John Chilton
4bd80ce6ef
Flush out documentation and service-info for DRS API a bit.
2022-12-08 10:08:01 -05:00
John Chilton
8ff9fe2610
Implement initial GA4GH DRS Support.
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- Implement APIs for serving Galaxy's public datasets as DRS objects.
- Implement support in galaxy.files.uris for DRS URIs so that upload, etc... can use DRS URIs from other data repositories.
The ways this can be improved are endless:
- New object ID patterns can be implemented to allow access to composite data, metadata files from a bundle view of datasets.
- New object ID patterns can be implemented to allow access to collections as bundles of datasets.
- More auth types and AccessMethods could be implemented for loading datasets from clients.
- Some sort of scheme for providing authenticated URLs to non-public data could be implemented to provide access to more of Galaxy's data if user's can implement.
Despite all these limitations - I think having the guts in like this provide useful points for interested parties to go and add functionality to enable their desired usecases.
2022-12-08 10:07:11 -05:00
guerler
72fd52f087
Deprecate brand title text option, logo now contains text
2022-11-30 17:19:07 -05:00
Linelle
9c5f5bc3a2
changed references from sample XML to sample YML
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added a sentence about where to find the XMLs as well in case people are still using those (it's me, i'm people)
2022-11-30 14:50:19 -05:00
Linelle
ec504562e3
change resubmission example link from xml to yml
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Test case for resubmission location used to be https://github.com/galaxyproject/galaxy/blob/dev/test/integration/resubmission_job_conf.xml which leads to 404, have changed it to https://github.com/galaxyproject/galaxy/blob/dev/test/integration/resubmission_job_conf.yml and made it linked text instead of plain URL
2022-11-30 14:29:52 -05:00
Nate Coraor
1cdb7b5bcd
Replace XML job conf sample with YAML.
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Prefer loading job_conf.yml, fall back to job_conf.xml with a warning if
it exists.
2022-11-17 19:58:24 -05:00
John Chilton
1a2a534695
Merge pull request #14965 from jmchilton/remove_no_longer_useful_wsgi_middleware
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Remove old WSGI middleware that is no longer useful.
2022-11-10 23:13:45 +01:00
John Davis
b11c18eb21
Merge pull request #14825 from neoformit/dev-html-email
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Looks great! Thanks, @neoformit
For future ref/todo: we do need a more systematic/unified approach to handling path construction that handles tests that are arun both as standalone unit tests and as part of package tests (as per observation by @neoformit)
2022-11-10 11:30:42 -05:00
John Chilton
92a885e280
Remove old WSGI middleware that is no longer useful.
2022-11-10 05:28:24 -05:00
Cameron Hyde
e2119e4750
Update config description
2022-10-20 14:25:49 +10:00
Cameron Hyde
dc27533344
Account activation email rendered from text/html templates
2022-10-20 14:06:17 +10:00
Dannon
c7216e4b85
Merge pull request #14776 from mahendrapaipuri/add_request_obj_authmanager
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Make HTTP request object available to `AuthManager`
2022-10-18 09:23:10 -04:00
Marius van den Beek
672ed4984f
Merge pull request #14694 from sveinugu/dev
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Allow path-based interactive tools using nginx proxy
2022-10-17 11:24:38 +02:00
Marius van den Beek
241da69672
Merge pull request #12288 from dannon/sorted-tools-in-sections
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Automatically sort tools in sections by name
2022-10-17 10:49:17 +02:00
Marius van den Beek
ce26561b33
Merge pull request #14708 from jdavcs/dev_celery_config
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Enable fine-grained celery configuration
2022-10-17 10:37:24 +02:00
Marius van den Beek and Nicola Soranzo
a5dc788bf3
Tweak wording and example for verifying remote_ip in custom LDAP authenticator
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2022-10-17 10:33:29 +02:00
John Davis
d310635895
Celery config option result_backend is required
2022-10-14 19:28:17 -04:00
John Davis
d26ad37e97
Remove celery_backend from config_schema, use celery_conf instead
2022-10-14 19:28:17 -04:00
John Davis
b6b49897dc
Remove celery_broker from config_schema, use celery_conf instead
2022-10-14 19:28:17 -04:00
John Davis
2de79dd7d1
Add default task routes to config schema
2022-10-14 19:28:17 -04:00
John Davis
71829ae6af
Add more details to setting db engine options to config schema
2022-10-14 13:18:35 -04:00
mahendrapaipuri
c0002c1ffb
Update authentication documentation with an example on how to use request object in auth flows
2022-10-14 09:46:59 +02:00
Nicola Soranzo
6069023d86
Merge pull request #14740 from bernt-matthias/topic/doc-security-datatables
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Extend security docs
2022-10-13 14:29:52 +01:00
M Bernt and Marius van den Beek
ffc26d5ddd
Update doc/source/admin/security.md
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2022-10-13 13:53:06 +02:00
Nicola Soranzo
a81d680cca
Merge branch 'release_22.05' into dev
2022-10-11 21:34:31 +01:00
Dannon Baker
c8659d1d4a
Add toolbox_auto_sort config option, expose in config manager.
2022-10-06 22:20:06 -04:00
M Bernt and Nicola Soranzo
e8adc13324
Apply suggestions from code review
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2022-09-30 22:38:49 +02:00
M Bernt
37594348f9
Update doc/source/admin/security.md
2022-09-30 19:00:54 +02:00
John Davis
06744d4d0f
Document use of release tags in manage_db.sh
2022-09-30 10:42:01 -04:00
Matthias Bernt
eddd8e89a6
extend security docs
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by adding data referred by data tables
2022-09-30 14:33:40 +02:00
John Davis
8538ab7fcb
Fix same error in sample code in the rst doc file
2022-09-29 12:23:28 -04:00
John Davis
84f22bac77
Add db migration documentation to docs
2022-09-27 15:03:12 -04:00
John Davis
5a748bb867
Display 'Config Options' as subheading of 'Galaxy Configuration'
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This corrects a (supposedly) typo that prevented this to be displayed as
a subheading on this page: https://docs.galaxyproject.org/en/master/admin/index.html
2022-09-27 15:03:03 -04:00
Sveinung Gundersen
4ec8c4654e
Added info on galaxy.yml config
2022-09-23 17:54:01 +02:00
Sveinung Gundersen
89bf7b1e52
Adding documentation and example nginx config to allow path-based interactive tools
2022-09-23 17:19:31 +02:00
Nicola Soranzo
e08deef224
Merge pull request #14592 from nsoranzo/misc_fixes_202209
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Misc fixes 202209
2022-09-09 21:34:38 +01:00
Nicola Soranzo
157d9647ea
Update docs on adding Python dependencies
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to use Wheelforge instead of Starforge.
2022-09-09 17:26:30 +01:00
Nicola Soranzo
404da60afa
Fix Tool Shed link
2022-09-09 17:20:24 +01:00
Nicola Soranzo
cb012c7fb2
Merge branch 'release_22.05' into dev
2022-09-09 17:14:20 +01:00
Nicola Soranzo
d8986239a1
Merge branch 'release_22.01' into release_22.05
2022-09-09 17:12:29 +01:00
Marius van den Beek and Nicola Soranzo
b05462a188
Add sbin to PATH
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2022-09-09 13:06:35 +02:00
mvdbeek
0256b34b34
Include /bin in sample systemd unit path
2022-09-09 12:52:05 +02:00
Dannon
c7a275b13c
Merge pull request #14570 from guerler/logout_url
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Add config option for post logout redirect url
2022-09-07 08:00:33 -04:00
guerler
8350ff212e
Add post logout url to configuration
2022-09-05 14:12:50 -04:00
Nicola Soranzo
0df5c9a5fb
Updates for Poetry 1.2.0
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Also:
- Export only dev requirements to `lib/galaxy/dependencies/dev-requirements.txt` .
- Packages don't have a `requirements.txt` file.
2022-09-05 17:23:18 +01:00
John Chilton
52d982bf74
Merge pull request #14558 from jdavcs/dev_schema_rename_option_ref
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Fix reference to config option in schema
2022-09-02 14:39:42 -04:00
Nicola Soranzo
e7d7c62de6
Merge branch 'release_22.05' into dev
2022-09-02 19:28:55 +01:00
Nate Coraor
86e42b5483
Update Gravity to 0.13.4 and document setting env vars on dynamic
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handlers.
2022-09-01 10:40:54 -04:00
John Davis
241647c1f1
Run make config-rebuild
2022-08-31 18:08:26 -04:00
mvdbeek
2e22b9e1f8
Merge branch 'release_22.05' into dev
2022-08-22 19:17:35 +02:00
John Chilton