opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-24 12:13:33 +08:00
Code Issues Packages Projects Releases Wiki Activity
80,454 Commits 63 Branches 243 Tags
631e33f5bd469eaed3ce99647d785e44de6f6ec3
Commit Graph
8695 Commits
Author SHA1 Message Date
John Chilton 631e33f5bd Merge pull request #19716 from jmchilton/fix_citation_handling 
[24.2] Fix #19515 - invalid citation handling changed with 24.2.
 2025-05-13 13:04:22 -04:00
mvdbeek b99112c337 Fix DataCollectionParameterModel factory 2025-05-06 14:23:23 +02:00
Dannon e7d8e66b48 Merge pull request #20134 from mvdbeek/fix_edam_selenium_test 
[24.2] Fix edam selenium test
 2025-05-05 10:41:51 -04:00
Marius van den Beek 18c68b067f Merge pull request #20144 from mvdbeek/fix_param_value_restriction 
[24.2] Skip ``param_value`` filter if ref value is runtime value
 2025-05-05 13:42:20 +02:00
mvdbeek a53b4125aa Skip `param_value` filter if ref value is runtime value 
Fixes https://github.com/galaxyproject/galaxy/issues/20136
 2025-05-04 16:48:33 +02:00
mvdbeek 4d71d88081 Improve edam test robustness 
No guarantee that the title won't change, and I think it has recently.
 2025-05-02 17:46:08 +02:00
mvdbeek 327bd3e391 WIP: if not accessing input.name, allow input.name to differ 2025-04-23 09:09:42 +02:00
Marius van den Beek 7a1ea09e9c Merge pull request #19949 from jmchilton/parameter_model_fixes_0 
[24.2] Fix various parameter validation issues.
 2025-04-15 15:08:28 +02:00
mvdbeek 4f9180604f Make dbkey_filter_input more realistic, regression test for https://github.com/galaxyproject/galaxy/issues/19975 2025-04-10 16:59:09 +02:00
John Chilton f37075c1a5 Fix various parameter validation issues. 
I previously failed to include a bunch of validation checks I assumed had been covered so fixed that first and got a bunch of new issues detected. Also added a parameter specification test case for https://github.com/galaxyproject/galaxy/issues/19908 and fixed that.
 2025-04-02 12:49:09 -04:00
Nicola Soranzo 1c8fbbb958 Fix mypy issues 
```
test/unit/tool_util/test_parsing.py:954: error: Argument 1 to "get_tool_source" has incompatible type "Traversable"; expected "str | PathLike[str] | None"  [arg-type]
        tool_source = get_tool_source(tool_path)
                                      ^~~~~~~~~
test/unit/tool_util/test_parsing.py:960: error: Argument 1 to "get_tool_source" has incompatible type "Traversable"; expected "str | PathLike[str] | None"  [arg-type]
        tool_source = get_tool_source(tool_path)
                                      ^~~~~~~~~
```
 2025-03-26 15:18:55 +00:00
mvdbeek 648239a31f Merge branch 'release_24.1' into release_24.2 2025-03-26 09:48:18 +01:00
mvdbeek 953a972349 Merge branch 'release_24.0' into release_24.1 2025-03-26 09:44:07 +01:00
Nicola Soranzo 8f0e11b929 Use `best_search_result()` function instead of parsing anaconda.org web pages 
Fix the following mulled unit test:

```
FAILED test/unit/tool_util/mulled/test_get_tests.py::test_hashed_test_search - AssertionError: assert ['samtools --help'] == ['bamtools --help', 'samtools --help']
  At index 0 diff: 'samtools --help' != 'bamtools --help'
  Right contains one more item: 'samtools --help'
  Full diff:
  - ['bamtools --help', 'samtools --help']
  + ['samtools --help']
```

that started not finding bamtools-2.4.0 inside
https://anaconda.org/bioconda/bamtools/files any more.

Also:
- Add type annotation to `CondaInDockerContext` and fix ensuing issues.
 2025-03-25 19:45:07 +00:00
mvdbeek 3c12acb270 Assert column_types 2025-03-25 10:29:01 +01:00
Nate Coraor ecc4b47804 Merge pull request #19824 from mvdbeek/fix_limit_bypass 
[24.2] Fix various job concurrency limit issues
 2025-03-24 17:37:26 -04:00
John Chilton ff011fbe01 Handle directories with percents in export_remote.xml. 2025-03-20 16:25:09 -04:00
John Chilton ef5ee033f3 Fix #19515 - invalid citation handling changed with 24.2. 2025-03-20 10:39:31 -04:00
mvdbeek 3e767c940e Add unit tests for queue_with_limit 2025-03-18 14:10:09 +01:00
mvdbeek a19e4eb091 Lower pulsar transport_timeout param instead of extending wait 2025-03-17 10:21:43 +01:00
Nicola Soranzo 4421f43483 Store maxseconds on GalaxyTestDriver 2025-03-16 22:42:58 +01:00
mvdbeek ada691492a Extend tool test timeout for pulsar resubmission 2025-03-16 21:01:23 +01:00
Marius van den BeekandNicola Soranzo c732a365e7 Improve test assertion 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-03-16 20:51:19 +01:00
mvdbeek e2135d6e16 Mock unit test doi.org requests 
We're testing the cache, not the requests here.
 2025-03-16 13:54:20 +01:00
John Chilton 808d5f9448 Merge pull request #19807 from mvdbeek/use_materialized_datasets_in_pulsar 
[24.2] Use materialized datasets in pulsar job runner
 2025-03-13 13:48:48 -04:00
mvdbeek 31aeefd65f Use materialized datasets in pulsar 2025-03-13 17:28:28 +01:00
mvdbeek 858593a8ba Fix transfer of $_TOOL_DIRECTORY subdirectories 
Goes together with https://github.com/galaxyproject/pulsar/pull/385
 2025-03-13 16:19:10 +01:00
John Davis 104a375ea4 Add get_private_role_user_emails_dict, test 
Retrieves a mapping of private role ids to associated users' emails.
Used to lookup a user's email when generating a displayed_name for
private roles.
 2025-03-11 00:34:22 -04:00
John Davis c4c66078d8 Factor out get_displayable_roles, add test 2025-03-10 11:13:13 -04:00
John Davis f2f55131b2 Fix unit tests 2025-03-10 11:13:13 -04:00
John Davis dfe1536a5d Update test fixture 
Specify correct role name for private roles. See comment in make_role
definition for why this must be set.
 2025-03-10 11:13:13 -04:00
Marius van den Beek 54de00e2cf Merge pull request #19694 from mvdbeek/bwa_index_directory_datatype 
[24.2] Add bwa_mem2_index directory datatype, framework enhancements for testing directories
 2025-03-08 11:14:52 +01:00
Marius van den Beek 2832585a34 Merge pull request #19672 from jmchilton/fix_actions_recording 
[24.2] Fix recording transform action name.
 2025-03-08 11:12:57 +01:00
Marius van den Beek 5fcc4585fe Merge pull request #19715 from jmchilton/assertion_linter_fixes 
[24.2] Assertion linter fixes
 2025-03-08 11:09:51 +01:00
Matthias Bernt 9f86a7db62 linter allow datatype auto in output tags 2025-03-06 17:25:05 +01:00
John Davis 0d81abe114 Skip slow tests for manage_db, db_dev scripts 2025-03-05 10:57:19 -05:00
John Chilton e6aee8b4cd Fix assertion model linter. 2025-02-27 10:48:29 -05:00
mvdbeek 9636983d44 Fix uploads in pulsar embedded test case 2025-02-26 14:55:08 +01:00
Marius van den BeekandBjörn Grüning e6b27a32b2 Adjust test tool and datatype config to best practices 
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
 2025-02-26 13:18:25 +01:00
mvdbeek 07a4a7c058 Fix directory uploads, use `__FETCH_DATA__` api 
for tool tests, which were still using upload1.
 2025-02-25 18:10:10 +01:00
John Chilton 387ce7dd37 Add failing test case for #19678 2025-02-25 11:39:58 -05:00
John Chilton 3b4ffd5de9 Fix recording transform action name. 
The upload option is space_to_tab, but we've always recorded in the source transform json blob as spaces_to_tabs. I guess the past tense version - it sort of makes sense but anyway we don't want any of these inconsistent values in the database.
 2025-02-22 14:10:00 -05:00
mvdbeek 8c4149b094 Fix dependency structure for ParameterOption 2025-02-19 17:57:49 +01:00
mvdbeek 6512b4c366 Add bwa_mem2_index datatype 2025-02-19 17:26:09 +01:00
mvdbeek c3cf80fc75 Fix data table filters that operate on `value` field 
This is a little cleaner. Also replaces the `list[tuple[str, str,
bool]]` return type of get_options with a NamedTuple.

Fixes https://github.com/galaxyproject/galaxy/issues/19609
 2025-02-19 15:05:35 +01:00
Nicola Soranzo e3942053f4 Merge branch 'release_24.1' into release_24.2 2025-02-16 17:26:50 +00:00
Nicola Soranzo ca9bf294f4 Merge branch 'release_24.0' into release_24.1 2025-02-16 17:19:15 +00:00
Nicola Soranzo 18312cfc69 Fix CondaSearch.get_json() to skip all header lines 
Fix the following `test_conda_search` failure:

```
______________________________ test_conda_search _______________________________

    @external_dependency_management
    @skip_unless_executable("conda")
    def test_conda_search():
        t = CondaSearch("bioconda")
        search1 = t.get_json("asdfasdf")
        search2 = t.get_json("bioconductor-gosemsim")
        assert search1 == []
>       assert all(r["package"] == "bioconductor-gosemsim" for r in search2)
E       assert False
E        +  where False = all(<generator object test_conda_search.<locals>.<genexpr> at 0x7f5be7fc34a0>)

search1    = []
search2    = [{'build': 'Version', 'package': '#', 'version': 'Name'},
 {'build': '0', 'package': 'bioconductor-gosemsim', 'version': '1.28.2'},
 {'build': 'r3.3.1_0', 'package': 'bioconductor-gosemsim', 'version': '1.29.0'},
 {'build': 'r3.3.1_0', 'package': 'bioconductor-gosemsim', 'version': '1.30.3'},
 ...
 {'build': 'r43hf17093f_0', 'package': 'bioconductor-gosemsim', 'version': '2.28.0'},
 {'build': 'r43hf17093f_1', 'package': 'bioconductor-gosemsim', 'version': '2.28.0'},
 {'build': 'r44he5774e6_0', 'package': 'bioconductor-gosemsim', 'version': '2.32.0'}]
```
 2025-02-15 13:34:44 +00:00
Marius van den Beek 82c428d347 Merge pull request #19563 from mvdbeek/replace_sanitize_html 
[24.2] Set content-type to text/plain if dataset not safe
 2025-02-14 10:28:39 +01:00
davelopez 937645c187 Add integration tests for non-vault user preferences handling 
There is a bug in the user preferences handling when the user preferences
contains fields defined as "secret" but the field is not stored in the
vault. This commit adds integration tests to cover this case.
 2025-02-13 18:40:55 +01:00