Sergey Golitsynskiy
0305428cd7
Add integration test verifying job_id
2021-03-30 19:07:41 +02:00
Dannon Baker
857171e787
Globally swap MininmalManagerApp to MinimalManagerApp (thanks for
...
noticing the first one @nsoranzo -- I am surprised how many of these
were in here)
2021-03-29 09:29:25 -04:00
mvdbeek
1afe1e1211
Break UniverseApplication into smaller parts
...
so we can use a variant of app that loads managers in Celery.
2021-03-29 09:29:25 -04:00
mvdbeek
f1debeacc9
Add purge dataset task
2021-03-29 09:29:25 -04:00
mvdbeek
ac3fcf911e
Merge branch 'release_21.01' into dev
2021-03-24 20:34:06 +01:00
Sergey Golitsynskiy
bb9547a1a3
Merge pull request #11696 from ic4f/dev_no_sqlalchemy_utils
...
Replace sqlalchemy-utilities with local implementation
2021-03-24 10:36:46 -04:00
Sergey Golitsynskiy
57782d5ff6
Add MySQL functionality, tests; refactor
2021-03-24 02:02:49 -04:00
Sergey Golitsynskiy
49ca9358bc
Add view tests, refactor
2021-03-23 23:23:45 -04:00
John Chilton
ca0b9bf36a
Merge pull request #11697 from mvdbeek/split_discovery_into_chunks
...
Break up dynamic dataset collection into chunks
2021-03-23 09:34:31 -04:00
mvdbeek
88074d5df6
Add test for paired discovery and fix paired discovery
...
If we break between forward and reverse read we would fail validation.
I guess if we want to do validation we should do that at a level before
building the collection ?
2021-03-23 10:29:34 +01:00
mvdbeek
2e6906d28d
Add integration test for test_flush_per_n_datasets
...
Which breaks down for nested collections ...
2021-03-23 10:15:41 +01:00
mvdbeek
f5800bed50
Break up dynamic dataset collection into chunks
...
Addresses https://github.com/galaxyproject/galaxy/issues/11488 .
One drawback here is that if multiple jobs are concurrently creating
datasets in a history the HID is not guaranteed to be sequential
between chunks. We can address this, but this is also a problem
when breaking workflow executions at
``maximum_workflow_jobs_per_scheduling_iteration``.
If we consider this to be a problem (personally I don't think it is, but
I could be convinved otherwise) I would work on this in a different PR.
On the upside the history panel will display an increasing amount of
datasets created during the dataset discovery.
2021-03-23 10:15:41 +01:00
mvdbeek
a9389ecd08
Drop test that does not apply to multiple="true" data_column parameters
2021-03-22 09:28:47 +01:00
Sergey Golitsynskiy
d40dabbe12
Fix linting errors
2021-03-21 22:32:54 -04:00
Sergey Golitsynskiy
66f4e81cef
Downgrade from SA 1.4 to SA 1.3
2021-03-21 22:19:07 -04:00
Sergey Golitsynskiy
fdc1852201
Replace refs to sqlalchemy-utils
2021-03-21 22:08:21 -04:00
Sergey Golitsynskiy
8af78a3342
Make test/unit/model a package
2021-03-21 22:03:35 -04:00
Sergey Golitsynskiy
db34dddbbd
Add create/drop/exists db functions; tests
2021-03-21 22:00:35 -04:00
mvdbeek
70934cd276
Add selenium test for data column parameters in workflow editor
2021-03-19 22:42:57 +01:00
John Chilton
1ed27ac609
Merge pull request #11637 from OlegZharkov/library_permissions
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Rewrite Library Permissions
2021-03-19 10:41:36 -04:00
Matthias Bernt
350ce8db37
lint for options with duplicated values
...
- unify messages a bit
- make everything fstring
2021-03-18 18:07:02 +01:00
M Bernt
826ae386b7
Update test/unit/tool_util/test_tool_linters.py
2021-03-18 15:30:01 +01:00
M Bernt and Nicola Soranzo
94ec02578f
Apply suggestions from code review
...
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-03-18 15:29:15 +01:00
Matthias Bernt
9cc84dc325
fix test and py linter error
2021-03-18 12:10:20 +01:00
Matthias Bernt
558d346de2
add test
2021-03-18 10:37:45 +01:00
Oleg Zharkov
3f4094948e
fix python style
2021-03-17 15:50:09 +02:00
Oleg Zharkov
d7504a2cba
make selenium tests happy
2021-03-17 15:46:00 +02:00
mvdbeek
d03c7af02a
Merge branch 'release_21.01' into dev
2021-03-15 14:53:07 +01:00
John Chilton
8f9bdd6eb5
Failing test case for output problem.
2021-03-14 19:58:31 -04:00
Nicola Soranzo
6c540932c7
Merge branch 'release_21.01' into dev
2021-03-12 19:01:35 +00:00
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
davelopez
e3cd70f352
Discard unit test attempt
2021-03-10 18:35:58 +01:00
davelopez
1315758c09
WIP add FastAPI unit test
2021-03-10 16:28:07 +01:00
davelopez
357a7e5c6c
Replace API test with integration test
2021-03-10 12:54:41 +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
b8eaa1a2c0
add test tool testing collection default format
2021-03-05 14:47:31 -05:00
davelopez
218e00ead5
Add a couple more tests just to be sure
2021-03-05 14:47:31 -05:00
davelopez
81d057c37a
Add failing test
2021-03-05 14:47:31 -05:00
Matthias Bernt
5b92a04cba
add test tool testing collection default format
2021-03-04 18:37:17 +01:00
John Chilton
e09e04bb69
Merge pull request #11514 from kxk302/csv_columns
...
Handle the case where column list is a comma-separated string
2021-03-04 09:41:30 -05:00
Dannon Baker
b4acf94e0c
Merge remote-tracking branch 'upstream/release_21.01' into dev
2021-03-03 18:22:07 -05:00
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
Kaivan Kamali
423a95435b
Added a default value to fix a broken framework test.
2021-03-02 17:35:42 -05:00
Kaivan Kamali
28c89ac950
Added another test for when columns are a comma separated string
2021-03-02 14:02:55 -05:00
mvdbeek
f730592215
Merge branch 'release_20.09' into release_21.01
2021-03-02 19:14:58 +01:00
Nate Coraor
a2d1625780
Merge remote-tracking branch 'upstream/release_21.01' into dev
2021-03-01 16:52:02 -05:00
Nate Coraor
7ed0f5337f
Merge remote-tracking branch 'upstream/release_20.09' into release_21.01
2021-03-01 16:47:23 -05:00
Sergey Golitsynskiy