mvdbeek
1e48e15ffb
Record input parameter invocation inputs
...
as they become available. Fixes the test in in the previous commit and
also means that inputs are properly recorded, something that's always
been unavailable for subworkflow invocations.
2025-12-13 13:37:50 +01:00
mvdbeek
e63ac527a0
Maintain columns on sample sheet map over
2025-12-12 08:27:39 +01:00
Nicola Soranzo
388b4a56b6
Merge branch 'release_25.0' into release_25.1
2025-11-25 19:40:13 +00:00
Nicola Soranzo
522546cfc3
Merge branch 'release_24.2' into release_25.0
2025-11-25 17:29:43 +00:00
Nicola Soranzo
42fda3adcd
Use anaconda API to find package download URL
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Fix the following failing mulled unit test:
```
FAILED test/unit/tool_util/mulled/test_get_tests.py::test_find_anaconda_versions - AssertionError: assert '/bioconda/2pg_cartesian/1.0.1/download/linux-64/2pg_cartesian-1.0.1-0.tar.bz2' in []
```
2025-11-25 16:33:37 +00:00
mvdbeek
3ef66cf65a
Merge branch 'release_25.0' into release_25.1
2025-11-17 15:20:25 +01:00
Nicola Soranzo
dd34c6d0ff
Merge pull request #21013 from mvdbeek/store_pulsar_job_prep_error_messages
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[25.0] Store pulsar job prep error messages
2025-11-14 22:11:09 +00:00
Marius van den Beek and Nicola Soranzo
aaf9965038
Fix linting issues
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2025-11-14 20:29:17 +01:00
mvdbeek
7256e5df48
Store pulsar job prep error messages
2025-11-13 18:39:40 +01:00
Nicola Soranzo
ba0bf2e868
Merge branch 'release_25.0' into release_25.1
2025-11-12 12:15:23 +00:00
John Chilton
7d251e76b2
Fixtures for manually ensuring we don't lexiographically sort tool versions.
2025-11-04 11:32:38 -05:00
Nicola Soranzo
fb9926ab44
Merge branch 'release_25.0' into release_25.1
2025-10-31 11:58:58 +00:00
John Chilton
ded7f0b567
Try to improve error messages for workbook upload parsing problems.
2025-10-30 10:59:58 -04:00
davelopez
5f92026d98
Adds test for RO-Crate export with unset optional parameter
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Ensures exporting a workflow invocation with an optional text parameter
left unset does not raise errors, addressing a previous issue with
handling None output values during RO-Crate creation.
2025-10-29 16:31:40 +01:00
mvdbeek
20b691b7cd
Resolve possible symlink before establishing tool file location
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I don't think this is a security issue because adding entries to the
tool config files is controlled by admins.
Fixes pulsar tests that fail after required_files was added to the
Filter1 tool. Also allows dropping the the symlink to the tool script.
2025-10-27 18:12:52 +01:00
Marius van den Beek
f91bca0ccd
Merge pull request #21091 from davelopez/25.1_fix_invocation_export_dataset_exclusion
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[25.1] Fix invocation export dataset exclusion
2025-10-17 18:20:30 +02:00
mvdbeek
0fae2608a4
Merge branch 'release_25.0' into release_25.1
2025-10-17 16:53:42 +02:00
davelopez
c166087597
Adds integration test for invocation export dataset flags
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Adds an integration test to verify the correct inclusion and exclusion of hidden and deleted datasets during export of workflow invocations.
2025-10-16 20:23:20 +02:00
Matthias Bernt
9203996550
extend test
2025-10-16 14:52:56 +02:00
Alireza Heidari
145acb2c27
Updates API routes to use plural 'groups' for credential group endpoints
2025-10-07 16:07:59 +02:00
Alireza Heidari and Arash Kadkhodaei
25347eee7f
Refactors credentials API to include user credentials ID
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Updates the credentials update and delete endpoints to require user credentials ID in the URL path, improving API consistency and enabling proper resource identification.
Modifies the PUT endpoint from `/credentials/group/{group_id}` to `/credentials/{user_credentials_id}/group/{group_id}` and updates the DELETE endpoint to include `/group/` segment for better REST API design.
Updates all related client code, tests, and API schema to handle the new endpoint structure with the additional user credentials ID parameter.
Co-authored-by: Arash Kadkhodaei <arash77.kad@gmail.com >
2025-10-07 16:07:58 +02:00
Alireza Heidari
eb088c0be8
Unify credential modals naming for clarity
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Updates type names to be more descriptive and consistent across the codebase.
2025-10-07 16:07:44 +02:00
Arash
51e2ec737e
Adds group update_time; removes aggregate field
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Adds explicit last-updated timestamp at credential group level and removes aggregated user credentials update_time to avoid misleading semantics.
Ensures group timestamp always refreshes on updates (even when only name unchanged) and returns it in responses for more precise change tracking.
Expands integration tests: adds granular update sequencing assertions, comprehensive update scenarios, and validation/error case coverage with helper methods for updating groups.
Improves clarity of schema, accuracy of audit data, and robustness of update validation.
2025-10-07 16:07:34 +02:00
Arash
b709fc48db
Adds update_time field to user credentials and implements tests for its functionality
2025-10-07 16:07:23 +02:00
davelopez
3b65a05241
Add vault integration tests for credentials
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Introduces tests to validate integration between user credentials and the vault, ensuring secure storage and deletion of secrets.
2025-10-07 16:07:09 +02:00
Arash
3385e91189
Refactor credential validation tests to handle invalid group names and improve error handling
2025-10-07 16:07:08 +02:00
davelopez
332e61f182
Simplify response handling in credentials API test
2025-10-07 16:07:08 +02:00
Arash
8c2a6901c1
Refactors credential management tests to improve group handling and validation scenarios
2025-10-07 16:07:07 +02:00
Arash
8d5b5ce74d
Enhances credentials management by adding update functionality for user credentials and groups, refactoring related methods and data structures for improved clarity and efficiency.
2025-10-07 16:06:27 +02:00
Arash
3900b74dd8
Refactor user credentials to allow optional current group values
2025-10-07 16:06:12 +02:00
Arash
31c5b6dec8
Refactor requirement parsing in multiple files to streamline credential handling
2025-10-07 16:06:04 +02:00
Arash
d81a9fa556
Refactor error handling in CredentialsService to raise ObjectNotFound for undefined services and enhance test coverage for invalid credential scenarios
2025-10-07 16:05:48 +02:00
Arash
afc933ba3f
Add source_version, service_name, and service_version to user credentials and removing service_reference, optional, and multiple from user credentials definition and add optional tag to the credential definition and update related functionality
2025-10-07 16:05:45 +02:00
Arash
f2b598ae78
Replaces Secret and Variable with Credential
2025-10-07 16:05:42 +02:00
Arash
015a526aa1
Renames 'reference' to 'service_reference'
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Applying suggestions from John Davis
2025-10-07 16:05:40 +02:00
Arash
3381ecf8c0
Refactor test_CredentialsManager to consolidate imports
2025-10-07 16:05:40 +02:00
Arash
85bcbf3a96
Refactor test_CredentialsManager to improve type annotations for rows_to_delete
2025-10-07 16:05:39 +02:00
Arash
201e78fcd8
Refactors credential management and improves type annotations
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Renames variables for clarity and consistency
2025-10-07 16:05:38 +02:00
davelopez
378b394e1e
Add test to ensure other users cannot list credentials
2025-10-07 16:05:37 +02:00
davelopez
3ef0ee369a
Add test to ensure anonymous users cannot provide credentials
2025-10-07 16:05:37 +02:00
Arash
35892c6b70
Add unit tests for CredentialsManager functionality
2025-10-07 16:05:36 +02:00
Arash
9cc8a39f66
Add tool_id attribute to MockTool class to fix the test
2025-10-07 16:05:35 +02:00
davelopez
ba3de7eb5c
Refactor + add more integration tests for user credential management
2025-10-07 16:05:34 +02:00
Arash
13880364c0
Refactor integration tests for user credentials
2025-10-07 16:05:34 +02:00
Arash
34f7edc31c
Add integration test for adding a new group to user credentials
2025-10-07 16:05:30 +02:00
Arash
52fe41b31c
Enhance test coverage for credential management
2025-10-07 16:05:22 +02:00
Arash
f22bd6b723
Add ondelete cascade to user credential group foreign keys and update integration tests
2025-10-07 16:05:19 +02:00
Arash
6139dbc2b1
Fix API endpoint string formatting in integration tests for user credentials
2025-10-07 16:05:18 +02:00
Arash
5bf23d76d4
Add integration tests for user credentials API
2025-10-07 16:05:18 +02:00
Arash
3081179c94
rename parse_requirements_and_containers to parse_requirements,
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remove unused tests,
add credential yaml test,
refactor tool evaluator (needs more work)
2025-10-07 16:05:13 +02:00
mvdbeek