Nicola Soranzo
eeb8a4e6bd
Fix path handling in imported conformance tests
2021-11-25 13:37:44 +00:00
John Chilton
9a586a58b9
Add CWL conformance API tests
...
1) Download conformance tests to `test/functional/tools/cwl_tools` where
they can be used also by framework and unit tests in the future.
2) Add populators to enable executing CWL conformance tests
3) Generate CWL conformance API tests only when needed for tests
2021-11-23 14:10:21 +00:00
mvdbeek
bc329c7b84
Merge branch 'release_21.09' into dev
2021-11-02 11:54:42 +01:00
mvdbeek
c657675d07
Adjust check_blocking_issues to PyGithub usage
2021-11-01 13:01:02 +01:00
mvdbeek
c378d08f19
Add release-diff.py to process
2021-11-01 12:37:53 +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
3b0c86f563
Fix and update bootstrap_history
2021-10-31 16:24:38 +01:00
Nicola Soranzo
90a729e431
New pyupgrade fixes
...
Found by running `ack --type=python -f | grep -v '^tools/' | xargs pyupgrade --py36-plus`
2021-10-24 12:10:34 +01:00
mvdbeek
5cfa818207
Merge branch 'release_21.09' into dev
2021-10-22 22:21:17 +02:00
Dannon Baker
2dd0eed46b
Fix several 'to to' redundant word typos.
2021-10-21 12:28:45 -04:00
Sergey Golitsynskiy
5acbb140b1
Remove refs to ToolShedRepository.metadata in scripts/
2021-10-20 17:15:39 -04:00
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
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
0e1ff5a30c
Adjust endpoint so it can receive tusd hooks
...
Without any proxying and tusd running as a separate service:
``
tusd -upload-dir=./database/tmp -hooks-http=http://localhost:8000/api/upload/_resumable_upload -hooks-http-forward-headers=X-Api-Key --hooks-enabled-events=post-finish
```
Adjust ./database/tmp to new_file_path, and this should work. Now we
just need to proxy `api/upload/resumable_upload` to `<tusd_port>/files`
and we're good for a production setup.
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
John Chilton
cd2e6527fc
Merge pull request #12255 from bernt-matthias/topic/deprecate_datamanager_version
...
Deprecate data manager version
2021-09-08 14:36:01 -04:00
mvdbeek
ecc54ba00c
Merge branch 'release_21.05' into dev
2021-08-09 18:45:05 +02:00
Nate Coraor
038045a600
Add a GDPR-friendly user purge to pgcleanup.
2021-07-23 14:55:54 -04:00
Matthias Bernt
c2a113bc85
add script for fixing shed_data_manager_conf.xml
2021-07-14 17:13:26 +02:00
mvdbeek
fdb36c7ed7
Run client-y tests with --frozen-lockfile
...
Seems to be best-practice and may be a little faster
2021-06-30 13:06:24 +02:00
mvdbeek
24d825856a
Merge branch 'release_21.05' into 'release_21.09'
2021-06-10 21:23:23 +02:00
Marius van den Beek
f115fee4a7
Merge pull request #11938 from mvdbeek/21.05_release_notes
...
Release notes for 21.05
2021-06-10 20:34:50 +02:00
mvdbeek
91795d198d
Lint fix
2021-06-10 19:41:24 +02:00
Helena Rasche
364286df04
munge filenames
2021-06-10 18:59:56 +02:00
Helena Rasche
3093c2dcef
handle subsections of configurations a bit better
2021-06-10 18:56:17 +02:00
Helena Rasche
1c66b755a6
include config schemas in diffing
2021-06-10 18:52:59 +02:00
Sergey Golitsynskiy
680db562f7
Do not use legacy string interpolation on URL obj
...
This fixes the pgcleanup script and an integration test.
The test fails because of an error in the script.
The error is caused by incorrect string formatting.
The new SQLAlchemy URL object extends collections.namedtuple, and a
tuple is incompatible with printf-style formating.
Ref:
https://github.com/sqlalchemy/sqlalchemy/blob/18dbd6aa12a7eca0acb1e2c4f752088e24d6adae/lib/sqlalchemy/engine/url.py#L36
https://docs.python.org/3/library/stdtypes.html#printf-style-string-formatting
2021-05-18 19:00:55 -04:00
Sergey Golitsynskiy
3cd1c7f1c7
Handle DedupedColumnCollection in db_indexes
...
This should fix the `scripts/check_model.py` script and the database
indexes github workflow.
Accessing index columns has changed: index.columns gives access to a
DedupedColumnCollection instead of a ColumnCollection.
Columns can be accessed by key; keys are accessed via keys() attr.
Ref:
https://docs.sqlalchemy.org/en/14/changelog/migration_14.html#select-objects-and-derived-from-clauses-allow-for-duplicate-columns-and-column-labels
https://docs.sqlalchemy.org/en/14/core/sqlelement.html?highlight=dedupecolumncollection#sqlalchemy.sql.expression.ColumnCollection
2021-05-18 19:00:55 -04:00
mvdbeek
37a15c5319
Merge branch 'release_21.05' into dev
2021-05-18 09:52:08 +02:00
Dannon Baker
22e7601653
First pass fstring conversion
2021-05-11 13:47:00 -04:00
mvdbeek
9e9343ccd2
Fix cleanup_datasets.py script
2021-05-11 18:34:30 +02:00
mvdbeek
bb3e9bffab
Don't set default pool
2021-05-07 11:17:02 +02:00
Nate Coraor
9ee437d57f
Fix usage of sed -i on macOS in release script
2021-05-06 11:27:48 -04:00
mvdbeek
de8ef76092
Make sure web handlers don't become job handlers if handlers section exists
...
And add a default pool, so that exisiting job setups that don't specify
a pool (for instance those that previously used db-preassign) will just
continue working.
2021-04-13 10:13:42 +02:00
John Chilton
c313635676
Merge pull request #11772 from mvdbeek/run_sh_gunicorn
...
Add circus + gunicorn option when using run.sh
2021-04-12 10:31:30 -04:00
mvdbeek
8157300d1d
Restore pastescript, make new stack depend on APP_WEBSERVER=dev
2021-04-07 14:39:06 +02:00
mvdbeek
d97c6e1e21
Set up default logging if running run.sh with --daemon
2021-04-07 14:39:06 +02:00
Marius van den Beek
32cb259274
Merge pull request #11641 from natefoo/release-process-overhaul
...
Overhaul make-based release process
2021-04-06 16:45:12 +02:00
mvdbeek
47d4e18c3b
Replace paster with circusd, add basic functionality to run.sh
2021-04-02 18:47:41 +02:00
mvdbeek
201b1e5e9f
Drop scripts/paster.py and pastescript
2021-04-02 18:47:41 +02:00
mvdbeek
c8c08ca84c
Merge branch 'release_21.01' into dev
2021-03-31 12:09:44 +02:00
Nate Coraor
cc1f471490
Release process overhaul
...
- Convert release Makefile targets to a script
- Update package versions from Galaxy version instead of leaving them
uncoupled
- Use next-dev-version process on release branches when in between point
releases
- Automatically detect and increment versions
- Test merging release branches forward before pushing releases
- Support multiple rc versions (will be more useful for package testing)
- Support building local versions of packages
- Tests for the release script
2021-03-30 12:11:48 -04:00
mvdbeek
ca6f2fa68e
Create install database with create_db.sh
2021-03-30 13:44:36 +02:00
mvdbeek
8d5c7003ce
Fix linting error in bootstrap script
2021-03-16 18:41:40 +01:00
Dannon Baker
3ae00d18e6
Merge remote-tracking branch 'upstream/release_21.01' into dev
2021-03-16 11:25:32 -04:00
Sergey Golitsynskiy
72c3cee00e
Update wording
2021-03-15 12:10:54 -04:00
mvdbeek
6ce5b63275
Add release testing credits to template
2021-03-15 15:22:42 +01:00
mvdbeek
75b641b89c
Tweak release issue template
2021-03-10 18:36:48 +01:00
mvdbeek
09de447b6d
Skip PRs that are already in the release notes
...
When updating the (already edited) release notes during the PR process
it is a major pain which PRs are really new. This makes that much
easier. Just be sure to keep the anchors (`.. bug`, `.. enhancement`) in until we are ready to
publish the release
2021-03-10 16:55:42 +01:00
Dannon Baker
00270ace03
Drop CLIENT_DEV_SERVER from webserver internals completely (we just proxy instead)
2021-03-05 09:52:02 -05:00
Nicola Soranzo