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Author SHA1 Message Date
Nicola Soranzo ffeca95f29 Merge pull request #12551 from jmchilton/galaxy-job-metrics-unit-tests 
Establish galaxy-job-metrics unit test directory.
 2021-09-25 01:41:51 +01:00
Nicola Soranzo e45ef7e6cb Merge pull request #12550 from jmchilton/galaxy-job-execution-unit-tests 
Establish galaxy-job-execution unit test directory.
 2021-09-25 01:36:12 +01:00
John Chilton 9debc5e529 Move test_verify.py into tool_util's test suite so it is properly packaged and tested in its package. 2021-09-24 14:09:25 -04:00
John Chilton 89e41b34d3 Fix unit test dependencies around tool_util sample data. 2021-09-24 14:09:25 -04:00
Björn Grüning d0f4d4f6ea Merge pull request #12547 from OlegZharkov/sel-fix 
fix test_sharing_valid_by_id  selenium test
 2021-09-24 19:57:31 +02:00
John Chilton 84785b7a1d Package test-data needed for test_model_store to run as packaged. 2021-09-24 12:16:55 -04:00
John Chilton c58fe574a8 Move more galaxy-data tests into test/unit/data so they are tested as part of galaxy-data tests. 2021-09-24 12:16:55 -04:00
John Chilton f1e50f34ee Remove dependencies in test_model_store.py on galaxy-app. 2021-09-24 12:16:54 -04:00
John Chilton 336cf7b918 Package objectstore's unittest helpers and drop hacks for running test_model_copy.py in galaxy-data. 2021-09-24 12:16:54 -04:00
John Chilton 9a0f850798 Remove import of tiny test utility _create_datasets. 2021-09-24 12:16:54 -04:00
John Chilton d7c50bd2e5 Remove dependency on Dummy in test_model_store. 2021-09-24 12:16:54 -04:00
John Chilton 84220b6b55 Establish unittest utils for galaxy-data packages. 
Progress toward https://github.com/galaxyproject/galaxy/issues/8364. Cleans up dependency into a proper DAG so we can move for instance test_model_discovery.py into galaxy-data's unittests.
 2021-09-24 12:16:54 -04:00
John Chilton a2e8194afd Establish galaxy-job-metrics unit test directory. 
One unit test directory per package is the convention I want to establish and I don't think this test file belongs with other galaxy-app tests. A similar refactoring job-execution exists as https://github.com/galaxyproject/galaxy/pull/12550. Both of these packaging issues were preventing the app test refactoring in https://github.com/galaxyproject/galaxy/pull/12549.
 2021-09-24 12:13:48 -04:00
Sergey Golitsynskiy 4c7d5ee25f Merge pull request #12468 from ic4f/dev_model_relationships 
Remove unused relationships from model
 2021-09-24 12:07:34 -04:00
John Chilton 425b3b5ec1 Establish galaxy-job-execution unit test directory. 
One unit test directory per package is the convention I want to establish and I don't think this test file belongs with other galaxy-app tests.
 2021-09-24 12:06:48 -04:00
davelopez acdfccb9f7 Move SharableService to services package 2021-09-24 17:07:52 +02:00
Oleg Zharkov 40841372b9 fix test_sharing_valid 2021-09-24 16:59:53 +02:00
davelopez 89895164de Move VisualizationsService to services package 
Some additional rename refactoring and adaptations to remove unused MinimalManagerApp dependency.
 2021-09-24 16:16:50 +02:00
Marius van den Beek 6d571840e6 Merge pull request #12538 from ic4f/dev_sa_1.4.25 
Update SQLAlchemy to 1.4.25
 2021-09-24 12:16:05 +02:00
davelopez 5838380f76 Move LibraryFolderContentsService to services package 
Some additional rename refactoring and adaptations to remove StructuredApp dependency.
 2021-09-24 11:47:59 +02:00
mvdbeek 019488005d [PROCEDURES] Add David López to committers group 
David has taken on the migration to fastAPI as his first big project
within the Galaxy codebase and has gained a very good understanding of
Galaxy's backend and the new server stack. His PRs are well-crafted and
contain rigorous tests.
David is also the maintainer of the [Galaxy language
server](https://github.com/galaxyproject/galaxy-language-server), has
presented his work at this years' GCC and is a member of the backend
working group. So I'm proposing to add David to the committers group.
 2021-09-24 11:27:43 +02:00
mvdbeek 5a91c04840 [PROCEDURES] Add Oleg Zharkov to committers group 
Oleg has contributed many large pieces of new and modernized frontend
components as well as complementary backend changes. He has included
many tests for new and old components, is an important member of the
UI-UX and testing working groups and has presented his work at multiple
GCC conferences. So let's make Oleg an official member of the committers
group.
 2021-09-24 11:16:25 +02:00
Marius van den Beek 4d91ba1df9 Merge pull request #12537 from jmchilton/test_hashes_and_sources 
Preserve important dataset metadata when importing/exporting histories.
 2021-09-24 10:52:37 +02:00
davelopez 036954c951 Move LibraryFoldersService to services package 2021-09-24 10:37:51 +02:00
Dannon 1e3855d74f Merge pull request #12540 from ic4f/dev_docs_label_database 
Modify description of the "database" label
 2021-09-23 14:35:46 -04:00
Sergey Golitsynskiy a302e988d5 Modify description of the "database" label 2021-09-23 14:04:35 -04:00
davelopez 7c1b62f9b9 Move QuotasService to services package 2021-09-23 20:04:02 +02:00
davelopez 10d407115d Move LibrariesService to services package 2021-09-23 19:52:45 +02:00
davelopez 70a3ad540f Move PagesService into services package 2021-09-23 19:31:55 +02:00
davelopez a9ca680dd7 Move HistoriesService and HistoryContentsService to services package 
Also move some of the shared pydantic models from managers package to schema package.
 2021-09-23 19:17:37 +02:00
mvdbeek 97c5bd8771 Merge API GalaxyInteractorTestCase into integration test 
This seems more appropraite as an integration test.
 2021-09-23 19:05:30 +02:00
mvdbeek 66fd430763 Include tool_version in API requests for test-data 
Should fix https://github.com/galaxyproject/ephemeris/issues/179.
 2021-09-23 19:05:30 +02:00
davelopez bd0db77abc Move ServiceBase to services package 2021-09-23 19:03:59 +02:00
mvdbeek 1b1b411acc Simplify and fix JobExportHistoryArchive / GenomeIndexToolData handling 
Output parameters must behave somewhat like a HDA, in that they need to
have a dataset attribute that points to a Dataset instance.
`GenomeIndexToolData` fits that requirement, `JobExportHistoryArchive`
provides the fda property that behaves like a HDA.
 2021-09-23 11:44:20 -04:00
Sergey Golitsynskiy e691ab866b Update SQLAlchemy to 1.4.25 2021-09-23 11:29:38 -04:00
Marius van den Beek e0fe836a94 Merge pull request #12531 from davelopez/add_request_wrapper 
FastAPI: Add request wrapper for `SessionRequestContext`
 2021-09-23 17:29:00 +02:00
Marius van den Beek 168509cb0a Merge pull request #12513 from jmchilton/admin_workflow_paths 
Test cases to verify only admins can import workflows from paths.
 2021-09-23 17:03:28 +02:00
Marius van den Beek b43929f932 Merge pull request #12512 from jmchilton/remove_installed_repo 
Remove workflow API hooks for tool shed.
 2021-09-23 17:02:50 +02:00
John Chilton 4602977fd8 Perserve dataset.sources when importing/exporting histories. 2021-09-23 10:57:40 -04:00
John Chilton 618a27b7fd Perserve dataset.created_from_basename when importing/exporting histories. 2021-09-23 10:57:40 -04:00
John Chilton 12e74a3390 Perserve dataset hashes when importing/exporting histories. 2021-09-23 10:57:40 -04:00
John Chilton 79cf2209b7 Typing for model store. 2021-09-23 10:57:40 -04:00
John Chilton d6ac2d2f7c Better exception handling. 2021-09-23 10:15:33 -04:00
John Chilton 2beeb00356 Useful comment? 2021-09-23 10:12:13 -04:00
mvdbeek 61a33f97bd Merge branch 'release_21.09' into dev 2021-09-23 15:59:47 +02:00
Marius van den Beek d2990db553 Merge pull request #12522 from kxk302/refactor 
Revised download() so parallel get() is utilized. Small refactor.
 2021-09-23 15:20:34 +02:00
Marius van den Beek 7128301d75 Merge pull request #12524 from natefoo/singularity-cache 
Add support for caching the Singularity cached images directory
 2021-09-23 15:16:14 +02:00
John Chilton cad79f46f8 Merge pull request #12532 from mvdbeek/fix_populated_optimized_on_empty_collections 
[21.09] Fix populated state for collections without members
 2021-09-23 08:53:38 -04:00
Marius van den Beek cd4bc5bef2 Merge pull request #12536 from mvdbeek/tolerate_extra_whitespace_in_from_work_dir 
[21.09] Add profile that strips whitespace in from_work_dir outputs
 2021-09-23 14:53:29 +02:00
mvdbeek 1fb2aa55dc Mention whitespace stripping change in 21.09 profile 2021-09-23 14:45:12 +02:00