John Davis
bd56131ebd
Split script into admin and dev
...
TODO: remove duplication between db.py and db_dev.py (split into
multiple commits is intentional)
2022-09-28 15:45:00 -04:00
John Davis
e43552fdc5
Rename db.sh > manage_db.sh, following code review feedback
2022-09-28 15:45:00 -04:00
John Davis
0c348a5759
Update test comments
2022-09-28 15:32:10 -04:00
John Davis
dfd32a2ee8
Add type hints
2022-09-28 15:32:01 -04:00
John Davis
6fcc58a85c
Drop LegacyScripts: no longer used
2022-09-28 15:31:25 -04:00
John Davis
d8e8a8efb6
Add --raiseerr option; hide error traceback by default
2022-09-28 15:25:14 -04:00
John Davis
b4b76c91a2
Add missing tests
2022-09-28 15:25:06 -04:00
John Davis
bf83b4347a
Fix mypy by asserting object before accessing its attributes
2022-09-28 15:24:40 -04:00
John Davis
e0e30a5744
Fix packages tests: script is one level up
2022-09-28 15:24:26 -04:00
John Davis
3be7c53eb9
Fix linting
2022-09-28 15:24:16 -04:00
John Davis
ab1854f3a7
Test against 1 or 2 databases
2022-09-28 15:23:50 -04:00
John Davis
887b882ff0
Add inline testing documentation
2022-09-28 15:23:42 -04:00
John Davis
b64fda7478
Add initial draft
2022-09-28 15:23:21 -04:00
John Davis
4cd3291598
Refactor get_alembic_cfg: make available to other code
2022-09-28 15:23:09 -04:00
John Chilton
ace1e13da3
Merge pull request #14641 from mvdbeek/fix_optional_data_input_submission_expanded_tool_form
...
[22.05] Fix delayed optional data input handling
2022-09-22 18:08:58 -04:00
mvdbeek
64cb245ddd
Fix running subworkflows with disconnected optional/default inputs
2022-09-21 19:31:41 +02:00
mvdbeek
aceaa698fc
Ensure guid is hexadecimal value
2022-09-08 14:04:35 +02:00
mvdbeek
d1b4f05345
Merge branch 'release_22.01' into release_22.05
2022-08-30 20:32:39 +02:00
Nicola Soranzo
6519604620
Add some type annotations
2022-08-30 14:34:54 +01:00
Nicola Soranzo
61b6eb1ee9
Fix more `discovered_datasets` typos
2022-08-30 09:57:26 +01:00
mvdbeek
60cda23970
Mock quay.io API calls, pass install=False to not pull docker images
2022-08-29 16:38:31 +02:00
mvdbeek
c4f576ccf3
Fix cache lookup condition
2022-08-29 16:38:31 +02:00
mvdbeek
c4a9050af9
Fix _namespace_has_repo if cache namespace cache key not present
2022-08-29 14:08:49 +02:00
Matthias Bernt
a8a80cf431
fix typo in test linter
2022-08-29 11:36:59 +02:00
mvdbeek
8a8acc625f
Fix refactor action dropping outputs on subworkflow connection
...
I thought it would be cleaner to make a distinction between the output
name and the output label when reasoning about a subworkflow step in
the context of a parent workflow
(https://github.com/galaxyproject/galaxy/pull/14473/commits/b0727be9e0b096a2dacacb767a1f4ac0fc3e6540#diff-a50bcc5c08ade11249449c4100ea8c286727df601b52a5b9588eb2a385d97da7R543 ),
in case we'd later want to do something with the label.
I don't think I thought about this correctly though,
and it breaks connections between steps that were made by referencing
the subworkflow's output name.
This wasn't necessary for the main goal of
https://github.com/galaxyproject/galaxy/pull/14473 , so I'm partially
reverting that here.
Fixes https://github.com/galaxyproject/planemo/pull/1262#issuecomment-1223874571
2022-08-23 14:12:29 +02:00
Marius van den Beek
cccdb496b8
Merge pull request #14482 from davelopez/22.05_fix_query_parameter_lists
...
[22.05] Fix Jobs API index to accept query parameters as lists
2022-08-19 13:23:32 +02:00
Dannon
d1c66d61b5
Merge pull request #14473 from mvdbeek/change_datatype_problems
...
[22.05] Fix effective datatype in workflow editor node terminals
2022-08-19 06:32:49 -04:00
davelopez
1d59487365
Add unit tests for query_parameter_as_list
2022-08-19 08:59:02 +02:00
Nicola Soranzo
9915a6eeeb
Merge pull request #14456 from mvdbeek/drop_tzinfo_when_parsing_datetime
...
[22.05] Fix data_range_{min,max} parsing
2022-08-17 20:06:43 +01:00
Marius van den Beek and Nicola Soranzo
973d0779b6
Include timezone testing
...
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2022-08-17 18:43:57 +02:00
mvdbeek
6eb034706f
Fix position of cleanenv flag in singularity command
...
Fixes https://github.com/galaxyproject/galaxy/issues/14408#issuecomment-1216742827
2022-08-17 09:53:08 +02:00
mvdbeek
b0727be9e0
Fix change_datatype not reflected in tool and workflow output terminals
2022-08-16 15:46:11 +02:00
mvdbeek
b0d9cff6c4
Add unit test
...
That was meant to go into the first commit ...
2022-08-16 13:12:28 +02:00
Marius van den Beek
df3d5a1992
Merge pull request #14429 from mvdbeek/singularity_no_host_env_vars
...
[22.05] Pass ``--cleanenv`` by default to singularity command
2022-08-12 15:58:05 +02:00
mvdbeek
0560e43a48
Fix cache image singularity resolver if path contains uppercase chars
...
Fixes https://github.com/galaxyproject/galaxy/issues/14425
2022-08-11 13:32:21 +02:00
mvdbeek
0eff482466
Pass --cleanenv by default to singularity command
2022-08-10 16:52:59 +02:00
davelopez
4846d04dad
Add unit test for quoted strings with spaces
2022-08-05 15:54:04 +02:00
davelopez
af949c2fd3
Revert adding __hash__ to BaseDatabaseIdField
2022-08-04 11:23:31 +02:00
davelopez
e5b11bb25b
Add unit tests for DabaseIdFields hashing
2022-08-02 11:10:35 +02:00
John Davis
def882932d
Add verify_db_is_initialized function; tests
2022-07-13 16:10:58 -04:00
John Davis
1e75d85fd4
Prevent accessing LegacyScripts.database before processing script args
2022-07-13 15:40:42 -04:00
Nicola Soranzo
9a08a76ac0
Merge pull request #14284 from mvdbeek/fix_json_encoding_things
2022-07-10 17:57:06 +01:00
mvdbeek
73c73e0822
Test Decimal/inf/nan value dumping
2022-07-08 19:39:38 +03:00
Nicola Soranzo
d4d3485b72
Fix mypy reexport error for testfixtures
...
Fix this mypy error for the galaxy-app package:
```
tests/app/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py:5: error:
Module "testfixtures" does not explicitly export attribute "log_capture";
implicit reexport disabled [attr-defined]
from testfixtures import log_capture
^
```
2022-07-08 02:33:28 +01:00
Evan Bolyen
184f0d8eaf
TST: fix qiime2.tabular auto-upload test
2022-07-05 09:43:30 -07:00
Evan Bolyen
9c06e232e1
lint: make format is neat
2022-07-05 09:43:30 -07:00
Evan Bolyen
88fed0ffff
TST: added more tests
2022-07-05 09:43:30 -07:00
Oddant1
38b1bfc417
QIIME 2: Strip properties from semantic types ( #2 )
2022-07-05 09:43:30 -07:00
mvdbeek
22f761aa10
Fix validation of nested element fetch data payloads
...
Fixes https://github.com/galaxyproject/galaxy/issues/14242
2022-07-01 13:52:06 +02:00
mvdbeek
84ea10767a
Unit test for No response returned error
2022-06-27 18:11:49 +02:00
John Davis