mvdbeek
a1ecabdfbc
Adjust API tests
...
Most of the time we just want an OK status code. 202, 204, 200 should
all be OK and some of this depends on the Galaxy instance config,
so this should be more robust to future changes.
2025-09-23 22:16:20 +02:00
Marius van den Beek
1ccf881190
Merge pull request #20838 from nsoranzo/pytest8
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Update pytest to v8
2025-09-23 17:00:13 +02:00
John Chilton
248ffcde05
Merge pull request #19086 from jmchilton/markdown_embedded_directives
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Allow several Galaxy Markdown directives to be embedded.
2025-09-23 10:48:32 -04:00
Marius van den Beek
50e39b245c
Merge pull request #20932 from mvdbeek/user_defined_tool_type
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Allow addressing user defined tools in job config
2025-09-22 15:01:11 +02:00
mvdbeek
99df41a49a
Merge branch 'release_25.0' into dev
2025-09-22 09:11:38 +02:00
mvdbeek
0c09aa9e5c
Add test for proposed prod-like deployment
2025-09-21 17:03:17 +02:00
mvdbeek
b204902146
Discriminate user defined tools via tool_type and tool_class
2025-09-21 15:28:27 +02:00
mvdbeek
e76e2f66c9
Fix collection element sorting in extended_metadata
2025-09-19 18:57:53 +02:00
mvdbeek
48841bd55e
Merge branch 'release_25.0' into dev
2025-09-19 17:19:41 +02:00
Marius van den Beek
c254d6cb2f
Merge pull request #20925 from mvdbeek/fix_sessionless_tag_creation
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[25.0] Fix sessionless tag creation
2025-09-19 17:19:20 +02:00
mvdbeek
253b1768e3
Test sessionless tag creation
2025-09-19 15:44:48 +02:00
Nicola Soranzo
45f2fd96a5
Disable celery tasks for Onedata tests
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Fix upload jobs not being picked up by the job handlers:
```
FAILED test/integration/objectstore/test_onedata_objectstore.py::test_tools[multi_output_assign_primary] - galaxy.tool_util.verify.wait.TimeoutAssertionError: Timed out after 60.25 seconds waiting on tool test run.
FAILED test/integration/objectstore/test_onedata_objectstore.py::test_tools[composite_output_tests] - galaxy.tool_util.verify.wait.TimeoutAssertionError: Timed out after 60.25 seconds waiting on tool test run.
FAILED test/integration/objectstore/test_onedata_objectstore.py::test_tools[metadata_bam] - galaxy.tool_util.verify.wait.TimeoutAssertionError: Timed out after 60.25 seconds waiting on tool test run.
```
2025-09-18 04:10:52 +01:00
Nicola Soranzo
0c2d349e35
Restore all environment variables at the end of Keycloak integration tests
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not just `OAUTHLIB_INSECURE_TRANSPORT`.
Fix the following error in integration tests that were run after
those in `test/integration/oidc/test_auth_oidc.py`:
```
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1147)
```
Introduced in https://github.com/galaxyproject/galaxy/pull/16977 .
2025-09-18 04:10:51 +01:00
David López
e44d3f096d
Merge pull request #20332 from davelopez/explore_short_term_storage_expiration_indicator
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Add short term storage expiration indicator to history items
2025-09-17 13:13:57 +02:00
Ahmed Hamid Awan
2d513e834c
Merge pull request #20911 from ahmedhamidawan/merge_25.0_into_dev_sept
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Merge 25.0 into dev
2025-09-15 21:06:30 -05:00
Ahmed Awan
f823afcc2a
Merge remote-tracking branch 'upstream/release_25.0' into merge_25.0_into_dev_sept
2025-09-15 14:46:12 -05:00
marius-mather
fff7a92d1c
Update unit tests to use attribute access
2025-09-15 13:30:38 +10:00
marius-mather
c11e7529c8
Merge remote-tracking branch 'upstream/dev' into oidc-pipeline-config
2025-09-15 11:05:44 +10:00
John Davis
b10409b2dd
Skip broken unit tests
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These tests require a rewrite of the entire test module, which is not a
quick fix, and so should not slow down the merging of the bug fix in
this PR.
2025-09-11 11:35:37 -04:00
John Chilton
2fa7b43ab5
Merge pull request #20859 from mvdbeek/multiple_true_data_collection_map_over
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Fix `multiple="true"` data collection map over for shell_command tools
2025-09-08 10:02:49 -04:00
Nicola Soranzo
06245f4f08
Fix test in `configfile_user_defined.yml`
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Introduced in commit 0308f25b43
2025-09-08 11:56:34 +01:00
John Davis
aed502d340
Merge pull request #20811 from ksuderman/20810-ipynb-sniffer
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Fix Ipynb datatype sniffer and add unit tests.
2025-09-05 14:11:02 -04:00
John Davis
763c859530
Ignore type error: function is defined in sniff.py
2025-09-05 14:00:29 -04:00
Keith Suderman
d0b4b9a1b4
Rebase with upstream changes
2025-09-05 13:22:19 -04:00
Keith Suderman
14188b8402
Run make format to fix linting errors
2025-09-05 11:27:40 -04:00
Tim Kok
7d21159a28
Fix linting + remove debug statement
2025-09-05 13:08:52 +02:00
Tim Kok
3f029fdf5e
Remove debug statement
2025-09-05 12:31:24 +02:00
Tim Kok
cc6da148c1
Add support for hierarchical module systems in lmod + modules dependency resolvers
2025-09-05 09:04:31 +02:00
Keith Suderman
b9f3b1f552
Simplify unit tests and add test data files.
2025-09-04 19:34:42 -04:00
mvdbeek
5ccf97752b
Verify collection is correctly consumed
2025-09-04 14:48:44 +02:00
Matthias Bernt
0b6cf742fb
Revert "add functional tool test for directory datatypes"
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This reverts commit 716e3607a9
2025-09-03 15:00:12 +02:00
Matthias Bernt
716e3607a9
add functional tool test for directory datatypes
2025-09-03 14:42:18 +02:00
marius-mather
da6bb6f8ba
Lint fixes
2025-09-02 11:41:50 +10:00
marius-mather
9436735034
Add tests of pipeline config
2025-09-02 10:42:40 +10:00
mvdbeek
eb823365bb
Don't load custom tools into toolbox
2025-09-01 17:36:11 +02:00
mvdbeek
0308f25b43
Implement templatable configfiles for yaml tools
2025-09-01 17:36:08 +02:00
davelopez
ef93b67cf3
Adds integration tests for object store expiration handling
2025-08-29 11:09:50 +02:00
davelopez
1b5673b6b8
Adapt test_export_dataset_collection_paired test
2025-08-29 10:43:25 +02:00
davelopez
f13a648b89
Patch serialize_object_store_ids in test_export_dataset_collection_paired test
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To handle mock datasets when serializing the collection during export
2025-08-29 10:43:24 +02:00
davelopez
92dfd18ce2
Enhance BaseFileSource test suite
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With comprehensive entry property verification
2025-08-25 09:48:29 +02:00
Keith Suderman
1cf079b56d
Fix Ipynb datatype sniffer and add unit tests.
2025-08-22 11:23:08 -04:00
Nicola Soranzo
7a65393d4b
Merge branch 'release_25.0' into dev
2025-08-21 16:25:52 +01:00
Nicola Soranzo
429366e7d0
Add unit test
2025-08-21 11:33:38 +01:00
Ahmed Hamid Awan
d26ddf3ff2
Merge pull request #20744 from itisAliRH/history-list-g-card-refactor
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New History List Using GCard
2025-08-20 18:35:36 -05:00
Marius van den Beek
fed092fe46
Merge pull request #20698 from davelopez/add_fsspec_support
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Add `fsspec` base implementation for File Source plugins
2025-08-20 10:58:47 +02:00
Marius van den Beek
41a72b2ab9
Merge pull request #20592 from jmchilton/tool_landing
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Implement Data Landing Requests
2025-08-19 14:55:55 +02:00
davelopez
552396cc7a
Add test suite for MemoryFilesSource
2025-08-19 14:01:11 +02:00
davelopez
060e4735f3
Refactor TempFilesSource tests to use generic test suite
2025-08-19 14:00:48 +02:00
davelopez
4826d63a3c
Add generic test suite for BaseFilesSource implementations
2025-08-19 14:00:17 +02:00
Alireza Heidari
aaee797337
Improves history import verification
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Replaces grid-based history name verification with a more robust check using the history card list.
Ensures tests are aligned with current UI behavior.
2025-08-19 11:51:39 +02:00
mvdbeek