Commit Graph
973 Commits
Author SHA1 Message Date
mvdbeek d08a08ac4c Backend Prototype for resumable uploads via TUS
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
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
Add config options for controlling handler and runner monitor thread sleep.
2021-09-16 18:08:18 -04:00
Nate CoraorandMarius 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
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
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
[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
[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
Add documentation on how to setup Pulsar's two-container job runner
2021-04-07 10:33:32 -04:00
Nicola Soranzo e1014acc9d Merge branch 'release_21.01' into dev 2021-04-07 13:13:29 +01:00
Nicola Soranzo 13d91da1f4 Fix typo in upstream_mod_zip admin docs 2021-04-06 20:04:19 +01:00
mvdbeek 8bda8d4110 Add enable_celery_tasks config option 2021-03-29 09:29:25 -04:00
mvdbeek f5800bed50 Break up dynamic dataset collection into chunks
Addresses https://github.com/galaxyproject/galaxy/issues/11488.

One drawback here is that if multiple jobs are concurrently creating
datasets in a history the HID is not guaranteed to be sequential
between chunks. We can address this, but this is also a problem
when breaking workflow executions at
``maximum_workflow_jobs_per_scheduling_iteration``.
If we consider this to be a problem (personally I don't think it is, but
I could be convinved otherwise) I would work on this in a different PR.

On the upside the history panel will display an increasing amount of
datasets created during the dataset discovery.
2021-03-23 10:15:41 +01:00
Ruben Vorderman 684978bc4f Add missing ssl keyword in nginx example
Otherwise it will use the http protocol instead of https.
2021-03-16 11:57:26 +01:00
vjalili 5d68570a85 Make docs on setting galaxy_infrastructure_url more generic. 2021-03-10 17:49:30 -08:00
Dannon Baker 7942402bd3 Merge remote-tracking branch 'upstream/dev' into proftpd 2021-03-09 09:46:22 -05:00
vjalili 9e7c1386a4 Add documentation on how to setup Pulsar's two-container job runner. 2021-03-05 12:21:21 -08:00
Nate Coraor a2d1625780 Merge remote-tracking branch 'upstream/release_21.01' into dev 2021-03-01 16:52:02 -05:00
Marius van den BeekandNicola Soranzo d61321d872 Improve enable_tool_cache option description
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
2021-02-23 10:22:52 +01:00
mvdbeek 82f26d40ac Disable tool document cache by default
It's kind of brittle, and https://github.com/galaxyproject/galaxy/pull/10804
has improved the parsing so much that it doesn't add much benefit.
Instances on Anvil start up in ~ 32 seconds, with all of main's toolbox.
2021-02-23 08:53:45 +01:00
Helena 85fafd5a06 Merge pull request #11384 from martenson/auth-docs
fix broken docs links
2021-02-16 11:20:28 +01:00
Martin Cech 99d0fae2fe fix broken links, clarify 2021-02-16 11:13:53 +01:00
setlen 4677cf9e0d Make sure the options are all documented, remove some logging. 2021-02-12 21:23:52 +01:00
mvdbeek dd7aa6ec38 Merge branch 'release_21.01' into dev 2021-02-08 16:01:53 +01:00
mvdbeek 7d0ec29fa0 Drop legacy metadata mode
And always serialize input dataset metadata using the model exports.
This means we don't have to pickle anymore, which breaks with weakrefs
used by sqlalchemy-json's Mutable class.
2021-02-05 11:38:50 +01:00
Nicola Soranzo 352c488aaf Merge pull request #11238 from mvdbeek/drop_unused_transfer_manager
Drop unused transfer_manager.py
2021-01-27 17:57:48 +00:00
mvdbeek c1b0fab1e8 Drop unused transfer_manager.py
scripts/transfer_manager.py had been deleted previously, so this can't
be functional.
2021-01-27 17:29:00 +01:00
Sergey Golitsynskiy 6b2220e1ac Add cache_dir to schema, rebuild 2021-01-21 10:30:12 -05:00
mvdbeek 4d984c5132 Add setting that lets admins enable/disable the tool document cache
Closes https://github.com/galaxyproject/galaxy/issues/11082
2021-01-20 10:12:07 +01:00
John Chilton b8c11ab21a Link in MQ docs stub. 2021-01-12 09:34:28 -05:00
John Chilton 6c79073eb4 Mark some Sphinx as orphans - they seem to be not linked to TOC for reasons. 2021-01-12 09:29:54 -05:00