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48c654d1b26e080fc3d13a96c91dc53182948314
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6935 Commits
Author SHA1 Message Date
mvdbeek 48c654d1b2 Add type hint for galaxy.workflow.{run, run_request} 
Trying out https://github.com/dropbox/pyannotate here.
It's still a lot of work even with pyannotate, but I think this fixes
some minor oddities, like assigning non-mapped attributes to
WorkflowInvocation instances.
 2022-09-23 09:33:47 +02:00
John Davis 4c7d6805e7 Drop integration test for config defaults 2022-09-16 15:31:55 -04:00
John Davis 5236b66382 Improve test of assignment of default config values 2022-09-16 15:15:03 -04:00
John Davis eb9dccef58 Drop unit tests for default config values 2022-09-16 15:05:20 -04:00
davelopez 0128e05a23 Fix export ro-crate to file source 
Write to the store the correct archive file
 2022-09-16 17:19:49 +02:00
John Chilton a887fc894d Merge pull request #14616 from jmchilton/ts_tests_1 
More tool shed API tests (+fixes)
 2022-09-15 09:08:31 -04:00
John Chilton f8c1c11016 API tests for tool shed search APIs. 2022-09-14 09:31:27 -04:00
John Chilton 3dbe2891e7 Implement RO Crate export of Galaxy histories and invocations. 2022-09-13 19:20:48 -04:00
John Chilton 42364892ac Merge pull request #14604 from bernt-matthias/topic/lint-duplicate-inputs 
linter: check for inputs with duplicated names
 2022-09-12 15:24:01 -04:00
Matthias Bernt ec04666cc1 linter: check for inputs with duplicated names 
and outputs
 2022-09-12 15:23:50 +02:00
John Chilton 1e664c3206 More tool data table typing and testing. 2022-09-09 13:12:30 -04:00
John Chilton 019db37411 Unit tests for tool_data... 2022-09-09 13:11:39 -04:00
Nicola Soranzo cb012c7fb2 Merge branch 'release_22.05' into dev 2022-09-09 17:14:20 +01:00
Nicola Soranzo dc0ac34fc4 Merge pull request #14588 from mvdbeek/fix_noisy_exception_logging_when_unicode_null_in_session_key 
[22.05] Ensure guid is hexadecimal value
 2022-09-08 19:05:54 +01:00
mvdbeek aceaa698fc Ensure guid is hexadecimal value 2022-09-08 14:04:35 +02:00
Marius van den Beek 28e03f0f10 Merge pull request #14362 from xtrojak/sybila-tools-datatypes 
Add datatypes for Sybila tools
 2022-09-08 12:05:04 +02:00
Nicola Soranzo fe83c7f99b Merge branch 'release_22.05' into dev 2022-09-06 12:31:22 +01:00
Nicola Soranzo 70b2ea429c Merge branch 'release_22.01' into release_22.05 2022-09-06 12:12:21 +01:00
Nicola Soranzo 9f1d8d053b Merge branch 'release_21.09' into release_22.01 2022-09-06 11:36:36 +01:00
Nicola Soranzo 06baa27d05 Merge branch 'release_21.05' into release_21.09 2022-09-06 11:24:20 +01:00
Nicola Soranzo 8069584d0f Merge branch 'release_21.01' into release_21.05 2022-09-06 11:12:59 +01:00
Nicola Soranzo 5ff960e9ae Fix comparing a boolean `InputValueWrapper` to "True"/"False" strings 
Fix the following framework test failures:

test/functional/test_toolbox_pytest.py::test_tool[output_action_change_format_test_1]

E           galaxy.tool_util.verify.interactor.JobOutputsError: Dataset metadata verification for [metadata_dbkey] failed, expected [hg19] but found [?]. Dataset API value was [{'id': '8ac6d96e308f61e5', 'name': 'output_action_change_format on data 1', 'history_id': '2cf235fc3a3387c3', 'hid': 2, 'history_content_type': 'dataset', 'deleted': False, 'visible': True, 'type_id': 'dataset-8ac6d96e308f61e5', 'type': 'file', 'create_time': '2022-09-01T18:07:56.177858', 'update_time': '2022-09-01T18:08:01.856249', 'url': '/api/histories/2cf235fc3a3387c3/contents/8ac6d96e308f61e5', 'tags': [], 'dataset_id': '8ac6d96e308f61e5', 'state': 'ok', 'extension': 'data', 'purged': False, 'misc_info': '', 'data_type': 'galaxy.datatypes.data.Data', 'creating_job': '7fbe67cfae825002', 'hda_ldda': 'hda', 'peek': None, 'created_from_basename': 'out1', 'display_types': [], 'download_url': '/api/histories/2cf235fc3a3387c3/contents/8ac6d96e308f61e5/display', 'display_apps': [], 'meta_files': [], 'file_ext': 'data', 'sources': [], 'copied_from_ldda_id': None, 'uuid': '6decb7d7-1e5a-4036-9895-6cea83a85737', 'file_name': '/tmp/tmpdsxagstf/tmp84ke9cq4/tmpv3mcqttw/database/objects/6/d/e/dataset_6decb7d7-1e5a-4036-9895-6cea83a85737.dat', 'api_type': 'file', 'misc_blurb': 'data', 'hashes': [], 'accessible': True, 'file_size': 4, 'model_class': 'HistoryDatasetAssociation', 'metadata_dbkey': '?', 'validated_state_message': None, 'resubmitted': False, 'permissions': {'manage': ['adb5f5c93f827949'], 'access': []}, 'annotation': None, 'validated_state': 'unknown', 'rerunnable': True, 'genome_build': '?'}].

test/functional/test_toolbox_pytest.py::test_tool[output_action_change_format_test_2]

E           galaxy.tool_util.verify.interactor.JobOutputsError: Dataset metadata verification for [metadata_dbkey] failed, expected [hg38] but found [?]. Dataset API value was [{'id': 'b316627aece188a7', 'name': 'output_action_change_format on data 1', 'history_id': 'a53aa9d4dc32b5ed', 'hid': 2, 'history_content_type': 'dataset', 'deleted': False, 'visible': True, 'type_id': 'dataset-b316627aece188a7', 'type': 'file', 'create_time': '2022-09-01T18:08:12.870025', 'update_time': '2022-09-01T18:08:18.490136', 'url': '/api/histories/a53aa9d4dc32b5ed/contents/b316627aece188a7', 'tags': [], 'dataset_id': 'b316627aece188a7', 'state': 'ok', 'extension': 'txt', 'purged': False, 'misc_info': '', 'data_type': 'galaxy.datatypes.data.Text', 'creating_job': '3607dcbef30930ec', 'hda_ldda': 'hda', 'peek': '<table cellspacing="0" cellpadding="3"><tr><td>1\t2</td></tr></table>', 'created_from_basename': 'out1', 'display_types': [], 'download_url': '/api/histories/a53aa9d4dc32b5ed/contents/b316627aece188a7/display', 'display_apps': [], 'meta_files': [], 'file_ext': 'txt', 'sources': [], 'copied_from_ldda_id': None, 'uuid': '4a58c935-6fea-4b55-b659-871e652021de', 'file_name': '/tmp/tmpdsxagstf/tmp84ke9cq4/tmpv3mcqttw/database/objects/4/a/5/dataset_4a58c935-6fea-4b55-b659-871e652021de.dat', 'api_type': 'file', 'misc_blurb': '1 line', 'hashes': [], 'accessible': True, 'file_size': 4, 'model_class': 'HistoryDatasetAssociation', 'metadata_dbkey': '?', 'validated_state_message': None, 'resubmitted': False, 'permissions': {'manage': ['adb5f5c93f827949'], 'access': []}, 'annotation': None, 'validated_state': 'unknown', 'metadata_data_lines': 1, 'rerunnable': True, 'genome_build': '?'}].

that started to appear after commit
94c75a083c was merged forward.
In particular, for the above tests the `ref` variable at

https://github.com/galaxyproject/galaxy/commit/94c75a083c25612b5f9e4aac6fc53d0ac2c77253#diff-0251b89ba313ad7ec78f79bfc21e416597cefd52447314029a728af5d775dbc6R85

is now a boolean `InputValueWrapper` instance, which could not be
meaningfully compared to `value` if it was a "True" or "False" string
because `ref` would be converted to the `truevalue` or `falsevalue` of the
parameter when casted to `str`.
 2022-09-02 18:26:01 +01:00
Nicola Soranzo 885f6f60c0 Fix test non testing what it was supposed to 2022-09-02 18:25:43 +01:00
Matej Troják 7d1807fc1e Merge branch 'dev' into sybila-tools-datatypes 2022-08-31 12:07:18 +01:00
Björn Grüning 7e76fdae82 Merge pull request #13977 from jmchilton/ts_api_tests 
Implement initial tool shed API tests.
 2022-08-30 21:51:33 +02:00
Björn Grüning 7ad3b40166 Merge pull request #13976 from jmchilton/remove_shed_datatypes 
Remove new shed datatypes
 2022-08-30 21:46:09 +02:00
mvdbeek b43dfa2613 Merge branch 'release_22.05' into dev 2022-08-30 20:37:56 +02:00
mvdbeek d1b4f05345 Merge branch 'release_22.01' into release_22.05 2022-08-30 20:32:39 +02:00
Nicola Soranzo 6519604620 Add some type annotations 2022-08-30 14:34:54 +01:00
Nicola Soranzo 4faa486c49 Merge pull request #14526 from bernt-matthias/topic/fix-test-linters 
[22.05] Fix typos in test linter
 2022-08-30 12:16:10 +01:00
Nicola Soranzo 61b6eb1ee9 Fix more `discovered_datasets` typos 2022-08-30 09:57:26 +01:00
John Chilton 439e3c68c4 Remove custom datatype installation from the tool shed. 
Existing custom datatypes will still be broken and available.
 2022-08-29 13:26:52 -04:00
mvdbeek 3b583a12c7 Give a hint about newlines when datatype test fails 2022-08-29 17:53:00 +02:00
mvdbeek 60cda23970 Mock quay.io API calls, pass install=False to not pull docker images 2022-08-29 16:38:31 +02:00
mvdbeek c4f576ccf3 Fix cache lookup condition 2022-08-29 16:38:31 +02:00
John Chilton a6a16811b2 master_api_key to bootstrap_admin_api_key 2022-08-29 09:51:19 -04:00
mvdbeek c4a9050af9 Fix _namespace_has_repo if cache namespace cache key not present 2022-08-29 14:08:49 +02:00
Matthias Bernt a8a80cf431 fix typo in test linter 2022-08-29 11:36:59 +02:00
Nicola Soranzo 26c41bb684 Fix B024 flake8-bugbear errors 2022-08-27 20:19:17 +01:00
John ChiltonandNicola Soranzo 2026d079b5 Update test/unit/util/test_properties.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-08-25 12:26:18 -04:00
Matthias Bernt 59f77048ce test case showing failing set_meta 
broke in https://github.com/galaxyproject/galaxy/commit/7d0ec29fa06ae6f04c0ae6fc193a390bc11cddcd
 2022-08-25 16:45:26 +02:00
mvdbeek 94c75a083c Fix setting metadata elements in conditional tool action 
Fixes https://github.com/galaxyproject/galaxy/issues/14509
 2022-08-25 14:27:44 +02:00
John Chilton ff80452421 Strong typing for galaxy.util.properties. 2022-08-24 17:37:08 -04:00
John Chilton be79f5ad3a Merge pull request #14436 from davelopez/refactor_pydantic_id_handling 
Refactor pydantic id handling
 2022-08-24 14:50:31 -04:00
mvdbeek 68d07cb890 Merge branch 'release_22.05' into dev 2022-08-24 15:24:04 +02:00
davelopez a7303e219e Fix API unit tests with ID encodings 2022-08-24 12:05:47 +02:00
davelopez a840696b93 Remove encoding in CreatesCollectionsMixin 2022-08-24 12:05:47 +02:00
davelopez 8355d5e12d Add more unit tests for ID fields 2022-08-24 12:00:26 +02:00
mvdbeek 8a8acc625f Fix refactor action dropping outputs on subworkflow connection 
I thought it would be cleaner to make a distinction between the output
name and the output label when reasoning about a subworkflow step in
the context of a parent workflow
(https://github.com/galaxyproject/galaxy/pull/14473/commits/b0727be9e0b096a2dacacb767a1f4ac0fc3e6540#diff-a50bcc5c08ade11249449c4100ea8c286727df601b52a5b9588eb2a385d97da7R543),
in case we'd later want to do something with the label.

I don't think I thought about this correctly though,
and it breaks connections between steps that were made by referencing
the subworkflow's output name.

This wasn't necessary for the main goal of
https://github.com/galaxyproject/galaxy/pull/14473, so I'm partially
reverting that here.

Fixes https://github.com/galaxyproject/planemo/pull/1262#issuecomment-1223874571
 2022-08-23 14:12:29 +02:00
mvdbeek 2e22b9e1f8 Merge branch 'release_22.05' into dev 2022-08-22 19:17:35 +02:00