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5591 Commits
Author SHA1 Message Date
mvdbeek 191a4b848e Merge branch 'release_21.01' into release_21.05 2021-05-11 18:28:04 +02:00
mvdbeek 2552ab47f1 Use f-strings in forward-merged code 2021-05-11 18:09:53 +02:00
mvdbeek 41aca51d2b Merge branch 'release_20.09' into release_21.01 2021-05-11 18:01:46 +02:00
Marius van den BeekandNicola Soranzo 8acf0d16a8 Use different string formatting option 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-05-11 14:57:21 +02:00
Marius van den BeekandNicola Soranzo d69a79f29e Use generator expression instead of list comprehension 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-05-11 14:56:50 +02:00
mvdbeek 75f5877951 Log exceptions IT port monitor fails and stop job 
That should make it significantly easier to debug issues when the
container monitor dies unexpectedly (which I sort of expect in the
future given that we parse output from the docker CLI).
 2021-05-10 17:43:46 +02:00
Marius van den Beek ef3c7e6615 Merge pull request #11904 from jmchilton/url_for 
Abstraction for fetching qualified app URL across webapp types
 2021-05-04 13:36:02 +02:00
Marius van den Beek eb3f3c816f Merge pull request #11832 from qiagu/dynamic_options 
Make tool parameter options capable of referring to metadata file
 2021-05-04 09:49:35 +02:00
John Chilton ad6b1ccb8c Merge pull request #11873 from mvdbeek/fix_file_source_uploads 
Fix "Choose remote files" uploads
 2021-05-03 20:54:39 -04:00
Marius van den Beek 9c69ab331e Merge pull request #11877 from jmchilton/rev_mypy 
Rev mypy.
 2021-05-03 19:03:42 +02:00
John Chilton c3b7f92b0e Fix url_for branch for actual test case. 2021-05-03 11:36:44 -04:00
John Chilton 7200a3920a Abstraction across app types for fetching qualified URL. 2021-05-03 11:36:44 -04:00
John Chilton 43941dedac Test qualified url_for. 2021-05-03 11:36:44 -04:00
mvdbeek 2edb301654 Move shared test setup to lib/galaxy_test/driver/integration_setup.py 2021-05-03 16:18:21 +02:00
Marius van den Beek 5e701b2bca Merge pull request #11911 from cat-bro/galaxy_interactor_encode_test_data_payload 
fix GalaxyInteractorApi get_tool_tests
 2021-05-03 12:25:12 +02:00
cat-bro 58f767d296 breaking test for GalaxyInteractorApi get_tool_tests 2021-04-29 23:50:12 +10:00
John Chilton 2a0474730b Rev mypy. 2021-04-23 14:49:53 -04:00
mvdbeek 35b200cd5a Add selenium test for file_source upload 2021-04-23 15:31:42 +02:00
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
qiagu b48e100216 Fix linter test 2021-04-20 12:58:04 -07:00
qiagu 5a787135fd Fix test error 2021-04-20 10:49:38 -07:00
guerler a10b3a2fab Add history_link markdown basic test case 2021-04-19 21:43:20 -04:00
qiagu 47c26f1deb Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dynamic_options 2021-04-19 15:27:01 -07:00
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
qiagu 02d6354e89 Merge branch 'dev' into dynamic_options 2021-04-19 10:09:18 -07:00
Matthias Bernt 8852d543cc fix test 
Despite lines in 4.maf like

```
e echTel1.scaffold_309554      3896 34801 +     42008 I
```

echTel1 seems not to be in the metadata table.

So I have chosen another one.
 2021-04-19 11:06:40 +02:00
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
Matthias Bernt 1a70bf5093 debug: switch test files cont. 2021-04-18 21:48:14 +02:00
Matthias Bernt 84fceaab6a debug: switch test files 2021-04-18 19:27:46 +02:00
Matthias Bernt 243091f046 use a different file for test 
to check if options are added
 2021-04-18 17:29:18 +02:00
Matthias Bernt bda13631d5 select linters: allow option definition by filters 
- options can be added by add_value (but this works apparently only
  if there are already values)
- data_meta is also documented to be able to generate values
 2021-04-18 17:20:46 +02:00
Matthias Bernt 29c5468f02 add tests for new linters 2021-04-17 13:34:25 +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
qiagu 3c05f0b85b Add test for options from metadata file of dataset_collection 2021-04-15 15:36:26 -07:00
qiagu 688f024193 Merge branch 'dev' into dynamic_options 2021-04-15 14:08:53 -07:00
Qiang GuandM Bernt 6645b4093b Update test/functional/tools/options_from_metadata_file.xml 
Co-authored-by: M Bernt <m.bernt@ufz.de>
 2021-04-15 13:56:08 -07:00
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
qiagu 6844607088 Fix tool styling 2021-04-13 20:21:24 -07:00
qiagu ca4e7ea83b Add simple doc for usage of meta_file_key 2021-04-13 19:43:11 -07:00
qiagu 455b838bd4 Make test tool for meta_file_key 2021-04-13 19:23:59 -07:00
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