Commit Graph
1511 Commits
Author SHA1 Message Date
mvdbeek 1a08eb57b3 Make tool_evaluation_strategy configurable on app and destination level 2021-11-30 12:27:14 +01:00
mvdbeek 6794d6be93 Resolve circular dependency for ToolEvaluator
by placing ComputeEnvironment and ActionBox under job_execution.
2021-11-29 11:22:42 +01:00
mvdbeek 9aec355752 Rename allow_tool_source_display to enable_tool_source_display 2021-11-23 12:05:46 +01:00
mvdbeek d7c34bfdb4 Return tool source language in header,
disable view unless admin or allow_tool_source_display is set
2021-11-15 11:33:13 +01:00
mvdbeek bc329c7b84 Merge branch 'release_21.09' into dev 2021-11-02 11:54:42 +01:00
mvdbeek a6207d043d Add last 2 PRs to release notes 2021-11-02 08:57:42 +01:00
mvdbeek 4257cd5531 Edits from Beatriz 2021-11-02 08:42:22 +01:00
mvdbeek 896bd88087 More punctuation fixes! 2021-11-01 18:10:44 +01:00
mvdbeek 1c75d43646 Capitalize Backbone 2021-11-01 17:42:47 +01:00
mvdbeek 317a8b5fc1 More whitespace and punctuation fixes 2021-11-01 17:27:26 +01:00
Marius van den BeekandDavid López 4a1e1021a7 Remove David from release testers for 21.09
Co-authored-by: David López <46503462+davelopez@users.noreply.github.com>
2021-11-01 16:05:48 +01:00
mvdbeek 55831413ce One more PR 2021-11-01 13:24:13 +01:00
mvdbeek 3b4cd15666 Add remaining open PRs 2021-11-01 12:47:02 +01:00
mvdbeek a9058c54ba Produce Literal Blocks for config value changes
These scroll correctly and don't fail when config description changes
includes newlines or long text.
2021-11-01 12:37:53 +01:00
mvdbeek ef2ace8e7f Write full release notes 2021-11-01 11:43:03 +01:00
mvdbeek 696a99bd53 More PR fixes 2021-11-01 11:31:40 +01:00
mvdbeek 11f1296d33 More fixes to PR titles 2021-11-01 10:10:13 +01:00
mvdbeek 46be208f30 Capitalize PR 2021-10-31 20:39:10 +01:00
mvdbeek 2aebc4f664 Add release testing team credits 2021-10-31 20:32:27 +01:00
mvdbeek 696331e3e8 Drop anchors 2021-10-31 20:18:01 +01:00
mvdbeek 9bfaf66603 Add release_21.09 to release toc 2021-10-31 16:25:03 +01:00
mvdbeek b3163b1d89 Update and finalize release notes 2021-10-31 16:10:04 +01:00
mvdbeek 497f6a9835 Merge branch 'release_21.09' into dev 2021-10-26 16:30:19 +02:00
Helena Rasche 653dd71170 Finish release notes 2021-10-25 12:56:33 +02:00
Marius van den Beek 6432945948 Merge pull request #12656 from mvdbeek/resumable_upload
Resumable file uploads with tus.io
2021-10-15 17:51:23 +02:00
Marius van den BeekandNicola Soranzo 5a9b95179c Clarify position of pytest arguments
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
2021-10-14 11:40:15 +02:00
mvdbeek 0b461c7bd7 Extend debugging test instructions for GHA 2021-10-14 11:29:18 +02:00
mvdbeek 9f463b6f82 Adapt scripts/resumable_upload.py to fetch API
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
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
Nicola Soranzo 92c49b9757 Merge branch 'release_21.09' into dev 2021-10-04 13:44:23 +01:00
Marius van den Beek 54df81a4f5 Merge pull request #12545 from mvdbeek/add_david_to_committers
[PROCEDURES] Add David López to committers group
2021-10-04 09:15:11 +02:00
Marius van den Beek 9a161cdef5 Merge pull request #12544 from mvdbeek/add_oleg_to_committers
[PROCEDURES] Add Oleg Zharkov to committers group
2021-10-04 09:14:56 +02:00
mvdbeek 9f99ea53ab Merge branch 'release_21.09' into dev 2021-09-30 13:51:06 +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
Dannon Baker 6393056ae4 Update both announce docs as well with prerelease tag 2021-09-28 08:13:33 -04:00
Dannon Baker d6449bfbde Add prerelease notes blurb so we can publish this early 2021-09-28 08:10:52 -04:00
mvdbeek c35a4679cb Release note draft 2021-09-27 18:03:33 +02:00
mvdbeek 019488005d [PROCEDURES] Add David López to committers group
David has taken on the migration to fastAPI as his first big project
within the Galaxy codebase and has gained a very good understanding of
Galaxy's backend and the new server stack. His PRs are well-crafted and
contain rigorous tests.
David is also the maintainer of the [Galaxy language
server](https://github.com/galaxyproject/galaxy-language-server), has
presented his work at this years' GCC and is a member of the backend
working group. So I'm proposing to add David to the committers group.
2021-09-24 11:27:43 +02:00
mvdbeek 5a91c04840 [PROCEDURES] Add Oleg Zharkov to committers group
Oleg has contributed many large pieces of new and modernized frontend
components as well as complementary backend changes. He has included
many tests for new and old components, is an important member of the
UI-UX and testing working groups and has presented his work at multiple
GCC conferences. So let's make Oleg an official member of the committers
group.
2021-09-24 11:16:25 +02:00
Sergey Golitsynskiy a302e988d5 Modify description of the "database" label 2021-09-23 14:04:35 -04:00
Dannon Baker b1b277ba22 Merge remote-tracking branch 'upstream/release_21.05' into dev 2021-09-20 08:40:41 -04:00
Nicola Soranzo be66e16ad3 Add PostgreSQL < 9.5 deprecation notice to 21.05 release announce
xref. https://github.com/galaxyproject/galaxy/issues/12095#issuecomment-921669954
2021-09-17 19:50:43 +01:00
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