mvdbeek
e5b300b9c1
Add job metrics per invocation
2024-11-04 17:53:17 +01:00
Marius van den Beek
339724e0aa
Merge pull request #19070 from mvdbeek/reuse_trs_import_in_workflow_contents_manager
...
Move TRS import into WorkflowContentManager
2024-10-30 15:27:21 -04:00
mvdbeek
48ed0682dc
Move TRS import into WorkflowContentManager
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which fixes missing source metadata when importing a workflow through a
landing page.
2024-10-30 17:32:23 +01:00
John Chilton
7f7710d392
Implement recovering normalized workflow request from invocation.
2024-10-15 09:12:05 -04:00
John Chilton
f80207d295
Revise workflow failure around materializing URLs.
2024-09-30 13:38:20 -04:00
John Chilton
660f78fe37
Implement workflow landings.
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Includes a lot of plumbing for tools but not the APIs - they are not ready to go yet.
2024-09-30 13:25:02 -04:00
John Chilton
2fe88a05ea
Allow workflows to consumer deferred {src: url} dicts..
2024-09-30 13:25:02 -04:00
John Chilton
b07750554d
Migrate mapover expression test to wf test framework.
2024-09-24 14:00:08 -04:00
mvdbeek
ac71c06854
Merge branch 'release_24.1' into dev
2024-09-13 16:59:22 +02:00
mvdbeek
076133b018
Add test case for updating workflow name of parent workflow
2024-09-12 10:59:24 +02:00
mvdbeek
9a231f7f79
Merge branch 'release_24.1' into dev
2024-09-04 17:05:21 +02:00
mvdbeek
4667cec17b
Add regression test for subworkflow that stops scheduling
2024-08-30 16:46:37 +02:00
mvdbeek
f6216355dc
Fix workflow invocation accessibility check
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Fixes https://github.com/galaxyproject/galaxy/issues/18695#issuecomment-2315782041
and fixes the test that didn't actualy test the published portion.
2024-08-28 19:06:28 +02:00
mvdbeek
160725a117
Merge branch 'release_24.1' into dev
2024-08-26 13:01:54 +02:00
John Chilton
5d5f537348
Merge pull request #18734 from mvdbeek/improve_yaml_exception_reporting
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[24.1] Catch and display exceptions when importing malformatted yaml workflows
2024-08-24 11:19:54 -04:00
mvdbeek
a2c304081a
Catch and display exceptions when importing malformatted yaml workflows
2024-08-23 21:56:00 +02:00
John Chilton
2c0a7033ad
Merge pull request #18707 from mvdbeek/allow_access_to_invocation_via_shared_history
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Allow access to invocation via shared or published history
2024-08-23 09:25:09 -04:00
mvdbeek
080a0c799b
Fail on expected subworkflow output not found
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This would currently just fail with an exception in the logs.
I ran into this while manually defining a gxformat2 workflow
and not referencing the right step.
2024-08-23 13:27:47 +02:00
mvdbeek
565911e85f
Add test workflow
2024-08-23 13:25:43 +02:00
mvdbeek
64bd95dd34
Merge branch 'release_24.1' into dev
2024-08-15 16:40:48 +02:00
mvdbeek
eca0cfbcfa
Allow access to invocation via shared or published history
2024-08-15 13:30:35 +02:00
mvdbeek
2d1680b042
Really do change PJA in test case
2024-08-13 15:22:10 +02:00
John Chilton
ad0ad8561b
Migrate another collection flatten workflow test to workflow test framework.
2024-07-29 09:19:10 -04:00
John Chilton
efedd7c89f
Migrate workflow flatten test to workflow test framework.
2024-07-29 09:19:10 -04:00
John Chilton
eeafa488ab
Move zip collection workflow test into workflow framework tests
2024-07-29 09:19:10 -04:00
John Chilton
dc14564b38
Replace API tests with workflow tests for various parameter replacement.
2024-07-29 09:19:09 -04:00
John Chilton
a7ce90d168
Rework and improve workflow tests for tools with different versions.
2024-07-29 09:19:09 -04:00
John Chilton
4a7d75071d
Migrate a workflow test case for output renaming to workflow test framework.
2024-07-29 09:19:09 -04:00
John Chilton
8697b61d45
Move empty sort workflow test into workflow test framework.
2024-07-29 09:19:09 -04:00
mvdbeek
b403bf8237
Add test case for runtime input map over
2024-07-14 20:53:52 +02:00
mvdbeek
33f27d5456
Merge branch 'release_24.0' into release_24.1
2024-07-01 18:23:55 +02:00
Marius van den Beek
6b8c7f75ba
Merge pull request #18456 from arash77/subworkflows_tags_fix
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[24.0] Fix subwofklow tags serialization type
2024-06-29 12:02:47 +02:00
Arash
9592520737
Add test
2024-06-28 13:42:08 +02:00
mvdbeek
093dcc8d3d
Merge branch 'release_24.0' into release_24.1
2024-05-28 14:34:20 +02:00
Ahmed Awan
f516679399
add api test for running workflow as anon user
2024-05-22 13:47:19 -05:00
Marius van den Beek
04485399aa
Merge pull request #17366 from jmchilton/cross_product
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Enable all-vs-all collection analysis patterns.
2024-05-14 16:17:44 +02:00
Martin Cech
bf14bcdaa3
validate the contents, not the path to file
2024-04-22 15:50:34 -07:00
Martin Cech
5fa2617727
readd a bco.json invocation export API test
2024-04-22 12:49:01 -07:00
Martin Cech
af4d4021ba
remove deprecated bco export endpoint
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instead clients shall POST api/invocations/{id}/prepare_store_download with payload:
{
model_store_format: bco.json
}
2024-04-18 15:35:27 -07:00
John Chilton
bbfc6041b3
Add API test that fails because outputs aren't skipped
2024-04-15 12:00:30 -04:00
mvdbeek
9b795ab28d
Merge branch 'release_23.2' into release_24.0
2024-04-10 09:39:34 +02:00
mvdbeek
8d52714199
Add test for implicit map over conversion in workflow
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This test fails because cut fails on the compressed input with
`cut: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpu8gqd71c/tmpmae9egoz/tmpz8sonmgx/database/objects/6/9/8/dataset_69847aef-7b3f-4915-a8ae-394921dbe388.dat: Illegal byte sequence`
2024-04-09 19:44:36 +02:00
mvdbeek
8e8d7fa0f9
Fix tool state in build_module and refactor action
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that can result form upgrading tools.
2024-04-08 20:28:39 +02:00
John Chilton
661d93ab2a
Merge pull request #17869 from mvdbeek/drop_dummy_replacement
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[24.0] Fix workflow run form failing on certain histories
2024-04-04 11:06:54 -04:00
Nicola Soranzo
1332eb1620
Fix `test_workflow_optional_input_filtering` API test to produce one output again
2024-04-03 13:10:53 +01:00
mvdbeek
969e995a9b
Add test tool w/ dynamic select in conditional
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Include this in a workflow, and notice that the run form breaks
if the history contains a dataset that trips up the dynamic parameter.
2024-04-02 19:10:20 +02:00
mvdbeek
23cf6a2e0a
Add test for changing dynamic collection datatype
2024-03-21 15:58:06 +01:00
mvdbeek
a689413a96
Ensure metadata is copied for expression tool outputs
2024-03-19 11:37:01 +01:00
mvdbeek
689bb0d88c
Test subworkflow response at /api/worflows/{workflow_id}
2024-03-14 17:07:43 +01:00
Marius van den Beek
b7c14c6559
Merge pull request #17294 from lldelisle/filter_paused
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[24.0] Add ``__KEEP_SUCCESS_DATASETS__``
2024-03-05 16:18:20 +01:00
mvdbeek