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6364 Commits
Author SHA1 Message Date
Marius van den Beek 2ecae06a83 Don't need to use a joinedload anymore 
The cache is only used on startup, not during dependency resolution.
Also rename _rebuild, since we only use it once now.
 2022-01-13 11:38:54 -05:00
mvdbeek 4b579c34c6 Limit lifetime of repository cache 2022-01-13 11:38:23 -05:00
Marius van den BeekandNicola Soranzo c19ef49957 Use different syntax 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-01-10 18:26:04 +01:00
mvdbeek 9ec830aad0 Don't template version command 2022-01-10 15:53:22 +01:00
mvdbeek 85d19caa16 Fix tell error 
Fixes https://github.com/galaxyproject/galaxy/issues/13090:
```
Sun, Dec 19 2021 9:01:49 pm | Traceback (most recent call last):
Sun, Dec 19 2021 9:01:49 pm | File "/galaxy/server/lib/galaxy/model/store/discover.py", line 203, in set_datasets_metadata
Sun, Dec 19 2021 9:01:49 pm | primary_data.set_meta()
Sun, Dec 19 2021 9:01:49 pm | File "/galaxy/server/lib/galaxy/model/__init__.py", line 3736, in set_meta
Sun, Dec 19 2021 9:01:49 pm | return self.datatype.set_meta(self, **kwd)
Sun, Dec 19 2021 9:01:49 pm | File "/galaxy/server/lib/galaxy/datatypes/interval.py", line 412, in set_meta
Sun, Dec 19 2021 9:01:49 pm | Tabular.set_meta(self, dataset, overwrite=overwrite, skip=i)
Sun, Dec 19 2021 9:01:49 pm | File "/galaxy/server/lib/galaxy/datatypes/tabular.py", line 404, in set_meta
Sun, Dec 19 2021 9:01:49 pm | if dataset_fh.tell() != dataset.get_size():
Sun, Dec 19 2021 9:01:49 pm | OSError: telling position disabled by next() call
```

Include a unit test that hits this error.
 2022-01-09 18:57:10 +01:00
mvdbeek 3cc94712a7 Fix header content-length, add test for send_file 
The uvicorn stack is a little less permissive and fails because
of the wrong content length.
 2022-01-05 19:36:57 +01:00
mvdbeek 43f9dbe760 Fix test_workflow_scheduling_options 2022-01-05 13:31:58 +01:00
mvdbeek 9a1b0753c5 Fix install_repo_request/delete_repo_request url 2022-01-05 13:31:55 +01:00
Sergey Golitsynskiy 7cc3a418ce Fix selenium test (bibtex rendering) 2022-01-03 16:18:20 -05:00
Marius van den Beek a3ac2ab611 Merge pull request #12940 from nuwang/vault_impl 
Vault abstraction for Galaxy
 2021-12-27 18:59:13 +01:00
Uehara.Keizo 992f18e127 Disable cleanup thread of cloud objectstore in set_metadata.py 
Apply the following fixes for s3.py to cloud.py
Be more explcit about starting cache monitor thread 494c15cb9d
Disable cleanup thread in set_metadata.py 6a56f3a5de
Fix S3 object store shutdown 7a63fd1db2
 2021-12-23 01:32:16 +00:00
Nuwan Goonasekera 01ca66fa98 Merge branch 'dev' into vault_impl 2021-12-22 23:55:37 +05:30
Marius van den Beek f041b13d36 Merge pull request #13048 from bernt-matthias/topic/fix-optional-column-select 
Fix dynamic optional + multiple select parameters: allow to select no option
 2021-12-21 10:13:57 +01:00
Marius van den Beek 9c92c1bde9 Merge pull request #12500 from nuwang/papercut_file_sources 
File sources for gdrive, gcs, onedata, basespace
 2021-12-21 10:08:24 +01:00
Nuwan Goonasekera 0924628d10 Refactor file source tests 2021-12-21 00:56:17 +05:30
Nuwan Goonasekera 5d72ddba11 Make gcsfs test optional 2021-12-21 00:43:39 +05:30
Nuwan GoonasekeraandEnis Afgan d4fe61a424 Update vault docs 
Co-authored-by: Enis Afgan <afgane@gmail.com>
 2021-12-20 18:40:20 +05:30
Nuwan Goonasekera be9f210901 Change vault api test case to integration test case and add missing conditional requirements 2021-12-20 18:23:00 +05:30
Nuwan GoonasekeraandMarius van den Beek 592603eb41 Add file upload test to vault 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2021-12-20 18:00:53 +05:30
Nuwan Goonasekera d1f804921c Add support for anonymous gcs file source access 2021-12-20 11:08:42 +05:30
Nuwan Goonasekera 15b7b88d8b Streamline access tokens needed to run gcsfs and gdrive storage tests 2021-12-20 11:08:42 +05:30
Nuwan Goonasekera cb22970426 Added support for illumina basespace filesource 2021-12-20 11:08:42 +05:30
Nuwan Goonasekera d1185fcd18 Added one data 2021-12-20 11:08:42 +05:30
Nuwan Goonasekera b8bdb6878e Added file source for google cloud storage 2021-12-20 11:08:42 +05:30
Nuwan Goonasekera 71862f540c Use separate env vars for each required param in google drive credentials 2021-12-20 11:08:42 +05:30
Nuwan Goonasekera ae8a832b7b Added unit tests for google drive file source 2021-12-20 11:08:42 +05:30
Uehara.Keizo 42b5971daf test: access_key and secket_key is optional in cloud objectstore(aws) 2021-12-19 09:35:39 +00:00
Matthias Bernt 34cd037df3 restructure tests 
- put them all in one test tool
- and add other select parameter types
 2021-12-16 09:55:12 +01:00
Matthias Bernt defbfbe8cf test for optional & multiple column select 
showing that its currently not possible to select no column

and the same for a select with dynamic options (wo legal_values)
that shows that it works here
 2021-12-16 09:55:12 +01:00
Simon Bray 505d94d21d add test for target_str_to_targets 2021-12-15 10:13:00 +01:00
Marius van den Beek a22184e7b2 Merge pull request #13044 from nsoranzo/fix_test_release.sh_on_dev 
Misc fixes - round 5
 2021-12-13 11:45:57 +01:00
Nicola Soranzo e7386d5230 Fix test_singularity_search unit test 
in a way that it doesn't break when a new version of the container
is released.
 2021-12-09 20:06:25 +00:00
Nicola Soranzo f7388c48fe Fix running test/release.sh on the dev branch 
Fix the following error:

```
# >>>> make_forks()
Cloning into '/tmp/galaxy_release_test_cQZHDb9B/work'...
done.
+ cd /tmp/galaxy_release_test_cQZHDb9B/work
+ git config user.name 'Test User'
+ git config user.email test@example.org
# Checking out ref '9bddbada0d3f7835ecafd12220a76dcfb6e3daca' as 'dev'
+ git checkout --no-track -b dev 9bddbada0d
fatal: A branch named 'dev' already exists.
```

Also:
- Add `log_exec` to a few git commands
 2021-12-09 19:46:40 +00:00
John Chilton 918302c23e Fix running pytest test/integration/test_remote_files.py::RemoteFilesIntegrationTestCase directly. 2021-12-08 11:33:13 -05:00
Nicola Soranzo 8c7477cab6 Test Galaxy release script 
xref. https://github.com/galaxyproject/galaxy/pull/11641#discussion_r764049621
 2021-12-08 10:43:09 +00:00
Nicola Soranzo 55b690ac99 Remove missing tool from functional test tool conf 2021-12-08 08:14:14 +00:00
Nicola Soranzo 9f89cd4d56 Fix errors in loading functional test tools 2021-12-08 08:14:13 +00:00
Nicola Soranzo 6c0036fb57 Fix wrong test tool file path 2021-12-08 08:14:13 +00:00
Nicola Soranzo cf1d036b1c Remove entry already in lib/galaxy/config/sample/tool_conf.xml.sample 
Cannot be imported from this directory any way.
 2021-12-08 08:14:12 +00:00
Nicola Soranzo 0bdc93a7cc Drop support for Python 3.6, add Python 3.10 2021-12-08 08:14:10 +00:00
John Chilton 44b8a45b34 Merge pull request #12996 from bernt-matthias/topic/is_multi_byte 
Remove is_multi_byte
 2021-12-06 16:17:45 -05:00
Marius van den Beek c00ed6f7a0 Merge pull request #13011 from nsoranzo/fix_job_env_vars 
Don't pass all Galaxy environment variables to jobs
 2021-12-06 20:37:53 +01:00
Nicola Soranzo eea0c8b673 Update pulsar-galaxy-lib to 0.14.13 and enable assert for EmbeddedPulsarDefaultJobEnvironmentIntegrationTestCase 2021-12-06 17:45:58 +00:00
Nicola Soranzo db566d4627 Check that jobs don't inherit env variables from Galaxy 
in integration tests.

Also:
- Merge `RunsEnvironmentJobs` class into
  `BaseJobEnvironmentIntegrationTestCase`
- Remove redundant checks in `DefaultJobEnvironmentIntegrationTestCase`
 2021-12-06 17:43:22 +00:00
Nicola Soranzo af46d773b5 Fix running test_config_defaults() unit tests locally 
If the `database/files/` directory exists, 2 unit tests would fail:

```
test/unit/config/test_config_values.py::test_config_defaults[file_path]

test_data = TestData(key='file_path', expected='/srv/galaxy/database/objects', loaded='/srv/galaxy/database/files')

    @pytest.mark.parametrize('test_data', get_config_data(), ids=get_key)
    def test_config_defaults(test_data):
>       assert test_data.expected == test_data.loaded
E       AssertionError: assert '/srv/galaxy/database/objects' == '/srv/galaxy/datatabase/files'
E         - /srv/galaxy/database/files
E         ?                      ^^^
E         + /srv/galaxy/database/objects
E         ?                      ^^^ ++
```

and

```
test_config_defaults[object_store_store_by]

test_data = TestData(key='object_store_store_by', expected='uuid', loaded='id')

    @pytest.mark.parametrize('test_data', get_config_data(), ids=get_key)
    def test_config_defaults(test_data):
>       assert test_data.expected == test_data.loaded
E       AssertionError: assert 'uuid' == 'id'
E         - id
E         + uuid
```

Also:
- Include tested option in assertion message
 2021-12-06 17:32:31 +00:00
Nicola Soranzo a0cf05ae71 Don't hide exception 2021-12-02 17:10:43 +00:00
Nuwan Goonasekera 7328ca0da9 Renamed vault migration script and some minor test fixes 2021-12-02 00:36:35 +05:30
Nuwan Goonasekera 85b6f6353b Fix vault table parent reference 2021-12-01 21:44:29 +05:30
Nuwan Goonasekera 7f663fad6e Add new secret type to user preferences that is not sent to client 2021-12-01 10:48:36 +05:30
Nuwan Goonasekera 2bc7bb45cf Added validation and prefixing decorators to vault 2021-12-01 07:00:18 +05:30