Marius van den Beek
eb3f3c816f
Merge pull request #11832 from qiagu/dynamic_options
...
Make tool parameter options capable of referring to metadata file
2021-05-04 09:49:35 +02:00
cat-bro
58f767d296
breaking test for GalaxyInteractorApi get_tool_tests
2021-04-29 23:50:12 +10:00
Matthias Bernt
8852d543cc
fix test
...
Despite lines in 4.maf like
```
e echTel1.scaffold_309554 3896 34801 + 42008 I
```
echTel1 seems not to be in the metadata table.
So I have chosen another one.
2021-04-19 11:06:40 +02:00
Matthias Bernt
1a70bf5093
debug: switch test files cont.
2021-04-18 21:48:14 +02:00
Matthias Bernt
84fceaab6a
debug: switch test files
2021-04-18 19:27:46 +02:00
Matthias Bernt
243091f046
use a different file for test
...
to check if options are added
2021-04-18 17:29:18 +02:00
qiagu
3c05f0b85b
Add test for options from metadata file of dataset_collection
2021-04-15 15:36:26 -07:00
Qiang Gu and M Bernt
6645b4093b
Update test/functional/tools/options_from_metadata_file.xml
...
Co-authored-by: M Bernt <m.bernt@ufz.de >
2021-04-15 13:56:08 -07:00
qiagu
6844607088
Fix tool styling
2021-04-13 20:21:24 -07:00
qiagu
ca4e7ea83b
Add simple doc for usage of meta_file_key
2021-04-13 19:43:11 -07:00
qiagu
455b838bd4
Make test tool for meta_file_key
2021-04-13 19:23:59 -07:00
Nicola Soranzo
d9188a4c3e
Merge pull request #11111 from bernt-matthias/topic/cheetah-qualified
2021-04-08 02:40:06 +01:00
M Bernt and Nicola Soranzo
47b6780fb9
fix typo
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-04-07 19:38:25 +02:00
Matthias Bernt
5034d6dd62
test qualified and unqualified access
2021-04-07 17:39:48 +02:00
John Chilton
66c1132ec0
Merge pull request #11307 from bernt-matthias/topic/recurse-dirs
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ignore subdirectories if recurse is false
2021-04-07 10:06:52 -04:00
M Bernt
08fbff5844
tests for multiple value splitter
2021-04-06 18:32:19 +02:00
mvdbeek
aa6e1dcc05
Merge branch 'release_21.01' into dev
2021-04-01 16:52:11 +02:00
John Chilton
a6f3b255cb
Merge pull request #11764 from mvdbeek/fix_format_input_implicit_conversion
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[21.01] Fix format="input" with implicit conversions
2021-04-01 10:45:55 -04:00
mvdbeek
7eb853d703
Fix format="input" with implicit conversions
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where the implicit converter uses galaxy.json.
Add test, fix fix
2021-03-31 22:06:39 +02:00
Anthony Bretaudeau
4adeca0e86
Merge remote-tracking branch 'upstream/release_21.01' into pulsar_tool_dir
2021-03-25 16:53:34 +01:00
mvdbeek
ac3fcf911e
Merge branch 'release_21.01' into dev
2021-03-24 20:34:06 +01:00
mvdbeek
a9389ecd08
Drop test that does not apply to multiple="true" data_column parameters
2021-03-22 09:28:47 +01:00
mvdbeek
70934cd276
Add selenium test for data column parameters in workflow editor
2021-03-19 22:42:57 +01:00
mvdbeek
d03c7af02a
Merge branch 'release_21.01' into dev
2021-03-15 14:53:07 +01:00
John Chilton
8f9bdd6eb5
Failing test case for output problem.
2021-03-14 19:58:31 -04:00
Nicola Soranzo
6c540932c7
Merge branch 'release_21.01' into dev
2021-03-12 19:01:35 +00:00
Nicola Soranzo
283ec1772f
Merge branch 'release_20.09' into release_21.01
2021-03-12 17:12:04 +00:00
Nicola Soranzo
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
Anthony Bretaudeau
b13a412133
Add test case for https://github.com/galaxyproject/pulsar/issues/249
2021-03-11 16:17:06 +01:00
Kaivan Kamali
b023970196
Added a default value to fix a broken framework test.
2021-03-10 10:26:41 +01:00
Kaivan Kamali
d423b29336
Added another test for when columns are a comma separated string
2021-03-10 10:26:41 +01:00
Matthias Bernt
b8eaa1a2c0
add test tool testing collection default format
2021-03-05 14:47:31 -05:00
Matthias Bernt
5b92a04cba
add test tool testing collection default format
2021-03-04 18:37:17 +01:00
John Chilton
e09e04bb69
Merge pull request #11514 from kxk302/csv_columns
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Handle the case where column list is a comma-separated string
2021-03-04 09:41:30 -05:00
Kaivan Kamali
423a95435b
Added a default value to fix a broken framework test.
2021-03-02 17:35:42 -05:00
Kaivan Kamali
28c89ac950
Added another test for when columns are a comma separated string
2021-03-02 14:02:55 -05:00
Nate Coraor
a2d1625780
Merge remote-tracking branch 'upstream/release_21.01' into dev
2021-03-01 16:52:02 -05:00
Nate Coraor
7ed0f5337f
Merge remote-tracking branch 'upstream/release_20.09' into release_21.01
2021-03-01 16:47:23 -05:00
Matthias Bernt
424ea656ac
add test
2021-02-25 18:08:27 +01:00
Matthias Bernt
8708e011cf
create a test file in $HOME
2021-02-25 12:28:21 +01:00
Matthias Bernt
11b7b369c4
simplify debugging
2021-02-25 12:27:26 +01:00
M Bernt and Marius van den Beek
21a5837677
fix quoting
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2021-02-25 12:25:21 +01:00
Matthias Bernt
742bae057c
test writing to job home and tmp
2021-02-25 12:24:42 +01:00
Nicola Soranzo
7ac4278feb
Merge branch 'release_20.09' into release_21.01
2021-02-19 18:01:13 +00:00
Nicola Soranzo
b93b81aaf2
Merge branch 'release_20.05' into release_20.09
2021-02-19 17:56:55 +00:00
Matthias Bernt
bd5e8f326c
fix profile logic for configfile generation
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some follow up fixes to
https://github.com/galaxyproject/galaxy/pull/9279/files
https://github.com/galaxyproject/galaxy/pull/9776/files
- wrong profile for the profile test tool (it used 20.01, but should
have used 20.05)
- the non-profile test tool used wrong assumptions. now fixed
and also tested against 19.09
- in the profile version `value_wrapper.value` needs to be casted
for `multiple==False` otherwise we gat `"None"` (which I do not
understand 100%)
2021-02-18 12:33:07 +01:00
Matthias Bernt
71dabed417
fix profile logic for configfile generation
...
some follow up fixes to
https://github.com/galaxyproject/galaxy/pull/9279/files
https://github.com/galaxyproject/galaxy/pull/9776/files
- wrong profile for the profile test tool (it used 20.01, but should
have used 20.05)
- the non-profile test tool used wrong assumptions. now fixed
and also tested against 19.09
- in the profile version `value_wrapper.value` needs to be casted
for `multiple==False` otherwise we gat `"None"` (which I do not
understand 100%)
2021-02-15 19:22:29 +01:00
John Chilton
e3dedd86bc
Performance metrics for tests.
2021-02-12 20:44:05 -05:00
Nicola Soranzo
d26b3d9848
Fix all E203, E741 and W504 flake8 errors
2021-01-18 10:35:41 +00:00
Marius van den Beek
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
Marius van den Beek