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merge 23.0 -> dev #15901

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wants to merge 67 commits into from
Closed

merge 23.0 -> dev #15901

wants to merge 67 commits into from

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bernt-matthias
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There were conflicts in

  • client/src/components/Workflow/Editor/modules/terminals.ts
  • lib/galaxy/dependencies/pinned-requirements.txt
  • lib/galaxy/webapps/galaxy/api/users.py

which I resolved by chosing the dev version

How to test the changes?

(Select all options that apply)

  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

jdavcs and others added 30 commits December 16, 2022 10:15
@jdavcs
Fix maintenance script bug
dd553e8
@jmchilton
Merge pull request galaxyproject#15222 from jdavcs/release_22.01_tabl…
d62235f 
…e_attr_err

[22.01] Fix maintenance script bug
@bernt-matthias
xsd: add forgotten comment attribute
92597e4 
for has_n_columns

follow up on galaxyproject#12528
@bernt-matthias @nsoranzo
Doc text improvement
90b3559 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
@mvdbeek
Display output dataset / collection type and map over on hover
b7df527
@mvdbeek
Pick concrete collection type if input collection type is any
b0cbb8a
@mvdbeek
Use textual description of collection type
8b31087
@martenson
add security checks to page and visualzation APIs
e2d0ef2
@mvdbeek
Test disconnecting output doesn't change map over
3fc4abf 
for previously connected step that should still be mapped over.
@mvdbeek
Don't lose step map over when disconnecting output
94123d5
@martenson
Merge pull request galaxyproject#15826 from martenson/release_22.01
5141a0f 
[22.01] add security checks to page and visualization APIs
@mvdbeek
Rebuild terminal when step changes
14eaee9 
We should track this in a finer grained way maybe,
but it'll work. This fixes displaying the right inferred
collection source type when you change connections.
@mvdbeek
Add selenium test for showing outpu type info
d7b173f
@anuprulez @ElectronicBlueberry
Partially fix galaxyproject#15723
3c6f93d 
This PR fixes tool recommendation galaxyproject#15723 partially, only in the workflow editor
@ElectronicBlueberry
run prettier
92cc29e
@ElectronicBlueberry
add thin wrapper to Recommendations
10ce335 
allows toggling Recommendations using v-if
@dannon
Merge pull request galaxyproject#15791 from bernt-matthias/topic/has_…
6f6e375 
…n_columns_comment

[22.01] xsd: add forgotten comment attribute
@dannon
Merge remote-tracking branch 'upstream/release_22.01' into release_22.05
f959f05
@dannon
Joinedload replaces eagerload 22.05 forward
caaa3e4
@jmchilton @dannon
Update Github RSA key in circle ci configuration -
82d5b4e 
xref
https://github.blog/2023-03-23-we-updated-our-rsa-ssh-host-key/
@dannon
Apply black to forward merge
9b1301e
@mvdbeek @cat-bro
Cast job_key to string
cc373c7 
Should fix galaxyproject#15211
@mvdbeek
Merge pull request galaxyproject#15842 from ElectronicBlueberry/backp…
d46f3ff 
…ort-patch-3

[23.0] Fix tool recommendation in the workflow editor
@dannon
Merge pull request galaxyproject#15850 from dannon/release_22.05
5300b13 
Merge 22.01 -> 22.05
@natefoo
Update Gravity to 1.0.2
a37f902
@natefoo
Merge pull request galaxyproject#15862 from natefoo/gravity-1.0.2
de030cd 
[23.0] Update Gravity to 1.0.2
@pauldg
ro-crate metadata fixes based on bugs
b184e11
@pauldg
Changes to tests according to ro-crate
e2882dc 
metadata changes
@pauldg
formatting
9105ba3
@pauldg
Change which parameters are included.
01782c0 
Remove duplicate dataset entries in Collections
martenson and others added 14 commits March 31, 2023 19:03
@martenson
Merge pull request galaxyproject#15883 from mvdbeek/tags_in_collectio…
905e89f 
…n_view

[23.0] List tags in ``/api/dataset_collections/{hdca_id}/contents/{parent_id}``
@mvdbeek
Merge pull request galaxyproject#15882 from davelopez/22.05_fix_ids_o…
42c9aff 
…n_errors

[22.05] Remove some IDs from error messages
@ElectronicBlueberry
increase webhook z-index
b855a81
@nsoranzo
Merge branch 'release_22.05' into release_23.0
bee3d2e
@bernt-matthias
cached_explicit_singularity: copy container description
e81fc67 
otherwise `container_description.identifier = cache_path` (at the end of the function)
will modify the original (i.e. the tools) container description which influences
i.e. (may break) successive container resolutions.
@davelopez
Fix extension lost after cleaning filename
8b715de
@davelopez
Guess mime type for short term storage files
d5bc7ff
@mvdbeek
Merge pull request galaxyproject#15893 from bernt-matthias/fix/cached…
f76d894 
…_explicit_singularity_container_description

[22.01] cached_explicit_singularity: needs to copy container description
@dannon
Merge pull request galaxyproject#15891 from ElectronicBlueberry/webho…
2acf212 
…ok-z-index

[23.0] Fix tool bar on top of pop-ups
@bernt-matthias
Merge branch 'release_22.01' into merge/22.01_22.05
a99c137
@davelopez
Add unit test for model_store_storage_target
0a04397
@jmchilton
Merge pull request galaxyproject#15894 from davelopez/23.0_fix_export…
0698979 
…_archive_extension

[23.0] Fix short term storage archive export extension on download
@mvdbeek
Merge pull request galaxyproject#15896 from bernt-matthias/merge/22.0…
f420a61 
…1_22.05

[22.05] merge 22.01
@nsoranzo
Merge branch 'release_22.05' into release_23.0
7452b2e
@github-actions github-actions bot added this to the 23.1 milestone Apr 5, 2023
@nsoranzo nsoranzo mentioned this pull request Apr 5, 2023
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@nsoranzo
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nsoranzo commented Apr 5, 2023

There were conflicts in

* client/src/components/Workflow/Editor/modules/terminals.ts

* lib/galaxy/dependencies/pinned-requirements.txt

* lib/galaxy/webapps/galaxy/api/users.py

which I resolved by chosing the dev version

I don't think that's correct, see #15902 for how I would solve the conflicts.

@bernt-matthias
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I don't think that's correct

Thought so :)

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