443c5cdd7c
Drop python wrapper for cat1, modernize
2025-09-25 17:38:31 +02:00
57633c35bb
Use consistent naming for added test csv
2025-05-04 09:04:15 -04:00
019a093a63
Add to upload test, test file is an actual geocsv
2025-05-03 18:30:08 -04:00
2c2efe8203
Make im8_uint16.tif tiled so we have a test for is_tiled=True
2025-03-25 14:36:42 +01:00
f3ded28c03
Rename im9_multipage.tif -> im9_multiseries.tif
2025-03-25 14:36:42 +01:00
eb1709fcbb
Merge branch 'release_24.2' into dev
2025-03-08 11:20:03 +01:00
07a4a7c058
Fix directory uploads, use `__FETCH_DATA__` api
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for tool tests, which were still using upload1.
2025-02-25 18:10:10 +01:00
9a8d944fbc
Remove im_corrupted.tif test case
2024-11-21 17:04:07 +01:00
02cb43bbeb
Merge branch 'dev' into image-metadata/dev
2024-11-12 22:34:05 +01:00
e79ec30d4f
Fix linting and add test
2024-10-21 13:35:15 +02:00
685f6538df
Add test for corrupted TIFF file and fix metadata extraction for that case
2024-10-09 09:21:23 +02:00
611739834e
Add test for empty TIFF file (no metadata available)
2024-10-09 08:45:38 +02:00
48b1808d06
Rename series -> page
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This is more consistent with the terminology used in https://github.com/cgohlke/tifffile/blob/8a25a0d4738390af0a1f693705f29875d88fc320/tifffile/tifffile.py#L4676
2024-10-09 08:29:56 +02:00
f9251ee658
Add support for TIFF files with multiple series
2024-10-08 23:44:58 +02:00
371264ca90
Add test for TYX axes
2024-09-25 18:02:05 +02:00
253b550e15
Add test for ZYX axes
2024-09-25 17:11:26 +02:00
1050983124
Add test for ZCYX axes
2024-09-25 16:59:32 +02:00
0bf9266627
Add support for YXCS axes in asserts/image.py
2024-09-25 13:21:47 +02:00
aeeef1d578
Update ruff to 0.6.1
...
Since 0.6.0, ruff checks also Jupyter notebook files by default:
https://astral.sh/blog/ruff-v0.6.0
2024-08-17 18:58:38 +01:00
4fffff6db6
Add float TIFF test case (fails with Pillow)
2024-03-19 22:03:34 +01:00
711fd6a262
Remove unrequired test file
2024-02-28 12:08:22 +01:00
e034928e2f
Fix bugs
2024-02-27 21:54:23 +01:00
3bb63ee5fa
Add functional test for image_diff
2024-02-27 19:22:33 +01:00
1f56fa37d7
WIP: metadata validation.
2023-06-06 10:02:29 +02:00
8dc38e6e4c
Add support for visualizing HDF5 datasets. This contribution is split into two parts: the visualization plugin and backend changes. The client code integrates the h5web visualizer into Galaxy ( https://h5web.panosc.eu ). The backend changes add the ability to access the contents of a dataset without needing to read the whole dataset, which is essential for large files. It is based on the h5grove API ( https://github.com/silx-kit/h5grove ).
2023-05-04 20:48:15 -04:00
a850a47419
Update pysam depedency to 0.20.0
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Fix `pysam.index()` calls which now use samtools 1.16 where
`samtools index input output` doesn't work any more if `output` is the path
of an already existing file, but `samtools index -o output input` works
fine.
Also:
- Pre-create the (empty) index file for mock test datasets as a unit test
reproducer of the above issue.
- Fix `test_cram` unit test that wasn't checking the return value of
`CRAM.set_index_file()`, which was in fact returning False because
`test-data/2.cram` was not sorted (updated now).
2023-01-01 03:37:53 +00:00
e736bedca6
Add connectivity table test dataset
2022-11-18 18:24:54 -05:00
9d18c91aca
Display dataset source transform information.
2021-11-12 11:42:21 -05:00
d88b72f1e0
added sniffer for yaml
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import order
Better sniff for big files, removed extraneous comments
Better test for bigger files
lint
safe load, yaml error
typo
2021-09-20 13:07:20 -07:00
bb9e7f49a1
fix the to_inchi converter
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which had the wrong id: CONVERTER_mol_to_mol2
therefore the test was not executed before
2021-07-01 15:08:49 +02:00
109ba3b698
move test data for molecules converters
2021-06-29 14:06:39 +02:00
fe5fd8282d
test-data: move 2.cram and link to datasets test
2021-06-29 10:47:23 +02:00
fad108f12f
add a bit of docs to the add tags tool
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and extend test for group tags
2021-04-21 11:45:07 +02:00
283ec1772f
Merge branch 'release_20.09' into release_21.01
2021-03-12 17:12:04 +00:00
3506abcc80
Fix `metadata_bcf` framework test
...
Somewhere between file/libmagic 5.36 and 5.39, the output of `file` on a
`.csi` file changed, breaking the ``metadata_bcf`` framework test with
the following error:
```
if found_exceptions:
> raise JobOutputsError(found_exceptions, job_stdio)
E galaxy.tool_util.verify.interactor.JobOutputsError: Output output_of_input_metadata: different than expected, difference (using contains):
E ( /tmp/tmpu1a3dgjcbcf_index_metadata_test.txt v. /tmp/tmpkt78tzggbcf_index_metadata_test.txt )
E Failed to find 'gzip compressed data, extra field' in history data. (lines_diff=0):
lib/galaxy/tool_util/verify/interactor.py:1222: JobOutputsError
```
So add a requirement for the latest `file` version and update the test
accordingly.
2021-03-11 20:21:00 +00:00
c148445e6c
Merge pull request #10880 from bernt-matthias/topic/options-fallback-name
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Dynamic select parameters: also allow to choose legal options by name
2021-01-13 12:00:08 +01:00
365e5a75c2
make 2nd column of 2.tabular test data unique values
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in preparation of a test for chosing selects per name
2021-01-12 13:44:58 +01:00
08810b2174
add empty test file
2021-01-08 12:43:37 +01:00
7c13c03dd6
Fix Galaxy tool/workflow staging and refactor for reuse in Planemo.
2020-08-01 10:34:46 -04:00
549c76a779
Add VCF_BGZIP to VCF converter
2020-07-25 01:33:02 +01:00
fcf5436717
column_param_configfile test: don't check json content
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dont compare the json file content but rely completely on the assertions on
the loaded json contents.
the json content test was superficial and did not work anymore since the order
of the keys differed. it worked before since the inputs contained only a
single key.
2020-02-01 14:15:20 +01:00
f25192b533
json configfiles: handle slect like data_column
...
- in particular the case of an empty select did yield "None" before
now its []
Problem was that the ValueWrapper is not None if nothing is selected
- but also non empty selects were "option1,option2" now its
["option1","option2"]
- renamed variable value -> value_wrapper
2020-02-01 14:15:20 +01:00
dd91b14b6d
Add testcase for new tag from file behavior
2019-05-27 14:58:16 +02:00
0c1334fea0
Fix grouping1 with modern sort, fix test data
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This tool currently fails with `sort: multi-character tab '$\\\\t'\n`
(https://jenkins.galaxyproject.org/view/All/job/docker-main-tools/lastCompletedBuild/testReport/test.functional/test_toolbox_pytest/test_tool_Grouping1_test_1_/ ).
This also removes test data that should be included in
galaxy-test-data instead (xref
https://github.com/galaxyproject/galaxy-test-data/pull/5 ),
and adds a test file that was missing from
https://github.com/galaxyproject/galaxy/pull/7205 .
2019-04-29 17:38:10 +02:00
bfc7b68848
Merge branch 'release_19.01' into dev
2019-04-12 23:18:49 +01:00
d545e88703
Add test case and use assertRaises()
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Also remove temporary directory.
2019-04-12 12:41:48 +01:00
54b9609896
Merge branch 'release_19.01' into dev
2019-04-08 18:29:11 +02:00
fd6198905b
Add test-data
2019-04-07 23:15:35 +02:00
af8ae098f4
Legacy history export tests and infrastructure.
2019-03-11 10:56:25 -04:00
091fe8121a
SQUASH: Adding in other archive containers
...
Per discussion with @bgruening
2019-02-26 16:43:23 -07:00
Nate Coraor