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Commit Graph
9091 Commits
Author SHA1 Message Date
mvdbeek 0308f25b43 Implement templatable configfiles for yaml tools 2025-09-01 17:36:08 +02:00
davelopez 92dfd18ce2 Enhance BaseFileSource test suite 
With comprehensive entry property verification
 2025-08-25 09:48:29 +02:00
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 
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 
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 
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 
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
davelopez ec80e9987d Add type assertions for TempFilesSource in test fixtures 2025-08-19 10:19:36 +02:00
David López c6e6b5b000 Merge pull request #20728 from davelopez/refactor_file_sources_framework_configuration 
Refactor Files Sources Framework for stronger typing using pydantic models
 2025-08-19 10:17:59 +02:00
John Chilton a252af81b9 Tool Landing API... 2025-08-18 11:08:06 -04:00
John Chilton d394f76580 Fix unit test names. 2025-08-18 11:08:05 -04:00
John Chilton 5eba4df33d Fix aliases in fetch_data. 2025-08-18 11:08:05 -04:00
davelopez cc12cf5c42 Refactor test_config_options to use template_config and resolved config 2025-08-18 11:21:11 +02:00
davelopez 6a7bf2454b Fix file source initialization by converting root LocalPath to string 
As the TestPosixConfiguredFileSources expects a string as root argument as well as the pydantic model for PosixFilesSource
 2025-08-18 11:21:05 +02:00
davelopez 9ba75f1dd2 Fix imports for models 2025-08-18 11:20:58 +02:00
davelopez f1b24c121c Adapt tests to new models 2025-08-18 11:20:54 +02:00
davelopez 7ccac30f43 Adapt some types 2025-08-18 11:20:37 +02:00
John Chilton ebd48c7516 Tests for preserving column definitions in different metadata collection strategies. 2025-08-14 09:57:45 -04:00
Marius van den Beek b7008a1f2f Merge pull request #20731 from mvdbeek/hierarchical_display_collection_dataset_states 
Hierarchical display collection dataset states
 2025-08-13 12:55:14 +02:00
mvdbeek ec7929c742 Construct CTEs using sqlalchemy core 2025-08-11 17:17:15 +02:00
mvdbeek a703c9b873 Mock out serialize_to_view, test doesn't add elements to database 2025-08-11 17:17:14 +02:00
mvdbeek 1de8f5a65e Fix pytest raises assertions 2025-08-11 17:17:14 +02:00
mvdbeek 2924f29a1e Use NamedTupe for collection state summary 2025-08-11 17:17:13 +02:00
mvdbeek c2ddea2217 Implement touch collection update time CTE 2025-08-11 17:17:10 +02:00
Ahmed Hamid Awan 57e16eeebd Merge pull request #20624 from ahmedhamidawan/add_error_tab_in_invocation_view 
Add a "Debug" (email report) tab to Workflow Invocations
 2025-08-11 09:37:30 -05:00
mvdbeek e83e6b72a1 Return states and deleted status with HDCA 2025-08-11 10:32:11 +02:00
Nicola Soranzo 1d9d93ea50 Merge branch 'release_25.0' into dev 2025-08-07 15:54:38 +01:00
Marius van den Beek 27fa54355e Merge pull request #20705 from jmchilton/color_param_fix 
[25.0] Fix parameter models for optional color params.
 2025-08-01 11:35:02 +02:00
Nicola Soranzo 7f89e0eab9 Code cleanups from pyupgrade 
Found by running:

```
make pyupgrade
ruff check --fix .
ruff check --preview --unsafe-fixes --select=F401 --fix .
make format
make update-client-api-schema
```

The bulk of the changes are replacements of typing deprecated aliases
such as `Dict` and `List` with the standard library classes. These
aliases became redundant in Python 3.9 when the corresponding
pre-existing classes were enhanced to support `[]`, see
https://docs.python.org/3/library/typing.html#deprecated-aliases

Also:
- Update the `pyupgrade` Makefile target to use `--py38-plus` for the
  packages needed by Pulsar, including the new galaxy-tool-util-models
  package.
 2025-07-31 11:17:22 +01:00
Nicola Soranzo e2777065eb Merge branch 'release_25.0' into dev 2025-07-30 17:45:20 +01:00
Nicola Soranzo 21d827f678 Merge branch 'release_24.2' into release_25.0 2025-07-30 17:33:15 +01:00
Ahmed Awan f7afe9daf0 fix security check return; exception vs False return 2025-07-30 10:48:46 -05:00
Ahmed Awan 0f700e1ac2 add unit tests for invocation feedback reporting 2025-07-30 10:48:46 -05:00
John Chilton a2af62966d Fix parameter models for optional color params. 2025-07-30 11:37:12 -04:00
Nicola Soranzo f28450cb75 Fix `test_base_image_for_targets` mulled test to use mzmine 
maker is not using the ``extended-base`` image since
https://github.com/bioconda/bioconda-recipes/commit/ce27c583fdd8fcaa60166fa3b0173083e352fd6b
 2025-07-30 14:53:04 +01:00
Marius van den Beek b48e97552f Merge pull request #19305 from jmchilton/sample_sheets 
Implement Sample Sheets
 2025-07-30 11:14:38 +02:00
Marius van den Beek 393e005ce9 Merge pull request #20510 from nsoranzo/remove_ToolDocumentCache 
Remove deprecated tool document cache
 2025-07-29 17:03:42 +02:00
Nicola Soranzo 02179acbef Merge pull request #20586 from Smeds/add-lexicmap-datatype 
[25.0] Add datatype for LexicMap index
 2025-07-29 11:04:57 +01:00
John Chilton 5447f98289 Rework sample sheets to use POSTs instead of GETs. 
Marius outlines why in the review of the PR.
 2025-07-28 13:43:14 -04:00
Arash ce52a72ebf Update HDASerializer test to validate copied_from_history_dataset_association_id with assertNullableEncodedId 2025-07-28 09:15:22 +02:00
John Chilton d26605517e Implement sample sheets. 2025-07-25 11:46:59 -04:00
John Chilton 7c09824364 Log format parsing info & column inferences when parsing workbooks. 2025-07-25 11:46:24 -04:00
John Chilton 8947cf8051 Generalize fetch workbook parsing on backend. 
Can now read a bunch of CSV/TSV files as easily as excel files.
 2025-07-25 11:46:24 -04:00
John Chilton 316d9817a8 Validate workflow inputs more directly on the backend. 2025-07-25 11:46:24 -04:00
Alireza Heidari 039e8457ac Merge pull request #20666 from davelopez/history_export_wizard 
Unify History export UX using wizard
 2025-07-22 16:26:50 +02:00
Leonid Kostrykin 65e5ed0d12 Revert "Merge pull request #20464 from mvdbeek/drop_num_unique_values" 
This reverts commit 6fe8a7bf6d, reversing
changes made to 8903af6964.
 2025-07-17 14:38:18 +02:00