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Commit Graph
558 Commits
Author SHA1 Message Date
Nicola Soranzo 97e7dceb73 Fix packages' requirements 2022-05-30 22:40:28 +01:00
Nicola Soranzo f2a42ba67e Run mypy on all packages' files 
Also:
- mypy fixes.
- Use `with` statement to open/close files.
 2022-05-30 22:38:55 +01:00
John Chilton d3719517e7 attempt to run CI on test_base so we can catch issues with packaging... 2022-05-30 12:19:29 -04:00
John Chilton c5bf63bc91 Add DEFERRED datasets to Galaxy 
- Improves options and display around discarded datasets.
- Adds new APIs for importing model stores.
- Adds support to model store layer for importing/exporting workflow invocations and APIs and tests to support this.
- Add new DEFERRED dataset state - with APIs for materializing them or the option to defer them on the worker node if using tool_evaluation_strategy=remote on the job destination.
- UI and API options for uploading deferred datasets individually or into collections.
 2022-05-23 19:48:47 -04:00
Nicola Soranzo 47d35a8cc5 Add missing pytest-asyncio test requirement to `webapps` package 
Otherwise all unit tests in `test_request_scoped_sqlalchemy_sessions.py`
are skipped.
 2022-05-12 16:38:14 +01:00
Michael R. Crusoe dd77026527 galaxy-tool-util: better link in the README 2022-05-04 15:25:42 +02:00
Marius van den Beek 2b3486bb25 Merge pull request #13793 from mvdbeek/fetch_data_almost_everywhere 
Port api/tools/fetch to FastAPI, add schema, and use `__FETCH_DATA__` in most tests
 2022-04-26 13:36:51 +02:00
mvdbeek 02ac5b3c9e Add FastAPI route for tools/fetch 2022-04-23 12:01:32 +02:00
Nicola Soranzo 6da2f0e98c Merge branch 'release_22.01' into dev 2022-04-22 18:23:33 +01:00
mvdbeek da61e77068 Fix persistent mulled cache unused for repo_has_name 2022-04-14 12:10:42 +02:00
John Chilton 800d49c467 Short term storage infrastructure. 2022-04-13 09:52:51 -04:00
Björn Grüning b81ea28df1 Merge pull request #13654 from mvdbeek/memoize_ffprobe 
Speed up sniffers by using lru_cache on ffprobe, skip binary sniffers on text files
 2022-04-09 14:13:00 +02:00
Nicola Soranzo 528f847d13 Remove file added by mistake 
in commit 9690680ec7 .
 2022-04-05 18:16:53 +01:00
mvdbeek 37b47e0304 Better binary detection with FilePrefix & libmagic 
FilePrefix reads the first Megabytes of a file, which is much more
than the previously used `check_binary` which read only 1KB.

Since we're re-using FilePrefix instance this shouldn't have any impact
on performace. In addition we're now using `python-magic` to detect
the encoding and mime-type. We're using the mime-type detection
for PDF only at this point, but we're also using the detected encoding
if we encounter non-utf8 content.
 2022-04-05 15:06:04 +02:00
Björn Grüning e5dd7b111e Merge pull request #13634 from jmchilton/job_metrics_revision 
Overhaul job metrics.
 2022-04-04 22:27:21 +02:00
Nicola Soranzo 7cf3ce97ec Unpin alembic in galaxy-data package 2022-03-31 18:50:07 +01:00
Nicola Soranzo d11bbf219d Update mypy to 0.942 . Fix new mypy errors. 
Remove unused `optional()` decorator function that had an annotation issue.
 2022-03-31 18:47:52 +01:00
John Chilton 2613512327 Remove job metrics CollectL plugin. 
The project seems to be a deadend and it was never adopted in production as far as I am aware. The cgroup plugin seems to provide similar information with much less overhead and with easier to manage dependencies.
 2022-03-31 09:25:52 -04:00
John Chilton f9940e35d1 Pin pysam since 0.19.0 seems to have incomplete type definitions. 2022-03-30 16:44:58 -04:00
mvdbeek 443119ccc9 Drop containers package, move to tool_util 2022-03-24 19:51:59 +01:00
mvdbeek 5ce08cc63f Add an alibi test for the containers package, drop another unused method 2022-03-23 19:06:57 +01:00
mvdbeek 08d3078382 Drop docker swarn gie support 2022-03-23 18:38:53 +01:00
mvdbeek 102a7eab63 Add apispec dependency 2022-03-20 14:26:28 +01:00
mvdbeek 4ca837d764 Merge branch 'release_22.01' into 'release_22.05' 2022-03-15 20:46:28 +01:00
mvdbeek 9690680ec7 Update version to 22.01. 2022-03-15 20:46:24 +01:00
John Chilton 72f3a6f465 Merge branch 'release_22.01' into dev 2022-03-15 14:51:10 -04:00
mvdbeek 6806a0f995 Make gravity import conditional 2022-03-15 16:59:58 +01:00
Marius van den Beek 550f47db9e Merge pull request #13540 from mvdbeek/dev 
Merge release_22.01 into dev
 2022-03-15 11:30:18 +01:00
mvdbeek faea1c8211 Merge branch 'release_22.01' into dev 2022-03-14 17:06:49 +01:00
Nicola Soranzo 0c80836c34 Upgrade syntax to Python 3.7 
using `ack --type=python -f | grep -v '^tools/' | xargs pyupgrade --py37-plus`

Also more refactoring of Python files in `packages/` .
 2022-03-14 14:57:43 +00:00
mvdbeek 3fa572d612 First pass at supporting --preload and worker_id 
We do need to include some kind of worker id in the server_name. If we
don't do this and we start with multiple workers the internal
QueueWorker won't work and multiple processes can pick up the same job
if the web process is also a job handler.
 2022-03-10 17:15:37 +01:00
Sergey Golitsynskiy 736c6c0048 Update data package (requirements, packages, includes) 
Note: manage_db entry point needs to be edited in model.orm.scripts.
 2022-03-09 18:41:03 -05:00
Sergey Golitsynskiy be53ebec6b Move triggers out of migrate directory 
(does not include an import in mapping.py: to be added in a separate
commit, grouped with other edits in mapping.py)
 2022-03-09 18:40:07 -05:00
Sergey Golitsynskiy 3be1f6fef3 Add alembic dir to ignore list in package tests 
Otherwise alembic/env.py gets executed out of context at test collection
stage (via tox -e unit >> run_tests.sh), which raises an AttributeError
(alembic.context is not set in this case)
 2022-03-09 18:40:07 -05:00
Sergey Golitsynskiy e248cbe35e Add alembic to dependencies 2022-03-09 18:40:07 -05:00
John Chilton 213f3a17fc Allow legacy EDAM mappings. 2022-03-07 16:54:54 -05:00
mvdbeek 873d43eac2 Move tool shed and reports config schema to config package 
And restore unit tests to proper place.
 2022-03-03 16:57:39 +01:00
Nicola Soranzo 2925277391 Simplify package testing code 2022-03-03 16:48:48 +01:00
Nicola Soranzo c0db14e195 Test the webapps package 
Also:
- Remove redundant `galaxy.schema` module from the `app` package (it's
  already in `data`)
- Fix requirements of the `app` and `webapps` packages
- Add missing `PyJWT` and `python-dateutil` to `tool.poetry.dependencies`
  (which were already included in the pinned requirements as deps of deps)
 2022-03-03 16:48:36 +01:00
Nicola Soranzo 7f04b5d698 Merge branch 'release_22.01' into dev 2022-03-02 20:08:55 +00:00
mvdbeek e89b47b7d6 Rename project_galaxy_config.py 2022-03-01 20:44:26 +01:00
Nicola Soranzo 6b32e23101 Reformat with black and pyupgrade 2022-03-01 19:35:56 +00:00
mvdbeek 022bae0654 Add pykwalify to `app` package test requirements 2022-03-01 19:27:21 +01:00
mvdbeek 4cffa78836 Drop pykwalify from app requirements 
Should be redundant as it is handled by the config package requirements.
 2022-03-01 19:25:07 +01:00
Marius van den BeekandNicola Soranzo 48e2ebe20f List transitive dependencies that are imported directly in config package 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-03-01 19:22:45 +01:00
mvdbeek cfd66f49b5 Switch license back to AFL 2022-03-01 16:50:07 +01:00
Marius van den BeekandNicola Soranzo 3c3e60d9b1 Use black style double quotes 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-03-01 16:50:07 +01:00
Marius van den BeekandNicola Soranzo 6b08108a88 Fix History formatting 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-03-01 16:50:07 +01:00
Marius van den BeekandNicola Soranzo 7ddf3ea075 Add galaxy-objectstore to app package requirement 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-03-01 16:50:07 +01:00
mvdbeek e3b7fe0805 Fix package symlinks 2022-03-01 16:50:06 +01:00