John Chilton
954c78f301
Disable implicit optional typing across the project.
2022-03-18 09:06:30 -04:00
Simon Bray
a362874f07
allow setting a workflow as (un)importable via the API
2022-03-17 17:20:21 +01:00
mvdbeek
faea1c8211
Merge branch 'release_22.01' into dev
2022-03-14 17:06:49 +01:00
mvdbeek
c523529411
Revert "Merge pull request #13285 from mvdbeek/null_text_values"
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This reverts commit 2549792d420223188e59https://github.com/galaxyproject/galaxy/issues/13516 , at the cost
of not respecting required text parameters.
2022-03-10 20:56:20 +01:00
John Chilton
3bb3e90e5d
Rework page creation in populators.
2022-03-10 10:51:27 -05:00
Marius van den Beek
ff72765507
Merge pull request #13376 from simonbray/add-trs-col
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Add source_metadata attribute for workflows imported using TRS ID or via URL
2022-03-09 15:53:39 +01:00
Dannon
13965b5a85
Merge pull request #13355 from guerler/new_history_consolidate_views
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Remove custom serialization views for new history, strip unused visualization details
2022-02-28 09:13:03 -05:00
Nicola Soranzo
f8bd5d4bea
Merge branch 'release_22.01' into dev
2022-02-21 17:00:55 +00:00
John Chilton
a0d555a6e6
Merge pull request #13396 from mvdbeek/a2wsgi
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[22.01] Use a2wsgi to serve WSGI app
2022-02-18 11:02:56 -05:00
Simon Bray
cc79e028ed
remove test_run_workflow_with_missing_tool() from API tests
2022-02-18 10:07:39 +01:00
Simon Bray
8078dab412
fix small bug in toolbox's get_tool() so non-shed tool can be used for missing tool workflow invocation test
2022-02-18 10:06:28 +01:00
Simon Bray
bbe90dd3f7
block workflow invocation if wrong tool versions installed
2022-02-18 10:06:04 +01:00
mvdbeek
2eb56c2bd0
Make history tests rerunnable by generating unique history names
2022-02-17 11:54:11 +01:00
Simon Bray
e906565108
generalize to source_metadata column and set for url uploads;
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add new column to test_model_mapping
2022-02-16 11:54:00 +01:00
Simon Bray
380d370b6d
store trs_tool_id and trs_version_id separately
2022-02-15 11:59:00 +01:00
Simon Bray
de017811d4
create trs_id attribute to be set when workflow is imported
2022-02-15 10:26:35 +01:00
guerler
1b65da81cf
Remove visualizations from dataset serialization test, run prettier, fix tests
2022-02-12 11:40:36 -05:00
mvdbeek
1c24f26dae
Merge branch 'release_22.01' into dev_test
2022-02-12 17:36:32 +01:00
mvdbeek
eb420329df
Merge commit '623a5e165ad79e15321b19b2a2afbf2f9224cc90~1' into release_22.01
2022-02-11 18:53:39 +01:00
mvdbeek
973f6679d6
Merge branch 'release_21.09' into release_22.01
2022-02-11 13:29:04 +01:00
Simon Bray
5b4b981c58
remove test_run_workflow_with_missing_tool() from API tests
2022-02-10 17:04:09 +01:00
Marius van den Beek
c1f959d909
Merge pull request #13330 from mvdbeek/exp_imp_anonymous
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[22.01] Fix history exports import by url
2022-02-10 12:11:19 +01:00
mvdbeek
96d89a4f5c
Drop API key from more places
2022-02-09 17:38:10 +01:00
Simon Bray
6de7d6f392
fix small bug in toolbox's get_tool() so non-shed tool can be used for missing tool workflow invocation test
2022-02-09 15:15:39 +01:00
Simon Bray
1659d0943c
block workflow invocation if wrong tool versions installed
2022-02-09 11:55:28 +01:00
mvdbeek
bec9d4b49f
Fix resuming job when job has optional data parameters
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This fixes
```
ERROR galaxy.tools.actions:__init__.py:683 Cannot remap rerun dependencies.
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 664, in _remap_job_on_rerun
self.__remap_parameters(job_to_remap, jtid, jtod, out_data)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 694, in __remap_parameters
input_values = {p.name: json.loads(p.value) for p in job_to_remap.parameters}
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 694, in <dictcomp>
input_values = {p.name: json.loads(p.value) for p in job_to_remap.parameters}
File "/usr/local/Cellar/python@3.9/3.9.10/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py", line 339, in loads
raise TypeError(f'the JSON object must be str, bytes or bytearray, '
TypeError: the JSON object must be str, bytes or bytearray, not
NoneType
```
Optional data inputs or optional selects are stored as `None` (super
inconsistent, since most other parameters are stored as JOSN. We should
create "basic_2.py" using pydantic at one point not too far into the
future ...). This means we can't call `json.loads` on these. Fortunately
this is the only place we do it, and we don't need to consider optional
parameters here anyway.
2022-02-08 15:45:01 +01:00
mvdbeek
acd56abee8
Return DatasetChainModel
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Fixes failure to serialize the response.
2022-02-08 11:33:05 +01:00
mvdbeek
6ee7d6bfe2
Merge branch 'release_22.01' into dev
2022-02-04 09:49:21 +01:00
Dannon Baker
623a5e165a
Apply black formatting.
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Apply isort.
2022-02-03 07:42:20 -05:00
mvdbeek
967dc07e9f
Fail invocation with null in required input parameter
2022-02-01 15:14:45 +01:00
mvdbeek
d0fdbabed0
Add test that verifies invocation non-optional text parameter handling
2022-02-01 15:14:45 +01:00
mvdbeek
962a945765
Add InvocationIndexPayload model
2022-01-28 19:31:41 +01:00
Marius van den Beek
c6bf4cfb3b
Merge pull request #13223 from gallardoalba/Add_compression_tools
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Add compression converter
2022-01-26 12:45:01 +01:00
mvdbeek
0b2ca51c17
Remove CONVERTER_interval_to_bed_0 from suitable converter
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There's no point in converting from bed to bed.
2022-01-26 09:40:24 +01:00
mvdbeek
0a0e835659
Make tests more robust
2022-01-25 21:07:33 +01:00
Dannon
976cbebe6c
Merge pull request #13159 from davelopez/fix_libraries_non_admin_permissions
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Assorted Data Libraries fixes
2022-01-24 13:50:07 -05:00
mvdbeek
f0baddd905
Merge branch 'release_21.09' into dev
2022-01-21 16:38:36 +01:00
davelopez
4f104cfbd7
Add API test for dataset collections batch update
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When merging forward replace `_raw_update_batch` to `_update_batch`
2022-01-20 19:25:45 +01:00
mvdbeek
7c4568fe90
Set collection update_time when replacing failed elements
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That allows the new history to update the collection.
2022-01-17 18:59:40 +01:00
mvdbeek
8a16c56cac
Fix re-run with rerun_remap_job_id hiding collection
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Fixes https://github.com/galaxyproject/galaxy/issues/13052
2022-01-17 18:59:39 +01:00
mvdbeek
fc8fb85530
Set collection update_time when replacing failed elements
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That allows the new history to update the collection.
2022-01-14 12:59:36 +01:00
mvdbeek
855e9f9f2f
Fix re-run with rerun_remap_job_id hiding collection
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Fixes https://github.com/galaxyproject/galaxy/issues/13052
2022-01-12 20:10:08 +01:00
davelopez
eff762cc1a
Allow users with modify permission to edit libraries
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This means only changing name, description and synopsis.
Includes API test
2022-01-12 18:28:34 +01:00
mvdbeek
9c4c4ee0b7
Drop unused url from reimport_history signature
2022-01-05 13:31:59 +01:00
mvdbeek
932c46576f
Use urljoin to join urls
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This will drop extra slashes when joining urls.
2022-01-05 13:31:56 +01:00
davelopez
b8745e9eea
Change field to a set of datatypes in collection
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- Rename the field to `elements_datatypes`
2021-12-16 18:56:00 +01:00
davelopez
4c92aaae7a
Add API test
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The test creates 2 collections, one with all elements of the same datatype and another with different datatypes and then checks the `homogeneous_datatype` field has the expected value in the response.
2021-12-16 18:56:00 +01:00
Marius van den Beek
024a533de7
Merge pull request #13060 from davelopez/allow_dataset_admin_access
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Allow admin access to datasets API
2021-12-15 11:06:22 +01:00
John Chilton
27e36e3fff
Merge pull request #12578 from davelopez/fastapi_history_contents_routes
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FastAPI: migrate history contents routes
2021-12-14 14:12:51 -05:00
davelopez
f1bccc6e49
Adapt API test to expect 403 status code
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After aplying the fix #13056 , `test_sharing_private_history_makes_datasets_public` will now return a proper 403 status code instead of 400.
2021-12-14 19:45:00 +01:00
John Chilton