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4801 Commits
Author SHA1 Message Date
Nicola Soranzo 8ffd6d76a9 Fix test_run_simple() test broken on Python 2 by virtualenv 20.0.5 
xref. https://github.com/pypa/virtualenv/issues/1670
 2020-02-28 04:38:18 +00:00
Sergey Golitsynskiy 2f264977f1 Make mutable_config_dir configurable + rename 
Also: do not run integration test on managed_config_dir: it depends on
config_dir, which is modified for testing.

Note: replaces previous commit from 9377
 2020-02-25 22:21:42 -05:00
Nicola Soranzo c9f806ffaa Merge branch 'release_20.01' into dev 2020-02-23 18:17:36 +00:00
Marius van den Beek e75163e10e Merge pull request #9279 from bernt-matthias/topic/inputs-multiple-test 
extend config file inputs tests
 2020-02-20 16:09:59 +01:00
mvdbeek cc0a71bc14 Make dataset discovery respect final_job_state 
Fixes https://github.com/galaxyproject/galaxy/issues/9394
 2020-02-20 15:31:49 +01:00
Nicola Soranzo 739ab59eaa Merge branch 'release_20.01' into dev 2020-02-20 00:23:19 +00:00
John Chilton 04b21a06ff Allow remote container port monitoring for ITs. 
Tested with Pulsar but not sure there is anything Pulsar specific about the implementation - simply set container_monitor_result on the job destination to 'callback' (instead of implicit default of 'file'). This causes the monitor.py script to hit a new job_ports API (that mirrors job_files API) and uses the same security mechanism (per-job keys that are only active while the job is active).

PR contains fixes for embedded Pulsar configuration handling, embedded Pulsar under uwsgi, and the introduction of new feature that allows dynamic expansion of ``$UWSGI_PORT`` inside of galaxy_infrastructure_url.
 2020-02-19 09:53:10 -05:00
Nicola Soranzo d4662fd952 Merge branch 'release_20.01' into dev 2020-02-19 12:43:07 +00:00
Nicola Soranzo d40c5ec9f4 Merge branch 'release_19.09' into release_20.01 2020-02-19 12:32:07 +00:00
John Chilton 8e9d6e685e Merge pull request #9354 from mvdbeek/parent_instance_detached_again_3 
[19.09] Expunge tool shed repository objects, prevents ParentInstanceDetachedError
 2020-02-18 08:54:04 -05:00
Nicola Soranzo 4e5ec84ff7 Skip `test_config_option[build_sites_config_file]` 
Fix:

```
_________________ test_config_option[build_sites_config_file] __________________

data = OptionData(key='build_sites_config_file', expected='config/build_sites.yml.sample', loaded='/home/runner/work/galaxy/galaxy root/lib/galaxy/config/sample/build_sites.yml')
driver = <galaxy_test.driver.driver_util.GalaxyTestDriver object at 0x7f0accbf93d0>

    @pytest.mark.parametrize('data', get_config_data(), ids=get_key)
    def test_config_option(data, driver):
>       assert data.expected == data.loaded
E       AssertionError: assert 'config/build...es.yml.sample' == '/home/runner/...ild_sites.yml'
E         - config/build_sites.yml.sample
E         + /home/runner/work/galaxy/galaxy root/lib/galaxy/config/sample/build_sites.yml
```

from https://github.com/galaxyproject/galaxy/pull/9353/checks?check_run_id=438827128
 2020-02-13 09:49:51 +00:00
Nicola Soranzo 6f0219e883 Merge branch 'release_20.01' into dev 2020-02-13 02:12:03 +00:00
Nicola Soranzo f16e5cb712 Merge branch 'release_19.09' into release_20.01 2020-02-13 02:11:15 +00:00
mvdbeek e1780cb20a Move logic of whether to load a config into can_load_config_file and fix unit tests 2020-02-12 11:53:28 +01:00
Nicola Soranzo 1893157fb9 Skip `test_config_option[build_sites_config_file]` 
Fix:

```
_________________ test_config_option[build_sites_config_file] __________________

data = OptionData(key='build_sites_config_file', expected='config/build_sites.yml.sample', loaded='/home/runner/work/galaxy/galaxy root/lib/galaxy/config/sample/build_sites.yml')
driver = <galaxy_test.driver.driver_util.GalaxyTestDriver object at 0x7f0accbf93d0>

    @pytest.mark.parametrize('data', get_config_data(), ids=get_key)
    def test_config_option(data, driver):
>       assert data.expected == data.loaded
E       AssertionError: assert 'config/build...es.yml.sample' == '/home/runner/...ild_sites.yml'
E         - config/build_sites.yml.sample
E         + /home/runner/work/galaxy/galaxy root/lib/galaxy/config/sample/build_sites.yml
```

from https://github.com/galaxyproject/galaxy/pull/9353/checks?check_run_id=438827128
 2020-02-11 17:27:39 +00:00
mvdbeek 8a8c0990dd Give ToolShedRepositoryCache.rebuild its own session 2020-02-11 14:57:24 +01:00
mvdbeek f4e32636e1 Make sure tool dependency relationships are accessibly as well 2020-02-11 12:35:16 +01:00
mvdbeek 82a06af664 Explain why the test does what it does 2020-02-11 12:24:40 +01:00
mvdbeek 098419b9b4 Ensure repository metadata isn't kept in memory 2020-02-11 12:21:39 +01:00
mvdbeek 2a66a39ace Add test that should provoke https://github.com/galaxyproject/galaxy/issues/9074 2020-02-11 12:09:49 +01:00
Nicola Soranzo 0a26ed38b2 Merge branch 'release_20.01' into dev 2020-02-05 15:26:27 +00:00
Nate Coraor acb9bc1ea1 Merge pull request #9306 from dannon/blue-elimination 
Clean up old 'blue' style path, update documentation and samples
 2020-02-05 09:31:34 -05:00
Nicola Soranzo 1dc1e5f219 Python3: unicodify the output of `subprocess.check_output()` 
By default it's a bytestring.

Also:
- don't use `shell=True`
- add a `splitlines()` forgotten in commit 670897ec5c
- raise exception instead of returning `error_info` in `docker_to_singularity()`
- use a random temp dir in `singularity_container_test()`
 2020-02-05 12:13:39 +00:00
Dannon 0045082085 Merge pull request #9299 from nsoranzo/update_contributing 
Update CONTRIBUTING.md
 2020-02-04 12:32:16 -05:00
Nicola SoranzoandDannon 2ad52474c5 Apply suggestions from code review 
Co-Authored-By: Dannon <dannon.baker@gmail.com>
 2020-02-04 15:28:26 +00:00
Dannon Baker f935c6206b Clean up old 'blue' style path, update documentation and samples to refer to plain old 'static' now. 2020-02-03 22:41:29 -05:00
Nicola Soranzo f32ece1e8d Faster and cleaner set creation 2020-02-03 15:42:09 +00:00
Nicola Soranzo 15a797c359 Update CONTRIBUTING.md 
- Update links
- Replace disappeared "Try Git" tutorial with Software Carpentry's one
- Include Python style guidelines and testing instructions from the Hub
 2020-02-03 14:14:45 +00:00
M Bernt 1f535a0779 remove remnant cat 2020-02-01 14:15:20 +01:00
M Bernt fcf5436717 column_param_configfile test: don't check json content 
dont compare the json file content but rely completely on the assertions on
the loaded json contents.

the json content test was superficial and did not work anymore since the order
of the keys differed. it worked before since the inputs contained only a
single key.
 2020-02-01 14:15:20 +01:00
M Bernt f25192b533 json configfiles: handle slect like data_column 
- in particular the case of an empty select did yield "None" before
  now its []
  Problem was that the ValueWrapper is not None if nothing is selected
- but also non empty selects were "option1,option2" now its
  ["option1","option2"]
- renamed variable value -> value_wrapper
 2020-02-01 14:15:20 +01:00
M Bernt 22a43aa5d8 extend config file inputs tests 
add cases for ooptional/multiple data/select inputs
 2020-02-01 14:15:20 +01:00
Sergey Golitsynskiy 5dc9fc680f Do not test config_dir default value 2020-01-30 17:08:27 -05:00
Dannon 299a729217 Merge pull request #9162 from machristie/idp-logout 
Add support for logging out of OIDC Identity Provider
 2020-01-28 19:56:02 -05:00
Dannon f94a5f5757 Merge pull request #9223 from nsoranzo/space_in_root_path 
Use a Galaxy root path with a space for integration tests
 2020-01-28 16:21:33 -05:00
Dannon Baker 947b9eca5b Merge remote-tracking branch 'upstream/dev' into idp-logout 2020-01-28 14:01:49 -05:00
Dannon Baker 13f4e1e3f1 Merge remote-tracking branch 'upstream/release_20.01' into dev 2020-01-28 13:24:09 -05:00
Dannon 8e16fcb4cc Merge pull request #9233 from dannon/external-auth-login-refinement 
[20.01] External auth login refinement
 2020-01-28 13:22:55 -05:00
Nicola Soranzo 80607164f4 Merge branch 'release_20.01' into dev 2020-01-24 17:13:06 +00:00
Nicola Soranzo 6fbe8c9031 Merge branch 'release_19.09' into release_20.01 2020-01-24 17:08:02 +00:00
Nicola Soranzo d67295162a Simplify and refactor 2020-01-23 21:57:54 +00:00
mvdbeek e227b1473f Fix unselected select parameter comparison to empty string 
`$wrapper == ""` and `$wrapper == "None"` had been valid ways
to check for unselected / optional select parameters.
This restores the `$wrapper == ""` form as used by gffcompare
https://github.com/galaxyproject/tools-iuc/blob/master/tools/gffcompare/gffcompare.xml#L41
 2020-01-23 19:24:52 +00:00
mvdbeek 5d379dc4a5 Fix unselected select parameter comparison to empty string 
`$wrapper == ""` and `$wrapper == "None"` had been valid ways
to check for unselected / optional select parameters.
This restores the `$wrapper == ""` form as used by gffcompare
https://github.com/galaxyproject/tools-iuc/blob/master/tools/gffcompare/gffcompare.xml#L41
 2020-01-23 16:02:56 +01:00
Nicola Soranzo f5cd88465e Make str.join()s more efficient 
by using generator expressions and tuples instead of lists.
 2020-01-23 11:06:32 +00:00
Dannon Baker f041eb2190 Fix lint in custos test 2020-01-22 16:43:42 -05:00
Dannon Baker 20a0777a25 Fix custos authnz tests. This should be swapped to use the standard mocked objects? 2020-01-22 11:44:27 -05:00
mvdbeek ceb214e1d9 Merge branch 'release_20.01' into dev 2020-01-22 16:14:30 +01:00
mvdbeek 83a8e1b7eb Test that working dir is intact on resubmission 2020-01-22 10:25:16 +01:00
M Bernt 5de147a181 re-remove the data input 2020-01-22 09:37:24 +01:00
M Bernt fff8d2ec7b inputs configfile: test for filename and data_style attributes 2020-01-22 09:37:19 +01:00