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1457 Commits
Author SHA1 Message Date
mvdbeek 974d7e58bf Tighten conversion target input 
This way we test that conversion to txt occurs via fasta, not the fasta
to tabular converter.
 2024-11-19 17:33:58 +01:00
mvdbeek b5d46aa943 Test workflow module building with dynamic parameters 
and parameter references and validators.
 2024-09-30 13:48:03 +02:00
Marius van den Beek f8175ef771 Merge pull request #18552 from dannon/update-h5web 
[24.1] Update h5web
 2024-08-06 18:00:56 +02:00
Dannon Baker ab90c943ff Load h5 datatype in reduced test datatypes set 2024-08-05 10:58:22 -04:00
Matthias Bernt 262b4b69ca remove test for actions from collection_creates_pair_format 
now in metadata_column_names
 2024-07-30 13:01:51 +02:00
Matthias Bernt 3cdbb8f64c test actions in statically defined collection elements 2024-07-30 13:01:51 +02:00
Matthias Bernt eeab749ef6 Revert "add test for filters in statically defined collection elements" 
This reverts commit c0ce2a7eb6beaacaf65a389273cae12244103591.
 2024-07-30 13:01:51 +02:00
Matthias Bernt 7b0972598b add test for filters in statically defined collection elements 2024-07-30 13:01:51 +02:00
Matthias Bernt 85d4b4235b add test for output actions for collection elements 2024-07-30 13:01:51 +02:00
Matthias Bernt 3b3a65d1d2 extend tool test for change_format in statically defined collection elements 2024-07-30 13:01:51 +02:00
Dannon Baker 6ec7521e1a Merge remote-tracking branch 'upstream/release_24.0' into release_24.1 2024-06-28 09:48:27 +02:00
Marius van den Beek 8a52443a0a Merge pull request #18428 from mvdbeek/replace_busybox 
[24.0] Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc
 2024-06-28 09:22:30 +02:00
mvdbeek 7c6fc1800f Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc 2024-06-21 16:58:21 +02:00
Nicola Soranzo 08d42ea24f Merge branch 'release_24.0' into release_24.1 2024-06-19 13:14:15 +01:00
mvdbeek dd171fe34d Add test tool for default ext handling in discovered collections 2024-06-13 12:53:28 +02:00
mvdbeek b8e2bfc9c7 Merge branch 'release_24.0' into release_24.1 2024-06-11 13:42:48 +02:00
mvdbeek 435a8cd37f Fix up test cases 
Add a sleep so we can delay output purging until command line is
templated. If we don't sleep we generate a command line where the
output path is just `''`. That needs another fix!
 2024-06-10 10:34:15 +02:00
mvdbeek 8bc3f2151a Add tool that produces all types of outputs 2024-06-08 16:27:49 +02:00
mvdbeek 093dcc8d3d Merge branch 'release_24.0' into release_24.1 2024-05-28 14:34:20 +02:00
mvdbeek fa5e852c67 Revert "Always create output" 
This reverts commit 90d04a017e.
 2024-05-21 09:06:22 +02:00
Marius van den Beek 04485399aa Merge pull request #17366 from jmchilton/cross_product 
Enable all-vs-all collection analysis patterns.
 2024-05-14 16:17:44 +02:00
mvdbeek 79be849f4f Make celery fixture available in framework tests 2024-04-18 15:33:29 +02:00
John Chilton 46e83e178d Implement a cross product collection operation tools. 
These are available in a list(n) x list (m) -> list(nxm) version (a cross product that produces two flat lists) and a list(n) x list(m) -> list(n):list(m) version (a cross product that produces two nested lists).

After two lists have been run through one of these two tools - the result is two new lists that can be passed into another tool to perform all-against-all operations using Galaxy's normal collection mapping semantics.

The choice of which to use will depend on how you want to continue to process the all-against-all results after the next step in an analysis. My sense is the flat version is "easier" to think about and pick through manually and the nested version perserves more structure if additional collection operation tools will be used to filter or aggregate the results.

Some considerations:

Apply Rules?

I do not believe the Apply Rules tool semanatics would allow these operations but certainly the Apply Rules tool could be used to convert the result of the flat version to the nested version or vice versa - so no metadata is really lost per se between the two versions. I think it is still worth including both versions though - they both have utility (both for instance are baked into CWL's workflow semantics - https://docs.sevenbridges.com/docs/about-parallelizing-tool-executions#nested-cross-product) and avoiding requiring complex Apply Rules programs for simple workflows is probably ideal.

One Tool vs Two?

Marius and I agree that few simpler tools for these kinds of operations are better. The tool help can be more focused and avoiding the conditional and conditional outputs make the static analysis done for instance by the workflow editor simpler.
 2024-04-15 12:00:30 -04:00
mvdbeek bfb31656dd Merge branch 'release_24.0' into dev 2024-04-09 17:08:48 +02:00
mvdbeek b3217607ea Fix version switching error in workflow editor 2024-04-08 17:16:56 +02:00
mvdbeek 6f2a04321d Merge branch 'release_24.0' into dev 2024-04-04 18:55:04 +02:00
John Chilton 661d93ab2a Merge pull request #17869 from mvdbeek/drop_dummy_replacement 
[24.0] Fix workflow run form failing on certain histories
 2024-04-04 11:06:54 -04:00
Nicola Soranzo 4a4ead2b5e Merge branch 'release_24.0' into dev 2024-04-04 12:57:27 +01:00
Marius van den Beek 28c8b2fdd2 Merge pull request #17866 from kostrykin/verify_imagediff_iou/upstream 
Add `pin_labels` attribute for `image_diff` comparison method
 2024-04-03 17:19:47 +02:00
Nicola Soranzo 4984523c39 Change test with no outputs to not fail 
``out_3`` has been removed in https://github.com/galaxyproject/galaxy/pull/17874 .
 2024-04-03 13:11:36 +01:00
Nicola Soranzo 406c22e980 Merge branch 'release_24.0' into dev 2024-04-02 18:18:53 +01:00
mvdbeek 969e995a9b Add test tool w/ dynamic select in conditional 
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
M Bernt e1ec2c8b28 Update test/functional/tools/output_filter.xml 2024-04-02 09:46:55 +02:00
M Bernt ae594c18bc Add back test output 2024-04-02 09:46:55 +02:00
Matthias Bernt 46abd27123 make test a bit more specific 2024-04-02 09:46:55 +02:00
Matthias Bernt 6687cdc3ca adapt output filter test 
- remove the output that is always present
- add a test that has no outputs
 2024-04-02 09:46:22 +02:00
Leonid Kostrykin cdfc3f0e57 Add pin_labels attribute for image_diff comparison method 2024-03-29 12:01:34 +01:00
Leonid Kostrykin 45a819ebc8 Adds tifffile support for image assertions 2024-03-20 10:12:17 +01:00
Leonid Kostrykin 4fffff6db6 Add float TIFF test case (fails with Pillow) 2024-03-19 22:03:34 +01:00
Leonid Kostrykin fc67b20444 Fix bug in assert_has_image_n_labels 2024-03-15 14:16:06 +01:00
Marius van den Beek e2b67da82c Merge pull request #17581 from kostrykin/files_assertions_images 
Add content assertion XML tags for test output verification using images
 2024-03-13 13:08:55 +01:00
Leonid Kostrykin 8a81593c53 Rename has_image_labels to has_image_n_labels 2024-03-13 09:34:34 +00:00
Leonid Kostrykin 5964f72dfc Rename assertion attribute value 2024-03-13 07:28:48 +00:00
Leonid Kostrykin fb7bbaaa83 Rename delta to eps for float-based assertions (#1) 
* Rename `delta` to `eps` for float-based assertions

* Fix tests
 2024-03-11 11:31:23 +01:00
Nicola Soranzo a2018a5e60 Enable flake8-comprehensions ruff rules 
but allow `dict()` calls that make use of keyword arguments (e.g.,
`dict(a=1, b=2)`).
 2024-03-09 19:11:20 +00:00
Nicola Soranzo 75f0618141 Merge branch 'release_24.0' into dev 2024-03-06 10:15:01 +00:00
Leonid Kostrykin 00485ccc52 Squashed commit of the following: 
commit 33b660ee19fa58e84643bba0b875c874a7d3da12
Author: Leonid Kostrykin <void@evoid.de>
Date:   Tue Mar 5 20:58:24 2024 +0000

    Fix XSD

commit 4ee6112b84d3406d6ba98dd190fe07fda2d90307
Author: Leonid Kostrykin <void@evoid.de>
Date:   Tue Mar 5 20:53:14 2024 +0000

    Add `labels` attribute for `has_image_labels` and `has_image_mean_object_size`

commit 4ff401c4f0731cc3aceb9c511f7c3c61abf2b19c
Author: Leonid Kostrykin <void@evoid.de>
Date:   Tue Mar 5 20:32:57 2024 +0000

    Replace `image_has_labels` by `has_image_labels` and `has_image_mean_object_size`

commit 09149d1394a1b81c8c3036316ab2be355db24cde
Author: Leonid Kostrykin <void@evoid.de>
Date:   Tue Mar 5 19:51:56 2024 +0000

    Fix bug

commit 28fedb98f19a35ab6a4747aa5b435c329277df50
Author: Leonid Kostrykin <void@evoid.de>
Date:   Tue Mar 5 19:44:12 2024 +0000

    Replace `image_has_intensities` by `has_image_mean_intensity` and `has_image_center_of_mass`

commit fe96916ca28752f5c5512658db53c4162d8d7d66
Author: Leonid Kostrykin <void@evoid.de>
Date:   Tue Mar 5 19:10:38 2024 +0000

    Replace `image_has_metadata` by `has_image_width`, etc.
 2024-03-05 22:04:55 +01:00
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
mvdbeek 184d880b11 Merge branch 'release_24.0' into dev 2024-03-05 17:05:06 +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