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Commit Graph
6713 Commits
Author SHA1 Message Date
Nicola Soranzo 9cd73e20c9 Fix typo in f-string 2022-05-06 13:29:13 +01:00
Nicola Soranzo 6ab35f4817 Fix error message from `ExpressionValidator` 
when the expression could not be evaluated. Previously the message
would be:
```
Validator '<code object <module> at 0x7fcfdf6737c0, file "<string>", line 1>' could not be evaluated on '%s'
```

Also, move doc tests to unit tests.
 2022-05-06 13:29:13 +01:00
Marius van den Beek 131e1d464d Merge pull request #13641 from simonbray/wf-step-index 
Expose input step order and rework calculation of node position in the workflow editor
 2022-05-06 12:37:52 +02:00
Marius van den Beek 0e96433199 Merge pull request #13833 from jdavcs/dev_dataset_declarative 
Map Dataset declaratively
 2022-05-05 17:06:33 +02:00
Simon Bray 77012ce7f5 Merge remote-tracking branch 'upstream/dev' into wf-step-index 2022-05-05 16:01:36 +02:00
John Chilton b84aec9ec3 Improved typing of Galaxy model store related stuff. 2022-05-04 12:11:17 -04:00
John Chilton 758f47343c Improved typing for output collect and its ilk... 2022-05-02 11:17:22 -04:00
John Chilton 5cd81741a7 Allow quoting in search library for exact matches (e.g. filtering on specific tags/tools). 2022-04-30 20:10:52 -04:00
John Chilton da8fe33e9a Typing and testing for baseline galaxy.util.search functionality. 2022-04-30 20:10:52 -04:00
Sergey Golitsynskiy 34e8b182d4 Map Dataset declaratively 2022-04-29 13:37:32 -04:00
Björn Grüning 131e27136e Merge pull request #13794 from jmchilton/selenium_fix_99 
Potential fix for certain kind of transient Selenium library errors.
 2022-04-26 21:02:16 +02:00
John Chilton 575a0b4476 Merge pull request #13588 from ic4f/dev_model_tests2 
Refactor model/mapping/migrations unit testing infrastructure
 2022-04-26 10:05:44 -04:00
John Chilton f315a7db5c Potential fix for certain kind of transient Selenium library errors. 
select_add_items_permission_option failed unexpectedly in a Selenium test https://github.com/galaxyproject/galaxy/runs/6130989843?check_suite_focus=true with this in the stack trace:

```
>       raise exception_class(message, screen, stacktrace)
E       selenium.common.exceptions.ElementClickInterceptedException: Message: element click intercepted: Element <ul class="multiselect__content" style="display: inline-block;">...</ul> is not clickable at point (324, 547). Other element would receive the click: <div data-v-5b55ce08="" class="col">...</div>
E         (Session info: headless chrome=100.0.4896.75)
```

I think this means something was preventing it from being clickable - presumably a toastr message or something. This attempts to fix that issue two ways - by making the retry dec
orator a little more aggressive and by ensuring the element is in fact clickable before clicking it.
 2022-04-26 09:50:53 -04:00
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 c1b3e56f64 Wait for datasets / collections 2022-04-26 11:12:37 +02:00
mvdbeek 9e091dc6a0 Don't do extra json.dumps of targets 2022-04-25 18:28:01 +02:00
mvdbeek 55e22ca8a9 Use separate model for fetch data form payload 2022-04-25 18:28:01 +02:00
mvdbeek 704af8fc59 Fix collection_creates_dynamic_list_of_pairs test 
The upload1 tool would have created a dataset in the history that would
have become auto-selected ... which is of course a bug when running
tools via the API, xref
https://github.com/galaxyproject/galaxy/issues/13799.
 2022-04-23 12:16:42 +02:00
mvdbeek 9abbac0180 Switch most tests to use `__DATA_FETCH__ instead of upload1` 2022-04-23 12:05:54 +02:00
mvdbeek 02ac5b3c9e Add FastAPI route for tools/fetch 2022-04-23 12:01:32 +02:00
Nicola Soranzo d5893b600b Merge pull request #13195 from bernt-matthias/topic/min-length 
Fix a bug in username minimum length transformation and set minimum length to 1
 2022-04-23 09:57:22 +01:00
Nicola Soranzo 6da2f0e98c Merge branch 'release_22.01' into dev 2022-04-22 18:23:33 +01:00
mvdbeek 1d5a52ec05 Schema for fetch_data 2022-04-22 17:08:41 +02:00
Marius van den Beek cf46c5c1fa Merge pull request #13777 from guerler/fix_tour_tests 
Adjust tours and tour tests to new history
 2022-04-22 15:38:27 +02:00
Marius van den Beek 46eb2e6b83 Merge pull request #13602 from bernt-matthias/fix/configfilename 
Fix config file generation if name and filename are given
 2022-04-22 12:31:12 +02:00
Martin Cech 5aad013172 Merge pull request #13718 from mvdbeek/fix_quay_io_cache_use 
[22.01] Fix persistent mulled cache unused for repo_has_name
 2022-04-22 10:45:55 +02:00
Marius van den Beek ed5dd149c4 Merge pull request #13755 from bernt-matthias/fix_mulled_conda 
Respect conda channels in mulled docker container building
 2022-04-22 10:43:31 +02:00
David López e788c3073c Merge pull request #13779 from jmchilton/sharing_error_handling 
Fixes for sharing component error handling.
 2022-04-22 10:39:41 +02:00
Nicola Soranzo 2f0f4c7e08 Replace 2 uses of deprecated `imp` module 
Also:
- Move doctests for `in_directory()` function to unit tests, add test
  for `local_path_module` parameter to exercise the posixpath/ntpath
  import code.
 2022-04-21 19:53:35 +01:00
Matthias Bernt cfc2043e00 fix black formatting 2022-04-21 16:58:58 +02:00
John Chilton 59038bc4bf Add navigates_galaxy.py convention for jumping to URLs not via navigating the landing to them. 2022-04-21 10:02:11 -04:00
M Bernt 4243ae86ad Merge branch 'dev' into topic/min-length 2022-04-21 11:26:51 +02:00
Matthias Bernt ad70b9bc4a fix config file generation 
always create the config file in `job_directory/configs/` and
if `filename` is given create a symlink to the actual config file

fixes https://github.com/galaxyproject/galaxy/issues/13586
 2022-04-21 11:15:07 +02:00
guerler 1c643a63ff Adjust tours and tour tests to new history, remove final occurance of use_legacy_history 2022-04-21 04:20:33 -04:00
Sergey Golitsynskiy cc1c2e4b94 Enable postgresql testing for new annotations module 2022-04-20 22:16:40 -04:00
Sergey Golitsynskiy e9eb6c1500 Proof of concept: replace annotation mapping tests 2022-04-20 18:14:43 -04:00
Sergey Golitsynskiy 254830a33b Add fixture for WorkflowStepAnnotationAssociation 2022-04-20 17:48:37 -04:00
Sergey Golitsynskiy ed2798e044 Fix module path for remote unit tests 2022-04-20 17:03:03 -04:00
Sergey Golitsynskiy 52bb6c90e6 Fix linting 2022-04-20 16:23:05 -04:00
Sergey Golitsynskiy 95a4fd5667 Use plugins instead of importing fixtures directly 
Also handle setting the fully qualified module name depending on wht's
the cwd from which the test is executed.
 2022-04-20 15:50:52 -04:00
Matthias Bernt 6f7a609665 explicitly set conda channels for CondaInDockerContext 2022-04-20 18:15:40 +02:00
Sergey Golitsynskiy c9e3d340f6 Move tmp_dir fixture one level up 
Otherwise url_factory is not usable outside of migrations
 2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy d091e5d390 Remove duplicate testing utils from TS tests 2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy 1228bfa769 Refactor code for dropping postgres 2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy 495dd6daaf Move last context managers out of migrations 2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy c3059de4a5 Move disposing_engine out of migrations 2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy eec0a87028 Move url_factory out of migrations 
Make available for use in other testing contexts.
 2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy 476da34b7a Move test revisions into testing_utils 2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy f5c962d8d7 Move common.py to testing_utils 2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy d2ecb7ee68 Fix linting (unused import) 2022-04-20 10:28:03 -04:00