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Author SHA1 Message Date
Matthias Bernt 3dae54a672 make it a warning 2024-03-11 15:23:52 +01:00
Matthias Bernt 4e1a6d3b94 tool tinter: check for valid bio.tools entries 2024-03-11 11:47:55 +01:00
Dannon 9ddb6ad44a Merge pull request #17630 from nsoranzo/type_annots_cwl 
Type annotation and CWL-related improvements
 2024-03-07 15:44:04 -06:00
Nicola SoranzoandMarius van den Beek 1e95836f54 Split `raw_to_galaxy()` trans requirement to app and history 
Marginal improvement, but might be nice not to be bound to
`trans.history`.

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2024-03-07 13:17:17 +00:00
Nicola Soranzo 833ad0631b Fix `do_eval()` function 2024-03-07 13:10:43 +00:00
Nicola Soranzo 1406a6111f Type annotation improvements 2024-03-07 12:58:20 +00:00
Marius van den Beek bc0d075d55 Merge pull request #17601 from nsoranzo/type_annots 
Type annotation improvements
 2024-03-06 16:05:44 +01:00
mvdbeek 1d5fb96af6 Merge branch 'release_24.0' into dev 2024-03-06 14:59:18 +01:00
mvdbeek 8b44fde05f Merge branch 'release_23.2' into release_24.0 2024-03-06 14:58:57 +01:00
Marius van den Beek 6728e482bf Merge pull request #17598 from mvdbeek/fix_pending_rollback_error 
[23.2] Anticipate PendingRollbackError in ``check_database_connection``
 2024-03-06 14:58:32 +01:00
mvdbeek c346bc02a3 Merge branch 'release_24.0' into dev 2024-03-06 14:39:42 +01:00
mvdbeek d1e654c1f7 Merge branch 'release_23.2' into release_24.0 2024-03-06 14:34:13 +01:00
Marius van den Beek 98c80e7380 Merge pull request #17613 from nsoranzo/release_23.2_get_or_create_default_history_twice 
[23.2] Don't call ``get_or_create_default_history()`` twice for invalidated sessions
 2024-03-06 14:25:03 +01:00
Nicola Soranzo fac8eedaf4 Add `DatasetCollectionElementWrapper` type alias 2024-03-06 12:52:46 +00:00
Nicola SoranzoandDavid López 05b467d5da Remove unnecessary conversion to str 
Co-authored-by: David López <46503462+davelopez@users.noreply.github.com>
 2024-03-06 12:52:45 +00:00
Nicola Soranzo 5cadcebd7f Remove unneeded and broken function 
since commit 4c7d6805e7 .
 2024-03-06 12:52:44 +00:00
Nicola Soranzo 0e1eb86d50 Remove unnecessary methods 2024-03-06 12:52:43 +00:00
Nicola Soranzo 159cb46c45 Add/fix type annotations 2024-03-06 12:52:42 +00:00
Dannon 88b5e657b2 Merge pull request #17607 from nsoranzo/unpin_social-auth-core 
Unpin social-auth-core dependency
 2024-03-06 05:58:03 -06:00
Nicola Soranzo 75f0618141 Merge branch 'release_24.0' into dev 2024-03-06 10:15:01 +00:00
Nicola Soranzo 3a8a124ee1 Merge pull request #17612 from nsoranzo/release_24.0_fix_test_oidc_login_existing_user 
[24.0] Fix ``test_oidc_login_existing_user`` test
 2024-03-06 10:10:51 +00:00
Nicola SoranzoandNuwan Goonasekera 11312a7c5d Add comment 
Co-authored-by: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
 2024-03-06 07:44:59 +00:00
Nicola Soranzo 7ffc2b75ce Don't call `get_or_create_default_history()` twice for invalidated sessions 2024-03-06 02:02:22 +00:00
Nicola Soranzo 0bad72a1b6 Fix `test_oidc_login_existing_user` test 
Fix the following error:

```
self = <test_auth_oidc.TestGalaxyOIDCLoginIntegration object at 0x7f00ca129150>

    def test_oidc_login_existing_user(self):
        ...
        _, response = self._login_via_keycloak("gxyuser_existing", KEYCLOAK_TEST_PASSWORD, save_cookies=True)

        # Should prompt user to associate accounts
        parsed_url = parse.urlparse(response.url)
        provider = parse.parse_qs(parsed_url.query)["connect_external_provider"][0]
        assert "keycloak" == provider
        response = self._get("users/current")
>       self._assert_status_code_is(response, 400)

test/integration/oidc/test_auth_oidc.py:229:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
lib/galaxy_test/base/api.py:199: in _assert_status_code_is
    assert_status_code_is(response, expected_status_code)
lib/galaxy_test/base/api_asserts.py:21: in assert_status_code_is
    _report_status_code_error(response, expected_status_code, failure_message)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

response = <Response [200]>, expected_status_code = 400, failure_message = None

    def _report_status_code_error(
        response: Response, expected_status_code: Union[str, int], failure_message: Optional[str]
    ):
        try:
            body = response.json()
        except Exception:
            body = f"INVALID JSON RESPONSE <{response.text}>"
        assertion_message = "Request status code (%d) was not expected value %s. Body was %s" % (response.status_code, expected_status_code, body)
        if failure_message:
            assertion_message = f"{failure_message}. {assertion_message}"
>       raise AssertionError(assertion_message)
E       AssertionError: Request status code (200) was not expected value 400. Body was {'total_disk_usage': 0.0, 'nice_total_disk_usage': '0 bytes', 'quota_percent': None}

lib/galaxy_test/base/api_asserts.py:48: AssertionError
```

This broke when commit 85630e2ca9 was
merged forward because now that the failed keycloak login session
still gets a history, this check

```
        if not trans.user and not trans.history:
            # Can't return info about this user, may not have a history yet.
            # return {}
            raise glx_exceptions.MessageException(err_msg="The user has no history, which should always be the case.")
```

in `_anon_user_api_value()` inside `lib/galaxy/webapps/galaxy/services/users.py`
does not raise the exception any more.
 2024-03-06 01:49:00 +00:00
John Davis 149e281a4c session may be a scoped_session and may not have a transaction 2024-03-05 17:18:01 -05:00
John Davis fb89a2651b Explicitly check for transaction state 2024-03-05 16:01:19 -05:00
John Davis 5e05e00656 Merge pull request #17016 from bernt-matthias/topic/stdio-regex-extend 
[24.0] Extend regex groups in stdio regex matches
 2024-03-05 14:32:57 -05:00
John Davis 0739b136e3 Fix client linting 2024-03-05 14:30:12 -05:00
Nicola Soranzo e4aae9407f Unpin social-auth-core dependency 
Needed to drop abandoned python-jose, which in turn depends on ecdsa,
a library that is not safe against side-channel attacks, xref.:

https://github.com/tlsfuzzer/python-ecdsa/security/advisories/GHSA-wj6h-64fc-37mp
 2024-03-05 18:12:33 +00:00
mvdbeek 184d880b11 Merge branch 'release_24.0' into dev 2024-03-05 17:05:06 +01:00
John DavisandM Bernt 415f419404 Update lib/galaxy/tool_util/xsd/galaxy.xsd 
Co-authored-by: M Bernt <m.bernt@ufz.de>
 2024-03-05 10:39:22 -05:00
mvdbeek fde1ec3543 Merge branch 'release_23.2' into release_24.0 2024-03-05 16:33:16 +01:00
Marius van den Beek 4752af0443 Merge pull request #17597 from mvdbeek/fix_tool_shed_tests 
[23.2] Fix tool shed webapp
 2024-03-05 16:32:36 +01:00
Marius van den Beek eeb2d04c78 Merge pull request #16885 from bernt-matthias/topic/dynamic-multiple 
Add test and doc showing how dynamic selects are used
 2024-03-05 16:25:14 +01:00
Marius van den Beek b7c14c6559 Merge pull request #17294 from lldelisle/filter_paused 
[24.0] Add ``__KEEP_SUCCESS_DATASETS__``
 2024-03-05 16:18:20 +01:00
Dannon fb30ddf12a Merge pull request #17125 from galaxyproject/dependabot/npm_and_yarn/client/yaml-2.3.4 
Bump yaml from 2.1.1 to 2.3.4 in /client
 2024-03-05 09:17:38 -06:00
Dannon 95eabbfc92 Merge pull request #17492 from bernt-matthias/topic/tabular-blurp 
Better display of estimated line numbers and add number of columns for tabular
 2024-03-05 09:14:05 -06:00
John Chilton ea359c36b4 Links to invocations. (by John Chilton via Michelle Savage Vue-component upgrade) 
Upgraded component to Vue 3. Extra space removed.
Remove index enumeration and indentation; separate multiple errors with border line instead. Prevent metadata from printing when there is no value.
Rebased and edited/removed accidental 'merge conflict markers' in file
 2024-03-05 10:13:42 -05:00
Marius van den Beek abe930a471 Merge pull request #17156 from SergeyYakubov/rucio-plugin 
Adding object store plugin for Rucio
 2024-03-05 16:11:03 +01:00
Matthias Bernt 450c93710e make the max discovered files error a "proper" job error message 2024-03-05 10:00:20 -05:00
Marius van den Beek c598c49f62 Raise NotImplementedError for TS get_or_create_default_history 2024-03-05 15:52:17 +01:00
Dannon 5c5f3aaabe Merge pull request #17531 from guerler/enable_activity_bar 
Enables activity bar by default
 2024-03-05 08:39:35 -06:00
Dannon f18739b0f7 Merge pull request #17555 from galaxyproject/dependabot/npm_and_yarn/client/es5-ext-0.10.63 
Bump es5-ext from 0.10.62 to 0.10.63 in /client
 2024-03-05 06:55:20 -06:00
Dannon 96b88f7ea8 Merge pull request #17567 from astrovsky01/colabfold_tar_datatype 
add colabfold tar file datatype
 2024-03-05 06:54:02 -06:00
mvdbeek feb38afccb Fix tool shed webapp 2024-03-05 12:50:35 +01:00
mvdbeek ffa58ae324 Anticipate PendingRollbackError in `check_database_connection` 2024-03-05 11:14:29 +01:00
Martin Cech e9e26b95c1 Merge pull request #17591 from jdavcs/version-24.0.rc1 
[24.0] Update version to 24.0.rc1
 2024-03-05 00:01:00 +01:00
Martin Cech 7280ecd9ab Merge pull request #17592 from jdavcs/version-24.1.dev 
Update version to 24.1.dev
 2024-03-04 23:59:33 +01:00
John Davis 04a8011697 Update version to 24.0.rc1 2024-03-04 13:14:33 -05:00
John Davis d70b8db736 Merge branch 'release_24.0' into 'dev' 2024-03-04 13:14:33 -05:00