Commit Graph
622 Commits
Author SHA1 Message Date
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 GuandM 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 BerntandNicola Soranzo 47b6780fb9 fix typo
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
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
John Chilton a6f3b255cb Merge pull request #11764 from mvdbeek/fix_format_input_implicit_conversion
[21.01] Fix format="input" with implicit conversions
2021-04-01 10:45:55 -04:00
mvdbeek 7eb853d703 Fix format="input" with implicit conversions
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 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
John Chilton 8f9bdd6eb5 Failing test case for output problem. 2021-03-14 19:58:31 -04:00
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 5b92a04cba add test tool testing collection default format 2021-03-04 18:37:17 +01:00
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 BerntandMarius van den Beek 21a5837677 fix quoting
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
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
Marius van den Beek c148445e6c Merge pull request #10880 from bernt-matthias/topic/options-fallback-name
Dynamic select parameters: also allow to choose legal options by name
2021-01-13 12:00:08 +01:00
Matthias Bernt 3bed882331 add test cases 2021-01-13 11:57:17 +01:00
Matthias Bernt 2ad6c6d194 test qualified and unqualified access to
variables in conditionals
2021-01-12 19:34:08 +01:00
Matthias Bernt 5f67c2075b fix name and value column in select_from_dataset.xml 2021-01-12 19:27:07 +01:00
Matthias Bernt 0c8c403bf4 add tests
showing that dynamic selects can be chosen by name for
from_data_table and from_dataset
2021-01-12 13:45:45 +01:00
Matthias Bernt d512049a4a more specific functional tool tests involving fasta_indexes.loc
rename entries such that they are suffixed by the column name
(execpt for dbkey).
this makes tests more specific, because this ensures that always
the correct column is used.
2021-01-12 13:44:58 +01:00
Matthias Bernt fd97fd4b5b fix output assertion in test tool 2021-01-08 12:44:39 +01:00
Matthias Bernt 5a01f060d9 add explicit formats to validation_empty_dataset.xml 2021-01-08 12:43:37 +01:00
Matthias Bernt 4343014792 add validation for collection parameters 2021-01-08 12:43:37 +01:00
Nicola Soranzo f99fbd4981 Merge pull request #11073 from mvdbeek/empty_work_dir_outputs_v3 2021-01-07 19:01:05 +00:00
Nicola Soranzo 3be6e1805e Lint collection_creates_pair_from_work_dir tool 2021-01-07 16:51:18 +00:00
Nicola Soranzo 82a66c59d2 Lint output_empty_work_dir tool 2021-01-07 16:47:15 +00:00