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Commit Graph
33712 Commits
Author SHA1 Message Date
pauldg 9105ba3ea5 formatting 2023-03-29 11:32:35 +02:00
pauldg e2882dc54c Changes to tests according to ro-crate 
metadata changes
 2023-03-29 11:32:34 +02:00
pauldg b184e11a4d ro-crate metadata fixes based on bugs 2023-03-29 11:32:34 +02:00
Nate Coraor a37f9021b6 Update Gravity to 1.0.2 2023-03-28 12:52:07 -04:00
Martin Cech bd82767681 Merge pull request #15829 from jmchilton/fastapi_fix 
[23.0] Fix API for latest FastAPI (0.95).
 2023-03-27 13:20:36 -04:00
Marius van den Beek b93f145197 Merge pull request #15846 from mvdbeek/missing_filter_job_cache 
[23.0] Add missing filter in job query
 2023-03-25 20:05:25 -04:00
mvdbeek 190824bc47 Add missing filter in job query 
On my instance this brings the query time down from 1.7 seconds to
0.9ms. Saturday afternoon hacking fun with John D.
 2023-03-25 17:47:13 -04:00
davelopez a54211b004 Fix get_metadata_file URL generation 2023-03-24 10:16:49 -04:00
davelopez 0dd4d3f835 Fix content type and filename parameters 2023-03-24 10:16:48 -04:00
John Chilton 9ea74b6537 Fix API for latest FastAPI (0.95). 
xref https://fastapi.tiangolo.com/release-notes/
 2023-03-24 10:16:48 -04:00
Martin Cech 66ea38ae8b Merge branch 'release_22.05' into release_23.0 2023-03-20 08:49:31 -07:00
Martin Cech e10320ce5d add security checks to page and visualization APIs 2023-03-19 20:52:18 -07:00
mvdbeek 6afcbe29c3 Display confirmation dialog when attepmting to save workflow with invalid connections 
Closes https://github.com/galaxyproject/galaxy/issues/15753
 2023-03-17 20:29:10 +01:00
Dannon Baker 85cf9735a6 Add eof newline to den_fmt test data 2023-03-17 10:50:33 -04:00
Dannon 6914d53208 Merge pull request #15797 from muon-spectroscopy-computational-project/den_fmt_charge_spin_fix 
[22.05] Account for charge and spin in den_fmt sniffer
 2023-03-17 10:24:32 -04:00
Dannon 346f90bc7e Merge pull request #15807 from guerler/fix_workflow_pages 
Show workflow errors in embedded markdown element
 2023-03-16 20:23:33 -04:00
guerler 66bf2c7d1f Properly display missing tools in subworkflows instead of throwing generic error 2023-03-16 05:56:42 +03:00
mvdbeek a534db364e Merge branch 'release_22.05' into release_23.0 2023-03-15 18:34:33 +01:00
mvdbeek c0ebe9fdb0 Bump tuswsgi middleware 
The middleware attempts to cleanup files on every upload,
this can be a problem if there are many files in the upload
directory, especially on NFS.
 2023-03-15 12:06:45 +01:00
Patrick Austin 054d2c71a2 Account for charge and spin in den_fmt sniffer 2023-03-14 15:38:41 +00:00
John Davis 446d312832 Fix typo in comment 2023-03-14 10:22:07 -04:00
Nicola Soranzo 89147e9eb1 Merge pull request #15787 from natefoo/gravity-1.0.1 
[23.0] Bump Gravity to 1.0.1
 2023-03-14 11:55:02 +00:00
Dannon 8f518ff60a Merge pull request #15758 from davelopez/23.0_add_missing_history_export_link 
[23.0] Add missing history export link
 2023-03-14 07:43:17 -04:00
Nate Coraor 767bb5c941 Bump Gravity to 1.0.1 2023-03-13 19:44:09 -04:00
John Davis 22939b4dda Fix bug exposed in new tests 2023-03-13 11:59:39 -04:00
John DavisandMarius van den Beek d690c59b99 Fix error 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2023-03-13 11:59:39 -04:00
John Davis dda56025cc Run make config-rebuild 2023-03-13 11:59:39 -04:00
John Davis 36b6c04510 Update config schema description 2023-03-13 11:59:39 -04:00
John Davis f35e8f8288 Add option to disable the fetch_data celery task 
To disable, set the task's route to "disabled" in galaxy.yml:

enable_celery_tasks: true
celery_conf:
  task_routes:
    galaxy.fetch_data: disabled
 2023-03-13 11:59:39 -04:00
Martin Cech c4795a839b fix premature return in user API 2023-03-12 22:08:09 -07:00
Nicola Soranzo 94fab1b320 Cast `url_for() output to str` 
Starlette 0.26.0 has changed the return type of `HTTPConnection.url_for()`
from `str` to `URL`, which breaks the Galaxy package mypy tests:

```
mypy . --enable-incomplete-feature=Unpack
galaxy/webapps/galaxy/api/__init__.py:180: error: Incompatible types in
assignment (expression has type "str", variable has type "URL")  [assignment]
                    url = f"{url}?{urlencode(query_params)}"
                          ^
Found 1 error in 1 file (checked 255 source files)
```
 2023-03-12 17:02:47 +00:00
Yakubov, Sergey 3ee6f17a53 fix hostname parsing for newer Docker versions 
newer versions seem to return "[::]" instead "::",
we check that as well
 2023-03-11 11:26:40 +05:30
Wolfgang Maier 1cb9133026 Avoid passing headers argument twice in datatypes display 
... in release_23.0
 2023-03-10 18:04:51 +01:00
John Davis c6c2e1b0dd Remove debugging code 2023-03-10 10:25:13 -05:00
davelopez 3f10b58ba9 Fix update of celery_conf for launch_gravity too 2023-03-10 13:15:24 +01:00
davelopez 01d3365b7f Fix Celery configuration for integration tests 
I think the intent was to have both `broker_url` and `result_backend` setup here. The previous code was setting just `result_backend` and leaving the rest as default.
 2023-03-10 13:15:14 +01:00
davelopez d15815a2b5 Add support for importing zip archives 2023-03-09 18:23:16 +01:00
Ahmed Awan 832e6f287d lint exception for hid-related ValueError 2023-03-08 11:01:02 -05:00
Ahmed Awan 3c3bbf6d0e Validate/Typecheck history Related filter in backend 2023-03-08 10:00:01 -05:00
Marius van den Beek 5a34325573 Merge pull request #15733 from jdavcs/release_23.0_wfrss_index 
[23.0] Add 2 indexes to WorkflowRequest* tables on the workflow_invocation_id field
 2023-03-08 15:39:20 +01:00
John Davis 7789c87b87 Update 23.0 release tags for migration scripts 2023-03-07 17:08:05 -05:00
John Davis 0bcc0172b2 Fix linting: remove unused imports 2023-03-07 15:29:42 -05:00
John Davis 8e4eda4a60 Add migration for index on workflow_request_input_parameters__workflow_invocation_id 2023-03-07 15:27:20 -05:00
John Davis 9ecea08428 Add migration for index on workflow_request_step_states__workflow_invocation_id 2023-03-07 15:27:20 -05:00
John Davis e16ad29ae4 Add migration helpers for handling indexes 2023-03-07 15:27:16 -05:00
John Davis 1a2c1f4fb3 Add index to WorkflowRequestInputParameter.workflow_invocation_id 2023-03-07 15:27:16 -05:00
John Davis ee112c6d12 Add index to WorkflowRequestStepState.workflow_invocation_id 2023-03-07 15:27:16 -05:00
davelopez e8e5d446e9 Fix attribute error on base models 
In some context (like Celery) the `table` in `__declare_last__` hook is not working and can end up in errors like:

AttributeError: type object 'History' has no attribute 'table'
 2023-03-07 20:25:22 +01:00
John Chilton be5f22d584 Merge pull request #15724 from davelopez/23.0_fix_sts_cleanup_metadata_lost 
[23.0] Fix Short Term Storage cleanup when metadata is lost
 2023-03-07 13:03:19 -05:00
davelopez f0ba2df752 Ignore errors when deleting the whole directory 2023-03-07 12:29:27 +01:00