Commit Graph
40356 Commits
Author SHA1 Message Date
John Chilton 224f573e83 Merge pull request #7896 from mvdbeek/add_local_namespace_cached_resolvers_to_default_resolver
[19.05] Add local namespaced resolver to default container resolvers
2019-05-06 14:23:23 -04:00
mvdbeek bfdc471435 Add local namespaced resolver to default container resolvers
The mulled container resolvers are building containers that are
namespaced to "local", so I think it makes a lot of sense to
include local in the defaults. This prevents planemo from
building the same image over and over again when run with
`--biocontainers`.
2019-05-06 14:09:25 +02:00
Nicola Soranzo 060a49f4e1 Merge pull request #7887 from mvdbeek/fix___call__cheetah_obj
[19.05] Update Cheetah dependency, fixes `AssertionError: Requested __call__ …
2019-05-03 18:04:55 +01:00
Martin Cech 598bdac004 Merge pull request #7885 from jmchilton/integration_fix
Fix failing integration test.
2019-05-03 10:48:28 -04:00
mvdbeek 65082653e9 Update Cheetah dependency, fixes AssertionError: Requested __call__ column missing from column def
Fixes
```
Traceback (most recent call last):
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/jobs/runners/pulsar.py", line 350, in __prepare_job
    job_wrapper.prepare(**prepare_kwds)
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/jobs/__init__.py", line 871, in prepare
    self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build()
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/evaluation.py", line 451, in build
    raise e
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/evaluation.py", line 447, in build
    self.__build_command_line()
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/evaluation.py", line 472, in __build_command_line
    command_line = fill_template(command, context=param_dict)
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/util/template.py", line 18, in fill_template
    return unicodify(Template(source=template_text, searchList=[context]))
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/util/__init__.py", line 1018, in unicodify
    msg = "Value '%s' could not be coerced to Unicode" % value
  File "/cvmfs/test.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1555443583_0915494_96112.py", line 261, in respond
  File "/cvmfs/test.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/NameMapper.py", line 288, in valueFromSearchList
    executeCallables=executeCallables)
  File "/cvmfs/test.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/NameMapper.py", line 231, in _valueForName
    if executeCallables and hasattr(nextObj, '__call__') and \
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/wrappers.py", line 138, in __getattr__
    self._fields[name] = self._input.options.get_field_by_name_for_value(name, self._value, None, self._other_values)
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/parameters/dynamic_options.py", line 658, in get_field_by_name_for_value
    assert field_name in self.columns, "Requested '%s' column missing from column def" % field_name
AssertionError: Requested '__call__' column missing from column def
```
reported by @natefoo and seen on test.galaxyproject.org.
This was fixed upstream in https://github.com/CheetahTemplate3/cheetah3/commit/354c885ae50c3d38b06928493ecd640c5d3bf768
by replacing `hasattr(nextObj, '__call__')` with `callable(nextObj)`.
2019-05-03 16:21:59 +02:00
John Chilton 754ca26f92 Fix failing integration test.
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
Dannon Baker ee89a482bc Merge remote-tracking branch 'upstream/release_19.05' into dev 2019-05-02 16:11:59 -04:00
Dannon af95770d60 Merge pull request #7877 from WilliamHolden/fix-quota-usage-click-target
[19.05] Fix click targeting for quota usage details
2019-05-02 16:11:32 -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
John Chilton b2eb394a7d Merge pull request #7870 from jmchilton/1901_fix_plugin
[19.01] Fix bug preventing handler runner plugin handling.
2019-05-02 11:39:39 -04:00
Martin Cech 918db5537e Merge pull request #7874 from jmchilton/cleanup_integration_tests
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
Dannon Baker e715f83364 Merge remote-tracking branch 'upstream/release_19.01' into release_19.05 2019-05-02 11:20:07 -04:00
Dannon d7b1479314 Merge pull request #7872 from mvdbeek/allow_not_uploading_optional_files
[19.01] Allow composite upload if all non-optional files are selected
2019-05-02 11:13:37 -04:00
Dannon 28a0d604e9 Merge pull request #7875 from mvdbeek/add_reset_button
[19.05] Add Reset button to composite upload interface
2019-05-02 11:09:29 -04:00
Martin Cech 9fac6e4340 Merge pull request #7859 from guerler/data_dialog_workflow
Fix flag for library dataset option in data selector
2019-05-02 11:08:50 -04:00
William Holden 2f0905273f add display block so a tag fills out whole div for click targeting 2019-05-02 14:42:47 +00:00
Dannon 046bbd3c50 Merge pull request #7866 from martenson/fav-for-logged
[19.05] Favorite filtering only for logged-in users
2019-05-02 10:30:03 -04:00
Dannonandmartenson e9c31a1624 use const instead of let
Co-Authored-By: martenson <marten@bx.psu.edu>
2019-05-02 10:18:02 -04:00
mvdbeek 01f43732d6 Add Reset button to composite upload interface
Fixes https://github.com/galaxyproject/galaxy/issues/5432
2019-05-02 15:01:41 +02:00
John Chilton c6fcd051c8 Cleanup integration test configuration code.
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
mvdbeek a52f3f30d8 Allow upload if all non-optional files are selected
Fixes https://github.com/galaxyproject/galaxy/issues/5326
2019-05-02 14:13:31 +02:00
Björn Grüningandjmchilton 175865740c Update test/unit/jobs/test_job_configuration.py
Co-Authored-By: jmchilton <jmchilton@gmail.com>
2019-05-02 08:08:23 -04:00
Helena Rasche c545aaf4d4 [19.05] Add shapefile datatype (#7819)
[19.05] Add shapefile datatype
2019-05-02 10:18:40 +02:00
guerler 4eeda6c58a Fix usage of const 2019-05-01 15:17:40 -04:00
guerler 3d30a5ef4e Merge branch 'dev' into data_dialog_workflow 2019-05-01 15:11:32 -04:00
John Chilton 98fa693a7c Fix bug preventing handler runner plugin handling. 2019-05-01 15:09:25 -04:00
John Chilton f6e54b49db Add job configuration test for resource groups and handler plugins. 2019-05-01 15:09:24 -04:00
Martin Cech 28a859e8dc hide favorite button for anons 2019-05-01 12:36:15 -04:00
Martin Cech 6230404623 Merge pull request #7865 from jmchilton/pulsar_fix
[19.05] Rev pulsar for latest fixes.
2019-05-01 11:53:31 -04:00
Dannon Baker 47e80ba630 Merge remote-tracking branch 'upstream/release_19.05' into dev 2019-05-01 11:04:12 -04:00
Nicola Soranzo 3b184d6fee Fix comment starttag in oidc sample (#7864)
Fix comment starttag in oidc sample
2019-05-01 16:01:50 +01:00
Dannon Baker 7677dbdc1c Fix comment starttag in oidc sample 2019-05-01 09:11:21 -04:00
John Chilton 6297ca6556 Rev pulsar for latest fixes.
Should fix the problem when that same input is sent to a tool more than once.
2019-05-01 09:03:33 -04:00
Dannon Baker ef0cfb5b2a Merge remote-tracking branch 'upstream/release_19.05' into dev 2019-05-01 08:57:22 -04:00
Dannon Baker 642c97e1b7 Merge remote-tracking branch 'upstream/release_19.01' into release_19.05 2019-05-01 08:54:27 -04:00
Dannon Baker 542b55c125 Merge branch 'revise_close_workflow' into dev 2019-05-01 08:46:01 -04:00
Dannon Baker 513fb016dc Sync client formatting. 2019-05-01 08:44:35 -04:00
guerler 0ca955a1ce Fix comment 2019-04-30 23:47:24 -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
Aysam Guerler dfce161169 Merge pull request #7860 from dannon/preferconst
Add linting and enforce prefer-const rule for client codebase
2019-04-30 19:07:12 -04:00
guerler e512db448c Leave data libraries visible for anon user for now 2019-04-30 16:59:04 -04:00
Dannon Baker 024424e6d4 Fix DisplayStructured let/const 2019-04-30 16:46:41 -04:00
Dannon Baker 852773ed27 Fix let/const usage in components. 2019-04-30 16:45:24 -04:00
Dannon Baker d13e4bd902 Add prefer-const linting 2019-04-30 16:45:03 -04:00
guerler c73ffe8085 Use const instead of let where appropriate in the data selector 2019-04-30 16:42:03 -04:00