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5557 Commits
Author SHA1 Message Date
Dannon a277c2421a Merge pull request #11789 from mvdbeek/history_export_task 
Run history export setup via celery, if configured
 2021-04-20 20:55:06 -04:00
Dannon ddbc67d83e Merge pull request #11863 from guerler/import_history 
Allow importing histories through pages / reports
 2021-04-20 20:46:31 -04:00
guerler a10b3a2fab Add history_link markdown basic test case 2021-04-19 21:43:20 -04:00
John Chilton d50579d37f Merge pull request #11849 from mvdbeek/restore_update_time_query 
Fix collection state updates by setting collection update time
 2021-04-19 14:41:39 -04:00
Marius van den Beek 87a71e061f Merge pull request #11856 from davelopez/unify_security_decode_id_exceptions 
Unify security decode id exceptions
 2021-04-19 09:15:37 +02:00
Marius van den Beek c8f881f0ba Merge pull request #11852 from jmchilton/less_transfer 
Test a better Pulsar configuration for extended metadata.
 2021-04-17 09:24:40 +02:00
mvdbeek a3f59a25ef Use SKIP LOCKED only if database supports it 2021-04-16 16:27:39 +02:00
davelopez 62de18fc35 Fix HistoryDeserializerTestCase::test_sharable to use expected exception 2021-04-16 15:35:12 +02:00
John Chilton cc41f30af6 Better extended metadata configuration for Pulsar (don't copy outputs) 2021-04-15 15:01:28 -04:00
John Chilton 289862d384 Merge pull request #11716 from OlegZharkov/library-collections-test 
[Selenium] Library collections export
 2021-04-15 10:31:16 -04:00
John Chilton 59fac33d06 Separate tests for "remote" and "remote + extended" metadata. 
We should be testing both these scenarios and ensure they both continue to work.
 2021-04-14 13:21:15 -04:00
mvdbeek 64b6f7fa95 Add export_history task 
Which prepares the export model store.
 2021-04-14 17:42:07 +02:00
Marius van den Beek b7078f51fa Merge pull request #11788 from jmchilton/pulsar_extended_metadata 
Fixes for extended metadata working with Pulsar.
 2021-04-13 18:39:45 +02:00
mvdbeek bb83f97af5 Move get_preferred_handler_assignment_method into ApplicationStack 
and simplify _set_default_job_handler_assignment_methods
 2021-04-13 10:13:42 +02:00
mvdbeek 333ebb75d9 Fix workflow_handler_configuration tests 2021-04-13 10:13:42 +02:00
mvdbeek f49ce548e6 Run kubernetes staging test against uvicorn 2021-04-13 10:13:42 +02:00
mvdbeek 1507cc80f4 Add generic GALAXY_WEB_PORT variable to infrastructure_url parsing 2021-04-13 10:13:42 +02:00
mvdbeek d0414eee5b Adjust unit tests for new setup 2021-04-13 10:13:42 +02:00
John Chilton b840092d2b Make tests green by dropping job_properties since it doesn't work yet. 2021-04-09 16:24:32 -04:00
John Chilton c502649104 Get extended metadata working with Pulsar. 
Work started in https://github.com/galaxyproject/pulsar/pull/192.
 2021-04-09 16:24:22 -04:00
Nicola Soranzo d9188a4c3e Merge pull request #11111 from bernt-matthias/topic/cheetah-qualified 2021-04-08 02:40:06 +01:00
Nicola Soranzo 7d32450ba8 Merge pull request #11727 from bernt-matthias/topic/lint-checkboxes 
lint for checkboxes select
 2021-04-07 23:19:18 +01:00
M BerntandNicola Soranzo 24ec1d603f Update test/unit/tool_util/test_tool_linters.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-04-07 22:23:53 +02:00
M BerntandNicola Soranzo 47b6780fb9 fix typo 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-04-07 19:38:25 +02:00
Matthias Bernt 5034d6dd62 test qualified and unqualified access 2021-04-07 17:39:48 +02:00
John Chilton 66c1132ec0 Merge pull request #11307 from bernt-matthias/topic/recurse-dirs 
ignore subdirectories if recurse is false
 2021-04-07 10:06:52 -04:00
Oleg Zharkov ee33b51ba4 implement export collection library->history 2021-04-07 16:03:53 +03:00
M Bernt 08fbff5844 tests for multiple value splitter 2021-04-06 18:32:19 +02:00
John Chilton 7773814c06 Merge pull request #11769 from davelopez/support_permissions_in_files_sources 
Support role and group permissions in file sources plugins
 2021-04-06 11:14:20 -04:00
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
davelopez e71b92a9f8 Add more tests for invalid expressions 2021-04-06 11:17:55 +02:00
davelopez f8ace37cb4 Add expression validation when the configuration is parsed. 
This will stop Galaxy from starting with an invalid expression defined in the configuration.
 2021-04-06 11:17:55 +02:00
davelopez 847db78aa1 Add test for using expression rules in posix file source 2021-04-06 11:17:55 +02:00
davelopez 03795b766e Add generic boolean expression evaluator + unit tests 2021-04-06 11:17:55 +02:00
davelopez 895c165414 Fix integration test failing by different response order 2021-04-06 11:17:55 +02:00
davelopez 6ef54d73c6 Add file sources access unit tests 2021-04-06 11:17:55 +02:00
davelopez 74ca28c3a8 Change requirement condition to both options. 
If the `requires_roles` and `requires_groups` options are defined, both must be satisfied.
 2021-04-06 11:17:55 +02:00
davelopez ed0af1aef1 Update integration tests 2021-04-06 11:17:55 +02:00
davelopez 7f23534461 Add integration tests. 
Basic tests for the new `requires_roles` and `requires_groups` settings for FileSources using the posix plugin.
 2021-04-06 11:17:55 +02:00
Sergey Golitsynskiy 179a6e4a17 Fix deprecated db urls in user config properties 2021-04-05 17:11:24 -04:00
Sergey Golitsynskiy be4429e4fb Replace: s/postgres/posgresql in db URLs 
Was deprecated in SQLAlchemy 1.3, removed in SQLAlchemy 1.4
https://docs.sqlalchemy.org/en/14/changelog/changelog_14.html#change-3687655465c25a39b968b4f5f6e9170b
https://github.com/sqlalchemy/sqlalchemy/issues/4643
 2021-04-05 15:02:26 -04:00
Nicola Soranzo 20a4bcd519 Use assertRaisesRegex() to fix new B017 linting errors 
Fix the following errors reported by flake8-bugbear 21.4.3:

B017 assertRaises(Exception): should be considered evil. It can lead to
your test passing even if the code being tested is never executed due to a
typo. Either assert for a more specific exception (builtin or custom), use
assertRaisesRegex, or use the context manager form of assertRaises.
 2021-04-03 20:09:02 +01:00
Marius van den Beek 0733ba3ddb Merge pull request #10222 from ic4f/dev_state5 
Store job_id on Dataset table.
 2021-04-02 13:29:47 +02:00
Sergey Golitsynskiy 349c0502ab Add unit test for testing dataset/job relationship 2021-04-01 17:18:44 -04:00
mvdbeek aa6e1dcc05 Merge branch 'release_21.01' into dev 2021-04-01 16:52:11 +02:00
John Chilton a6f3b255cb Merge pull request #11764 from mvdbeek/fix_format_input_implicit_conversion 
[21.01] Fix format="input" with implicit conversions
 2021-04-01 10:45:55 -04:00
almahmoud 619f1e7a11 galaxy.webapps.tool_shed to webapp.tool_shed 2021-03-31 17:37:36 -04:00
mvdbeek 7eb853d703 Fix format="input" with implicit conversions 
where the implicit converter uses galaxy.json.

Add test, fix fix
 2021-03-31 22:06:39 +02:00
Anthony Bretaudeau b5e2ea9877 try something else 2021-03-31 13:42:17 +02:00
mvdbeek c8c08ca84c Merge branch 'release_21.01' into dev 2021-03-31 12:09:44 +02:00