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30415 Commits
Author SHA1 Message Date
Sergey Golitsynskiy 41d7cf20e4 Merge pull request #13541 from ic4f/dev_13376_migration 
Add source_metadata column to workflow table as alembic revision
 2022-03-16 11:01:25 -04:00
John Chilton a132cf5892 Fix broken merge. 2022-03-15 17:40:46 -04:00
John Chilton 72f3a6f465 Merge branch 'release_22.01' into dev 2022-03-15 14:51:10 -04:00
Dannon 86f696cc0b Merge pull request #13546 from mvdbeek/fix_yaml_preview_firefox 
[22.01] Fix yaml preview in firefox
 2022-03-15 12:47:43 -04:00
mvdbeek 6806a0f995 Make gravity import conditional 2022-03-15 16:59:58 +01:00
mvdbeek 66406ffa72 Fix yaml preview in firefox 
by using standard text/plain content-type.
Fixes https://github.com/galaxyproject/galaxy/issues/13295.
 2022-03-15 16:04:10 +01:00
mvdbeek a8d9801785 Merge branch 'release_22.01' into dev 2022-03-15 15:21:15 +01:00
Marius van den Beek 083d94dfca Merge pull request #13531 from mvdbeek/include_gravity_in_sample_config 
[22.01] Include gravity in sample config
 2022-03-15 14:47:49 +01:00
mvdbeek 90672de88d Rebuild sample for gravity 0.11.0 2022-03-15 12:02:06 +01:00
Dannon 513c4c1bd1 Merge pull request #13529 from ic4f/dev_alembic_doc1 
Add link to issue to error message
 2022-03-15 06:38:24 -04:00
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
Sergey GolitsynskiyandDavid López 77254915a7 Fix dumb mistake 
Co-authored-by: David López <46503462+davelopez@users.noreply.github.com>
 2022-03-14 17:46:21 -04:00
Sergey Golitsynskiy 1b9be1e61a Factor out drop_column pattern into a util module 2022-03-14 16:12:33 -04:00
Sergey GolitsynskiyandMarius van den Beek 9db6c98fcb Update lib/galaxy/model/migrations/alembic/versions_gxy/b182f655505f_add_workflow_source_metadata_column.py 
Drop import

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-03-14 14:07:46 -04:00
Sergey Golitsynskiy 6bb0125664 Add source_metadata column to workflow table 
The context manager in the downgrade() function is a standard workaround
for dealing with the limitations of SQLite's alter_table statement.

Ref:
https://alembic.sqlalchemy.org/en/latest/ops.html?highlight=batch_alter_table#alembic.operations.Operations.batch_alter_table
https://alembic.sqlalchemy.org/en/latest/batch.html#batch-migrations
 2022-03-14 13:36:57 -04:00
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
Dannon 4e742cdfcf Merge pull request #13536 from mvdbeek/content_id_issue 
[22.01] Return actual tool id instead of specified tool id in workflow step
 2022-03-14 10:49:54 -04:00
Dannon c8901b1bb1 Merge pull request #13514 from mvdbeek/support_preload 
[22.01] Support ``--preload`` and worker_id for server processes
 2022-03-14 10:24:29 -04:00
mvdbeek 4bb6802d31 Return actual tool id instead of specified tool id in step 
We do also return the version changes in the module, so this should be
fine. Fixes https://github.com/galaxyproject/galaxy/issues/13524.
 2022-03-14 13:37:50 +01:00
Nicola Soranzo a6b1238be7 Fix CondaSearch to use conda from PATH and CondaContext.exec_search() 
The `conda` package on PyPI is severely outdated and unmaintained, and
the output of `run_command("search", ...)` did not parse correctly.

Fix broken `test_conda_search` unit test.
 2022-03-13 20:34:40 +00:00
Nicola Soranzo dabc6f6389 Add exec_search() method to CondaContext 
Rework `best_search_result()` and `CondaInDockerContext` to use it.
 2022-03-13 20:34:39 +00:00
Nicola Soranzo dbf7ac364a Check GitHub API rate limit in GitHubSearch. Deprecate get_json() search 
Follow-up on https://github.com/galaxyproject/galaxy/pull/13509 .
 2022-03-13 20:34:31 +00:00
mvdbeek 0f65081127 Rebuild galaxy.yml.sample 2022-03-13 16:44:35 +01:00
mvdbeek 07a763eede Include gravity sample schema in galaxy.yml.sample 2022-03-13 16:44:11 +01:00
galaxybot 74c531135e Update Python dependencies 2022-03-12 03:11:18 +00:00
Sergey Golitsynskiy 41a60c7a2a Add link to issue to error message 2022-03-11 12:00:04 -05:00
Marius van den Beek 63ab54651a Merge pull request #13513 from ic4f/dev_alembic20_rebase2_1 
Reorganized alembic branch
 2022-03-11 09:38:26 +01:00
Sergey Golitsynskiy 44d245f820 Improve error message when SA Migrate version is incorrect 
See inline comment ("version too old" is misleading if the incorrect
version is more recent than what the system expects).
 2022-03-11 00:53:49 -05:00
mvdbeek c523529411 Revert "Merge pull request #13285 from mvdbeek/null_text_values" 
This reverts commit 2549792d42, reversing
changes made to 0223188e59.

Fixes https://github.com/galaxyproject/galaxy/issues/13516, at the cost
of not respecting required text parameters.
 2022-03-10 20:56:20 +01:00
Marius van den BeekandNicola Soranzo c98e13befe Skip unnecessary list comprehension 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-03-10 19:41:03 +01:00
Sergey Golitsynskiy 84d5787aa2 Drop new migration script (see note) 
This will be added as an alembic revision as a separate commit
 2022-03-10 12:32:46 -05:00
Sergey Golitsynskiy 1421e7ad7b Apply formatting 2022-03-10 12:25:21 -05:00
Sergey Golitsynskiy 7535159289 Manually re-apply edits to app (from config), mapping 2022-03-10 12:25:15 -05:00
mvdbeek d655aa3e8a Replicate log_startup for GunicornApplicationStack 
Not loving it, but fixes https://github.com/galaxyproject/galaxy/issues/13515
 2022-03-10 17:15:37 +01:00
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
John Chilton 400c4ee465 Improved API exceptions for serializing views. 2022-03-10 10:51:30 -05:00
John Chilton 62dae772ec Add model stores manager. 
Reused for a bunch of things in the deferred data branch but it does simplify the tasks file for now and move more logic into managers - which I think is a better place.
 2022-03-10 10:51:28 -05:00
John Chilton 3bb3e90e5d Rework page creation in populators. 2022-03-10 10:51:27 -05:00
Sergey Golitsynskiy 67a4fa83b2 Remove vault table revision (part of 22.01) 2022-03-09 18:41:50 -05:00
Sergey Golitsynskiy 90d8140524 Change handling of unrecognized revisions; improve log messages 2022-03-09 18:41:50 -05:00
Sergey Golitsynskiy db07621925 One engine for 2 dbs logically equiv to 2 refs to same engine 2022-03-09 18:41:50 -05:00
Sergey Golitsynskiy 1a1ae8d3d2 Adapt manage_db.py for usegalaxy playbook; add tests 2022-03-09 18:41:50 -05:00
Sergey Golitsynskiy 3f8a223eb1 Change latest db version to 180 2022-03-09 18:41:50 -05:00
Sergey Golitsynskiy c8ce9c4fbb Remove old migrate files (fix rebase) 2022-03-09 18:41:50 -05:00
Sergey Golitsynskiy 92b2e67145 Apply black, isort (squashed) 
Squashed:
- pick 8a26c3c7af Fix import order in config
- squash ebe36de5fc Apply black, isort
 2022-03-09 18:41:49 -05:00
Sergey Golitsynskiy d2f766b311 Check for table existence for vault (see note) 
This was the last revision to the database that was handled with
SQLAlchemy Migrate prior to the move to Alembic (db version 180).
However, it was added to the dev branch after 21.09 was released, but
before 22.01. Therefore, this table should be created when upgrading
from 21.09, but not from dev.
 2022-03-09 18:41:03 -05:00
Sergey Golitsynskiy f32b220cf8 Modify behavior of legacy wrapper, add tests, refactor 
If the database is combined, running `./manage_db.sh upgrade` should upgrade
BOTH models: gxy and tsi. However, if tsi uses a separate database, only
the galaxy model should be updated.

Also, see this for context: https://github.com/galaxyproject/galaxy/pull/13108#discussion_r789108576

See inline comments for more details.

The new tests are examples of new behavior.

All refactoring is directly related to the changes in this commit.
 2022-03-09 18:41:03 -05:00
Sergey Golitsynskiy 337992e573 Update README: rename script, add legacy script, simplify upgrade steps. 2022-03-09 18:41:03 -05:00
Sergey Golitsynskiy 537cf5d2aa Preserve manage_db.sh, but do not hide alembic 
- Preserves usage of legacy script while not hiding the Alembic script.
    (see manage_db.sh and run_alembic.sh)
- Adds documentation (see top of script files)
- Includes misc. relevant refactorings
- Includes unit tests for testing legacy script handling
 2022-03-09 18:41:03 -05:00