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718 Commits
Author SHA1 Message Date
Nicola Soranzo 70b2ea429c Merge branch 'release_22.01' into release_22.05 2022-09-06 12:12:21 +01:00
Nicola Soranzo 9f1d8d053b Merge branch 'release_21.09' into release_22.01 2022-09-06 11:36:36 +01:00
Nicola Soranzo 06baa27d05 Merge branch 'release_21.05' into release_21.09 2022-09-06 11:24:20 +01:00
Nicola Soranzo 8069584d0f Merge branch 'release_21.01' into release_21.05 2022-09-06 11:12:59 +01:00
Matthias Bernt 59f77048ce test case showing failing set_meta 
broke in https://github.com/galaxyproject/galaxy/commit/7d0ec29fa06ae6f04c0ae6fc193a390bc11cddcd
 2022-08-25 16:45:26 +02:00
mvdbeek 94c75a083c Fix setting metadata elements in conditional tool action 
Fixes https://github.com/galaxyproject/galaxy/issues/14509
 2022-08-25 14:27:44 +02:00
Nicola Soranzo b5a75cac27 Merge branch 'release_22.01' into release_22.05 2022-08-19 15:28:58 +01:00
Matthias Bernt 8ef9ef4383 fix test 2022-08-18 14:28:55 +02:00
Nicola Soranzo e383e593e0 Merge branch 'release_22.01' into release_22.05 2022-07-27 15:38:19 +01:00
Matthias Bernt fe06eea75d fix test output 2022-07-15 10:49:12 +02:00
M BerntandNicola Soranzo d7272cc987 Update test/functional/tools/options_from_metadata_file.xml 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-07-14 23:30:11 +02:00
Matthias Bernt d642ce34c8 fix startswith attribute of <options> 
as documented in the xsd

in addition fix https://github.com/galaxyproject/galaxy/issues/14324,
i.e. document the `separator` attribute of options

also doc that only 1MB is used and lines starting with `#` are always
ignored
 2022-07-14 14:19:40 +02:00
mvdbeek df6551da78 Test that metadata validators work 2022-06-25 12:55:51 +02:00
Nicola Soranzo d3b4ef81d0 Merge branch 'release_21.09' into release_22.01 2022-06-23 14:30:57 +01:00
Dannon 155c1c6e48 Merge pull request #5378 from jmchilton/resource_requirements 
Allow specification of resource requirements in tools.
 2022-06-20 14:11:35 -04:00
mvdbeek 1df9646747 Add <resource/> tag set to schema, add tool 
I think this leaves us more room to write expressions without having to
escape everything.
 2022-06-15 13:53:58 +02:00
mvdbeek 55ecc382e7 Add selenium test for ucsc table browser data source 2022-06-13 11:03:13 +02:00
mvdbeek 5ea0a53538 Add selenium test for ucsc table browser data source 2022-06-09 15:03:45 +02:00
Marius van den Beek 7cb3f76c6e Merge pull request #12232 from bernt-matthias/topic/drilldown 
fix `drill_down` parameters
 2022-05-25 15:52:50 +02:00
Marius van den Beek ac510bc8dc Merge pull request #7894 from bernt-matthias/topic/count-pairs-correctly 
Fix docs for `expect_num_outputs` and add `count` attribute for test `output` and `element` tags
 2022-05-25 15:23:10 +02:00
mvdbeek 704af8fc59 Fix collection_creates_dynamic_list_of_pairs test 
The upload1 tool would have created a dataset in the history that would
have become auto-selected ... which is of course a bug when running
tools via the API, xref
https://github.com/galaxyproject/galaxy/issues/13799.
 2022-04-23 12:16:42 +02:00
M BerntandMarius van den Beek 803b9a5a5b Apply suggestions from code review 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-04-22 12:05:56 +02:00
M Bernt 228d07a9cc Merge branch 'dev' into topic/count-pairs-correctly 2022-04-21 13:03:59 +02:00
Matthias Bernt ad70b9bc4a fix config file generation 
always create the config file in `job_directory/configs/` and
if `filename` is given create a symlink to the actual config file

fixes https://github.com/galaxyproject/galaxy/issues/13586
 2022-04-21 11:15:07 +02:00
John Chilton c247b38b3d Fixup simple_constructs.yml... 2022-04-19 11:23:44 -04:00
Nicola Soranzo 8adc7ec870 Merge branch 'release_21.09' into release_22.01 2022-04-11 19:03:41 +01:00
Matthias Bernt 4bc560383f add test for correct sorting on recursive discovery 2022-04-08 19:38:50 +02:00
Matthias Bernt 0626e45b3c add test for correct sorting on recursive discovery 2022-04-07 14:42:19 +02:00
Matthias Bernt 4ac6c9f2e9 fix profile of multi_output_recurse 
feature was merged in july 21
 2022-04-07 12:24:12 +02:00
Nicola Soranzo a4053dc199 Merge branch 'release_22.01' into dev 2022-03-28 23:16:34 +01:00
Matthias Bernt a725e90a50 add more doc and test 2022-03-22 18:56:49 +01:00
Matthias Bernt f8a19bd761 drill_down: make values unique 
fix: if an option is selected that is contained in an already selected
subtree then the selected values contained duplicates
 2022-03-22 14:25:07 +01:00
Matthias Bernt 9c5cfed6f4 add functional test for drill down parameters 2022-03-22 08:57:42 +01:00
mvdbeek 2e61fccb1c Extend kubernetes logs to check that job logs are properly recorded 2022-03-19 12:11:41 +01:00
mvdbeek 1c24f26dae Merge branch 'release_22.01' into dev_test 2022-02-12 17:36:32 +01:00
mvdbeek 973f6679d6 Merge branch 'release_21.09' into release_22.01 2022-02-11 13:29:04 +01:00
mvdbeek 96e76c62d2 Don't record version command as part of command line 
Fixes https://github.com/galaxyproject/galaxy/issues/13306
 2022-02-08 15:52:06 +01:00
mvdbeek bec9d4b49f Fix resuming job when job has optional data parameters 
This fixes
```
ERROR    galaxy.tools.actions:__init__.py:683 Cannot remap rerun dependencies.
Traceback (most recent call last):
  File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 664, in _remap_job_on_rerun
    self.__remap_parameters(job_to_remap, jtid, jtod, out_data)
  File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 694, in __remap_parameters
    input_values = {p.name: json.loads(p.value) for p in job_to_remap.parameters}
  File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 694, in <dictcomp>
    input_values = {p.name: json.loads(p.value) for p in job_to_remap.parameters}
  File "/usr/local/Cellar/python@3.9/3.9.10/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py", line 339, in loads
    raise TypeError(f'the JSON object must be str, bytes or bytearray, '
TypeError: the JSON object must be str, bytes or bytearray, not
NoneType
```

Optional data inputs or optional selects are stored as `None` (super
inconsistent, since most other parameters are stored as JOSN. We should
create "basic_2.py" using pydantic at one point not too far into the
future ...). This means we can't call `json.loads` on these. Fortunately
this is the only place we do it, and we don't need to consider optional
parameters here anyway.
 2022-02-08 15:45:01 +01:00
mvdbeek 6ee7d6bfe2 Merge branch 'release_22.01' into dev 2022-02-04 09:49:21 +01:00
Dannon Baker 623a5e165a Apply black formatting. 
Apply isort.
 2022-02-03 07:42:20 -05:00
John Chilton 671ca0a7fe Implement bioconductor xref on the frontend. 
Cleanup xref rendering a bit.
 2022-02-02 14:56:07 -05:00
Matthias Bernt 4a5fd66a49 also check count also for element XML tags 
which allows to check the "structure" of nested collections
 2022-01-30 15:22:05 +01:00
Matthias Bernt 065e4e7509 add count attribute to test output tags 
which allows to count discovered data sets
 2022-01-30 15:22:04 +01:00
Matthias Bernt c194cc62f1 fix doc for expect_num_pairs and add test tool 
also the TOC for discovered_dataset was wrong
and fixed a minor typo in comments in xsd
 2022-01-30 15:21:34 +01:00
Matthias Bernt 71ea1d4bba revert changes to test tool 2022-01-30 15:21:34 +01:00
M Bernt 355eb33579 correct counting of paired output 
If a tool returns a paired collection the test for the expected
number of outputs seems to be wrong. It seems that the pair and
its contents are counted (the reported number is larger by 2 than
the expected number).

I added a test to show this.

Also added a test with automatically detected forward and reverse element
which surprisingly works.
 2022-01-30 15:21:01 +01:00
John Chilton 9f8223d845 Merge pull request #10304 from bernt-matthias/topic/test-sort-order-multiple 
Reimplement collection order test, add wrong order, add `expect_test_failure` attribute
 2022-01-20 12:31:01 -05:00
Matthias Bernt 2e33be78ac make param_value filter work with multi data inputs 
ie data with multiple=true and collections
 2022-01-11 15:54:42 +01:00
Matthias Bernt b53f29465f comment forward reference 
seems that it is not possible to refer other input parameters
that are defined below in the xml
 2022-01-11 15:54:42 +01:00
Matthias Bernt 07d66b8ae0 do not add hg38 to test data table 
interferes with another test
 2022-01-11 15:54:42 +01:00