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5373 Commits
Author SHA1 Message Date
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
davelopez 19bc082597 Add a couple more tests just to be sure 2021-03-03 18:40:54 +01:00
davelopez 6e7e2b0377 Add failing test 2021-03-03 18:25:25 +01:00
mvdbeek f730592215 Merge branch 'release_20.09' into release_21.01 2021-03-02 19:14:58 +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
mvdbeek 15cf05a8a5 Add testcase for explicit output collection step_outputs when reaching max_num_jobs 
This should recapitulate the error seen when running workflow tests
against https://github.com/galaxyproject/iwc/pull/23.
 2021-03-01 20:09:03 +01:00
John Chilton aacf2b08c1 Fix galaxy.files unit test file names so they are picked up by pytest. 2021-02-25 16:01:12 -05:00
John Chilton 3eb86d28fc More flushing to file source posix tests pass consistently. 2021-02-25 16:01:11 -05:00
John Chilton ab396bfd4e Allow anonymous access to S3 buckets via file sources plugins. 
```yaml
- type: s3fs
  id: genomeark
  doc: Access to Genome Ark open data on AWS..
  bucket: genomeark
  anon: true
```

0;95;0c# Please enter the commit message for your changes. Lines starting
 2021-02-25 16:00:57 -05:00
Matthias Bernt 241977854f Fix another integration test 
TmpDirAsShellCommandJobEnvironmentIntegrationTestCase.test_default_environment_1801

- actually create a dir
- create the dir in the job working dir
 2021-02-25 13:49:58 +01:00
Matthias Bernt 5c2ef80c6b fix chained dynamic destinations integration test 
- create a tmp dir as absolute path
- actually create a dir in the dyndest test
 2021-02-25 13:49:19 +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
guerler 427594be71 Fix test cases, naming issues 2021-02-19 14:56:49 -05:00
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
mvdbeek 79b6bdbc60 Add missing assert statement in unit test 2021-02-17 12:40:55 +01:00
Nicola Soranzo 80c423b684 Fix MetadataCollection attribute access for tools 
Follow-up on https://github.com/galaxyproject/galaxy/pull/11353 .
 2021-02-16 22:52:59 +00:00
Nate Coraor 99a40ebcfb Document tool and pulsar limits for coexecution pods 2021-02-15 14:15:31 -05:00
Marius van den Beek f813ee9103 Merge pull request #11366 from mvdbeek/revert_sqlalachemy_json_plus_mutable_list_fix 
[21.01] Revert sqlalachemy-json, add unit tests, fix 'MutationList' object has no attribute '_key'
 2021-02-14 13:48:48 +01:00
Marius van den Beek 073a67a24d Merge pull request #11349 from jmchilton/tool_environment_vars_puslar 
[21.01] Add tool environment variables to Pulsar client.
 2021-02-13 18:58:05 +01:00
mvdbeek af47800c49 Add unit test 2021-02-13 16:09:10 +01:00
mvdbeek 156950f9c8 Small unittest 2021-02-12 09:24:48 +01:00
John Chilton fd92160271 Maybe test? 2021-02-11 15:40:07 -05:00
John Chilton 02d6db7003 Merge pull request #11288 from mvdbeek/mutable_replacement 
[21.01] Use nested state tracking with sqlalchemy-mutable
 2021-02-08 09:18:55 -05:00
John Chilton b47a80004f Fix concrete objectstore methods for new/discarded datasets. 2021-02-05 13:08:55 -05:00
mvdbeek 029c017c69 Drop strip_control_characters_nested workaround 
Pretty sure https://github.com/galaxyproject/galaxy/pull/10390/ fixed
the null issue to start with.
 2021-02-05 13:13:23 +01:00
mvdbeek 7d0ec29fa0 Drop legacy metadata mode 
And always serialize input dataset metadata using the model exports.
This means we don't have to pickle anymore, which breaks with weakrefs
used by sqlalchemy-json's Mutable class.
 2021-02-05 11:38:50 +01:00
Dannon Baker 6c155bf2ef Standardize test format 2021-01-29 12:05:41 -05:00
Dannon Baker 0b84678f43 Add a couple basic tests for username/email validation 2021-01-29 12:04:51 -05:00
Dannon e16c95eb19 Merge pull request #11186 from mvdbeek/disable_tool_cache_optionally 
[21.01] Add setting that lets admins enable/disable the tool document cache
 2021-01-20 14:44:20 -05:00
Nicola Soranzo 72c08ccaad Merge branch 'release_20.09' into release_21.01 2021-01-20 18:15:49 +00:00
mvdbeek e428e4298e Fix pulling of singularity images 
That broke in https://github.com/galaxyproject/galaxy/pull/11134, since
the singularity container resolve() inherits from docker container
resolution it'd also check to see if `docker` was on path.
 2021-01-20 12:06:32 +01:00
mvdbeek 9ac472ecc5 Disable tool document cache in unit tests 2021-01-20 10:34:02 +01:00
John Chilton b6747dc5c3 Merge pull request #11151 from jmchilton/fix_wf_extract 
[21.01] Fix certain classes of workflow extraction on copied objects.
 2021-01-18 18:41:18 -05:00
John Chilton 15bde671e7 Fix certain classes of workflow extraction on copied objects. 2021-01-15 23:59:06 -05:00
John Chilton 53b9d35863 Integration selenium tests for history import/export of files plugins. 2021-01-15 23:40:50 -05:00
Nicola Soranzo 166087ea7a Merge branch 'release_20.09' into release_21.01 2021-01-15 17:05:47 +00:00
mvdbeek 588f2c49b6 Log exception but continue if cli is available but not functional 
That is a good idea, thanks Nicola!
 2021-01-15 15:47:16 +01:00
mvdbeek 40a7cd8f3c Don't attempt to use docker cli if it is not available 
This fixes https://github.com/galaxyproject/galaxy/issues/11125, which
became a problem with https://github.com/galaxyproject/galaxy/pull/10814
and the recent removal of the docker runtime from kubernetes.

This is the quick fix, but I don't like the guessing and disabling
that we do if docker is not available or not functional.

I'm hesitating between adding a config option for the resolver
(`docker_cli_available` or `docker_list_images` + `docker_pull_images`)
and adding a `KubernetesContainerResolver` / `RemoteContainerResolver`
class that doesn't assume docker is available for listing and pulling
iages.

Not wanting to list/pull images on the Galaxy node is probably a
reasonable thing outside of kubernetes as well, so I tend to
go with a `RemoteContainerResolver` class in dev ?
 2021-01-14 17:43:25 +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 5f67c2075b fix name and value column in select_from_dataset.xml 2021-01-12 19:27:07 +01:00
Marius van den Beek 520e097771 Merge pull request #11063 from bernt-matthias/topic/validate-collections 
add validation for collection parameters
 2021-01-12 16:40:06 +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