from more places
2024-09-02 14:03:18 +01:00
José Manuel Domínguez and John Davis
018e5417c2
Mention that interactivetools_map_sqlalchemy overrides interactivetools_map in the latter's description
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Co-authored-by: John Davis <jdavcs@gmail.com >
2024-08-09 09:58:30 +02:00
José Manuel Domínguez
ffa8ea4f4d
Fix typos in descriptions of interactivetools_map and interactivetools_map_sqlalchemy
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Authored-by: John Davis <jdavcs@gmail.com >
2024-08-09 09:42:30 +02:00
José Manuel Domínguez
c1fd2b569b
Merge branch 'dev' into interactivetoolssqlalchemy
2024-07-23 12:19:58 +02:00
José Manuel Domínguez
dddf5ba9f6
Add note in interactive tools docs page informing about interactivetools_map_sqlalchemy setting
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Refer to SQLite docs page describing situations where a client/server RDBMS works better and provide an example. Link to the `interactivetools_map_sqlalchemy` on the Galaxy configuration page.
2024-07-22 17:22:25 +02:00
José Manuel Domínguez
ce6d0f73c5
Configure SQLAlchemy interactive tool maps via new interactivetools_map_sqlalchemy setting
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Define a new configuration property `interactivetools_map_sqlalchemy` to store interactivetool proxy mappings on a RDBMS supported by SQLAlchemy.
If set, it takes precedence over `interactivetools_map`. When unset, a SQLite mapping file located at `interactivetools_map` is used (as usual).
2024-07-22 17:22:24 +02:00
Marius van den Beek
a7fb571143
Merge pull request #18499 from bgruening/obs_cache_size
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small docs enhancement
2024-07-11 11:33:32 +02:00
Martin Cech
7264a82589
regenerate config sample and docs
2024-07-05 09:19:40 -07:00
Björn Grüning
3724309809
small docs enhancement
2024-07-05 10:46:44 +02:00
José Manuel Domínguez
967b59140e
Merge branch 'refs/heads/dev' into interactivetoolssqlalchemy
2024-07-04 13:52:59 +02:00
José Manuel Domínguez
b54bf35518
Support using a table in any database supported by SQLAlchemy as mapping for interactive tools
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Replace the class `InteractiveToolSqlite` in lib/galaxy/managers/interactivetool.py with a new class `InteractiveToolPropagatorSQLAlchemy`. The new class implements a SQLAlchemy "propagator" for `InteractiveToolManager` (on the same file). This propagator writes the mappings to the table named after the value of `DATABASE_TABLE_NAME`, in the database specified by the SQLAlchemy database url passed to its constructor. Change the constructor of `InteractiveToolManager` so that it uses `InteractiveToolPropagatorSQLAlchemy`.
Change the method `_process_config` of `galaxy.config.GalaxyAppConfiguration` so that it converts the value of `interactivetools_map` to a SQLAlchemy database url if it is a path.
Update documentation to reflect these changes.
2024-07-02 11:24:34 +02:00
Dannon Baker
6ec7521e1a
Merge remote-tracking branch 'upstream/release_24.0' into release_24.1
2024-06-28 09:48:27 +02:00
mvdbeek
7c6fc1800f
Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc
2024-06-21 16:58:21 +02:00
Bjoern Gruening
5eec5cc7ae
rebuild Galaxy config
2024-06-04 21:30:24 +02:00
Dannon Baker