mvdbeek
26a98ae8f4
Implement max_discovered_files
2022-01-18 11:49:00 +01:00
mvdbeek
c9aa48ea25
Fix (per-domain) favicon url
2022-01-05 14:06:12 +01:00
mvdbeek
8ce2690ea9
Implement fastAPI prefix handling
...
Admins just need to set `galaxy_url_prefix`, the rest should just work.
2022-01-05 13:31:54 +01:00
Nuwan Goonasekera
01ca66fa98
Merge branch 'dev' into vault_impl
2021-12-22 23:55:37 +05:30
Sergey Golitsynskiy
bc6f766d5a
Update migrated_tools_config schema description, run config-rebuild
2021-12-21 10:54:28 -05:00
Sergey Golitsynskiy
91af9c51ed
Run make config-rebuild
2021-12-21 10:54:28 -05:00
Nuwan Goonasekera and Enis Afgan
d4fe61a424
Update vault docs
...
Co-authored-by: Enis Afgan <afgane@gmail.com >
2021-12-20 18:40:20 +05:30
Nuwan Goonasekera and Marius van den Beek
592603eb41
Add file upload test to vault
...
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2021-12-20 18:00:53 +05:30
Darren Cullerne
65f7259b29
Adding /doc/source/admin/reports_options.rst from make config-rebuild and additional change to file_path value in /lib/galaxy/webapps/reports/config.py
2021-12-17 09:23:03 +11:00
Nuwan Goonasekera and Marius van den Beek
3e993667e3
Typo in doc/source/admin/special_topics/vault.md
...
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2021-12-15 20:08:45 +05:30
Simon Bray
d6b0ee1900
add docs for mulled-hash, few other small fixes to existing docs
2021-12-15 10:22:23 +01:00
Nuwan Goonasekera
d9f2c0bf91
Added admin docs on configuring and using the vault
2021-12-01 21:44:44 +05:30
mvdbeek
1a08eb57b3
Make tool_evaluation_strategy configurable on app and destination level
2021-11-30 12:27:14 +01:00
mvdbeek
9aec355752
Rename allow_tool_source_display to enable_tool_source_display
2021-11-23 12:05:46 +01:00
Nuwan Goonasekera
e1535db412
Add vault conditional dependencies
2021-11-18 01:12:23 +05:30
mvdbeek
d7c34bfdb4
Return tool source language in header,
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disable view unless admin or allow_tool_source_display is set
2021-11-15 11:33:13 +01:00
mvdbeek
9f463b6f82
Adapt scripts/resumable_upload.py to fetch API
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Finding out that the `files` parameter is required took way more time
than I want to admit ... .
2021-10-13 18:05:42 +02:00
mvdbeek
e088b04b3e
Fix documented nginx location for tus
2021-10-12 18:06:09 +02:00
mvdbeek
03698ee4ac
Update docs with correct headers to forward
2021-10-12 16:43:14 +02:00
mvdbeek
600f59b0ee
Use client-logic to run upload tool
...
It is pretty cool to use hooks and an alternative tool submission
endpoint, but this is less invasive. We'd have to do this anyway for
cases where the upload is already on the server and the pre-finish hook
doesn't fire.
2021-10-12 13:43:45 +02:00
mvdbeek
82abf51069
Implement chunked upload using tus-js-client
2021-10-12 13:34:56 +02:00
mvdbeek
c13e3f49c5
Add admin documentation for running tusd + nginx
2021-10-12 13:34:55 +02:00
mvdbeek
d08a08ac4c
Backend Prototype for resumable uploads via TUS
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The middleware can be replaced by running a [tusd
server](https://github.com/tus/tusd ) or
[nginx tus location](https://github.com/mmatuska/lua-tus-server ) in
front of Galaxy.
Includes a sample script that can upload datasets into a Galaxy history.
2021-10-12 13:34:53 +02:00
mvdbeek
28511e262e
Use new sentry-sdk and adapt usage pattern
...
Replaces our custom Sentry WSGI middleware with middleware shipped by
sentry-sdk. Adds sentry-sdk ASGI middleware. Our custom sentry
middleware also allowed logging slow requests to sentry. I have dropped
this for now, and if we still want this in the future, we should
probably implement this as a custom logging middleware instead, which
would automatically appear in Sentry as well.
We used to hardcode the log level for events to WARNING, and the Sentry
default is ERROR now, which I think is a good idea. I've made this
configurable using the sentry_event_level config variable.
It does not seem to be possible to connect multiple dsn's in the same
app, unless we start hacking
(https://github.com/getsentry/sentry-python/issues/198 ), so I dropped
the custom_dsn from the sentry error reporting plugin (which has been
broken anyway, so shouldn't be a big deal).
2021-09-28 19:32:10 +02:00
Alexander OSTROVSKY
c5825e07db
remove webpack for initial version, fix default location
2021-09-16 23:23:03 -04:00
Alexander OSTROVSKY
9b9f379265
New User Welcome page
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make runnable from pr. Still need to debug
divs out
tree
broken into components
cleaning
formatting, file names, jest tests
jest
removed image files, will be retrieved via npm or separate repo
update
plugin via webpack
webpack plugin
change to plugin to prevent repeated image downloading
update
add actual page accessible from help and registration
Full draft
jest fix, next to make package customizeable
yarn lock
fix
update
Update
Refactor from here for the confiuration stuff -- this displays the bundle
drop plugin_build_hash -- these should never be committed
Update plugin gitignore
Oops, left in a debug
2021-09-16 23:22:57 -04:00
Dannon
4517657e90
Merge pull request #12473 from natefoo/papercut-job-queue-sleep-time
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Add config options for controlling handler and runner monitor thread sleep.
2021-09-16 18:08:18 -04:00
Nate Coraor and Marius van den Beek
b9333cd36d
Apply suggestions from code review
...
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2021-09-16 15:13:58 -04:00
Nate Coraor
44bc1469b0
Make the subject and body of the mailing list join message configurable.
2021-09-16 15:06:46 -04:00
Nate Coraor
1963bc7294
Add config options for controlling handler and runner monitor thread sleep.
2021-09-16 10:15:45 -04:00
John Chilton
f52c510c81
Rebuild config files.
2021-09-07 14:29:39 -04:00
Nate Coraor
db6944523f
Support setting container resolvers directly in the app config
2021-08-13 15:23:30 -04:00
Nate Coraor
7c9c7f8305
Rename containers_resolvers_config_file to container_resolvers_config_file
2021-08-13 14:24:16 -04:00
mvdbeek
11363a013e
Merge branch 'release_21.05' into dev
2021-06-24 12:22:55 +02:00
John Chilton
cd2e51fd5f
Merge pull request #12164 from lldelisle/ftp_doc
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change doc for ftp_upload_dir/site
2021-06-23 19:08:29 -04:00
almahmoud
b6092e8c4c
Use new config option for base path
2021-06-22 01:57:42 -04:00
Lucille Delisle
a93d3308bc
change doc for ftp_upload_dir/site
2021-06-18 11:08:48 +02:00
Dannon
1aeba32257
Merge pull request #12103 from guerler/restrict_user_account_management
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Add configuration option to hide user account management interfaces
2021-06-15 08:26:59 -07:00
Nate Coraor
15e1b06ba5
A few more updates to the tool deps documentation
2021-06-07 20:54:23 -04:00
Nate Coraor
2ddc310711
Update dependency resolver docs and drop sample XML file in favor of
...
direct configuration under the dependency_resolvers key of galaxy.yml.
2021-06-07 18:16:07 -04:00
guerler
d901dd48d3
Rename option to enable_account_interface
2021-06-07 15:20:06 -04:00
guerler
8d9d8363a7
Add configuration option to hide user account management interfaces for admin managed instances
2021-06-07 13:33:02 -04:00
Marius van den Beek
b84dccb7f9
Merge pull request #11973 from almahmoud/k8s_runner_its
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[21.05] Change default prefix
2021-05-13 18:07:00 +02:00
almahmoud
ab8bfe4b10
Change default prefix
2021-05-13 12:04:51 -04:00
Marius van den Beek
c5e00e49dd
Merge pull request #11914 from Nerdinacan/history-audit
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[21.05] Create history_audit table to avoid write deadlocks during history.update_time updates
2021-05-13 16:26:59 +02:00
almahmoud
d0971cc1b5
Move configs to schema
2021-05-11 16:43:46 -04:00
mvdbeek
3d59717142
Add celery setup that regularly cleans audit_table
2021-05-11 18:34:30 +02:00
mvdbeek
2f22a31a15
Update documentation for new defaults and recommendations
2021-04-13 10:13:42 +02:00
Helena
e5000e24c8
Merge pull request #11351 from selten/analytics
2021-04-08 16:45:34 +00:00
John Chilton
0b0b8c48b9
Merge pull request #11557 from VJalili/two_container
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Add documentation on how to setup Pulsar's two-container job runner
2021-04-07 10:33:32 -04:00
mvdbeek