mvdbeek
62f5572a43
Add carriage return unit test
2019-05-27 11:35:20 +02:00
Nicola Soranzo
d9b0f54906
Try to verify tool test output first as Unicode
2019-05-26 15:07:36 +01:00
mvdbeek
2d71b0bdfe
Use io.open with errors="repalce" instead of comparing byte strings
2019-05-23 11:07:06 +02:00
mvdbeek
ab7a38631e
Unit test verify module
2019-05-22 17:45:00 +02:00
mvdbeek
9c06527bbb
Simplify convert_newlines_sep2tabs
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Just call convert_newlines with a compiled regex
2019-05-19 09:30:26 +02:00
mvdbeek
b67ddbf036
Drop (seemingly?) unused sep2tabs function
2019-05-19 09:30:26 +02:00
mvdbeek
3c5c7a0da2
Parametrize sniff_test
2019-05-17 15:41:14 -04:00
mvdbeek
6878e3973a
Fix test_sniff unittest
2019-05-17 15:41:14 -04:00
John Chilton
0e707f2901
Improve sniffing test cases.
2019-05-17 15:41:13 -04:00
John Chilton
d3f2ce009e
Attempt binary conversion of newlines if UTF conversion fails.
2019-05-17 15:41:13 -04:00
John Chilton
85f9ead2a2
Improved newline conversion handling.
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- Fix bug where sep2tabs didn't work with '\r\n'
- Fix bug where sep2tabs didn't work with '\r' - we were opening it with universal newlines.
- Fix memory bug where convert_newlines would read unbounded buffers - other methods still do though :(.
- Simplify convert_newlines to just let universal newline handling handle the conversion.
2019-05-17 15:41:13 -04:00
John Chilton
6000f79b6d
Fix extra newlines in peek code.
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Behavior changes:
- Now includes a trailing new line if the input contained a trailing newline.
- Now returns only as many lines as are present if the file contains fewer lines than LINE_COUNT.
2019-05-17 15:41:13 -04:00
John Chilton
703c968788
Merge pull request #7944 from mvdbeek/expression_tool_improvements
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[19.05] Allow mapping over of expression tool params
2019-05-14 08:12:38 -04:00
mvdbeek
556ee003ae
Fix parse_values_from_file tool and tests
2019-05-14 00:14:34 +02:00
mvdbeek
974f45b043
Allow mapping over of expression tool params
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This allows feeding a collection of parameters values to a parameter
value. This enables https://github.com/galaxyproject/tools-iuc/pull/2404#issuecomment-491740393
for instance, where we normalize a collection based on a computed
parameter.
2019-05-14 00:14:34 +02:00
Nicola Soranzo
196e000191
Fix upload of gzipped VCF files
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which were mistakenly sniffed as `vcf_bgzip`.
Fix Fix https://github.com/galaxyproject/galaxy/issues/4892 .
2019-05-10 19:47:48 +01:00
mvdbeek
ccea1eeb8f
Delete running jobs after each API-style test
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Should prevent https://jenkins.galaxyproject.org/job/docker-integration-py3/159/testReport/junit/test.integration.test_upload_configuration_options/AdminsCanPasteFilePathsTestCase/test_admin_path_paste_libraries/
2019-05-08 13:40:59 +02:00
Nicola Soranzo
1d1f72799b
Use packaging.version.parse() instead of float() for version comparisons
2019-05-07 18:20:05 +02:00
mvdbeek
d25a5dda10
Only run python 3 fixers if profile version < 19.05
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or python_template_version < 3.
2019-05-07 18:20:05 +02:00
mvdbeek
510f23f85a
Non-list comprehensions can't refer to non-iteration variables from surrounding scope
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While fixable this seems to not work on python 2 either, so we will not
attempt to fix it.
2019-05-07 18:20:05 +02:00
mvdbeek
0062bce79f
Work around list comprehension scope issues
2019-05-07 18:20:05 +02:00
mvdbeek
5ef41e7dce
Run futurize on Compiled Cheetah Module
2019-05-07 18:20:05 +02:00
mvdbeek
85e13d2dc4
Add test that unfortunately shows that the global variable isn't updated
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Now if we could figure out the exact position in the template source
where a NotFound error is raised we could replace `$variable`
with `variable` and add `#variable = $variable` just before the failing
statement.
2019-05-07 18:20:05 +02:00
John Chilton
754ca26f92
Fix failing integration test.
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https://jenkins.galaxyproject.org/job/docker-integration/9044/testReport/junit/test.integration.test_job_recovery/JobRecoveryBeforeHandledIntegerationTestCase/test_recovery/
Likely transiently broken with #7874
2019-05-03 08:38:33 -04:00
John Chilton
5dd92d2421
Merge remote-tracking branch 'upstream/release_19.05' into dev
2019-05-02 14:19:49 -04:00
John Chilton
9bfb08f00c
Merge remote-tracking branch 'upstream/release_19.01' into release_19.05
2019-05-02 11:43:51 -04:00
John Chilton
9bc0a0cbe5
Add file missing from #7694
2019-05-02 11:41:44 -04:00
Martin Cech
918db5537e
Merge pull request #7874 from jmchilton/cleanup_integration_tests
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Cleanup integration test configuration code.
2019-05-02 11:32:10 -04:00
Dannon Baker
8b0bbba1a7
Merge remote-tracking branch 'upstream/release_19.05' into dev
2019-05-02 11:20:39 -04:00
John Chilton
c6fcd051c8
Cleanup integration test configuration code.
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Remove copy and paste problems, remote excess configuration unrelated to the what is being tested (handler configuration, multiple worker counts, etc..).
2019-05-02 08:45:11 -04:00
John Chilton
faae919af1
Add file missing from #7694
2019-05-02 08:27:04 -04:00
Björn Grüning and jmchilton
175865740c
Update test/unit/jobs/test_job_configuration.py
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Co-Authored-By: jmchilton <jmchilton@gmail.com >
2019-05-02 08:08:23 -04:00
Helena Rasche
c545aaf4d4
[19.05] Add shapefile datatype ( #7819 )
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[19.05] Add shapefile datatype
2019-05-02 10:18:40 +02:00
John Chilton
f6e54b49db
Add job configuration test for resource groups and handler plugins.
2019-05-01 15:09:24 -04:00
guerler
89cf0a48fc
Wait until workflow saving message disappears
2019-04-30 21:31:26 -04:00
guerler
2a0e0e1736
Remove close option from selenium tests
2019-04-30 19:14:25 -04:00
Bjoern Gruening
102b619c43
make tests stricter
2019-04-30 09:47:06 +02:00
Bjoern Gruening
bec0d87f4c
ordering matters
2019-04-30 00:12:28 +02:00
Bjoern Gruening
1d2126a84e
enable input composite data
2019-04-29 19:09:18 +02:00
Nicola Soranzo
ed18d34f08
Merge pull request #7838 from mvdbeek/use_getfullargspec_on_python3
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Use getfullargspec on python3
2019-04-29 13:50:45 +01:00
Björn Grüning
1e2528b754
fixing file names in tests
2019-04-29 14:09:33 +02:00
mvdbeek
b68dcb4507
Use getfullargspec on python3
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`getargspec` is marked for deprecation.
2019-04-29 11:52:33 +02:00
Marius van den Beek and bgruening
977c59fa0a
Update test/functional/tools/composite_shapefile.xml
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Co-Authored-By: bgruening <bjoern@gruenings.eu >
2019-04-29 10:55:12 +02:00
Bjoern Gruening
75c53409a0
add datatype and tool to the tests
2019-04-29 09:50:00 +02:00
Nicola Soranzo
084296c92a
Remove recursion from `expand_nested_tokens()`
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Also add test for recursive nested token.
2019-04-27 00:09:31 +01:00
John Chilton
003cdb83fd
Merge pull request #7823 from mvdbeek/fix_token_replacement_py3
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Fix nested macro/token expansion on python 3
2019-04-26 10:59:38 -04:00
mvdbeek
60d87107ee
Fix InputValueWrapper gt/ge/lt/le comparisons
2019-04-25 21:32:47 +02:00
mvdbeek
77ae679746
Fix nested macro/token expansion on python 3
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I noticed that in multiqc @ESCAPE_IDENTIFIER@ wasn't being replaced.
It's surprising that this didn't cause any issues on python 2,
but might have to do with the iteration order changes.
2019-04-25 19:51:25 +02:00
Bjoern Gruening
21a60e3020
add shapefile test
2019-04-25 16:43:06 +02:00
John Chilton
75ec6dba53
Merge pull request #7594 from martenson/workflow-ux
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improve workflow cog menu ux
2019-04-24 08:28:18 -04:00
mvdbeek