Marius van den Beek
03ff774f23
Merge pull request #11701 from OlegZharkov/share-to-users
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Refactor Sharing
2021-09-20 19:46:54 +02:00
Dannon
52cd891148
Merge pull request #12283 from davebx/sanitize_allow
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Vuefy and improve granularity for tool HTML sanitization
2021-09-20 12:48:06 -04:00
Dannon
1d72e02051
Merge pull request #12495 from mvdbeek/data_manager_fail_job_when_data_table_addition_fails
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Fail data manager job when processing table entry fails
2021-09-20 12:36:28 -04:00
Dannon
5fac82731f
Merge pull request #11738 from mvdbeek/ncbi_datasets_async_tool
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NCBI Datasets data source tool
2021-09-20 12:17:28 -04:00
mvdbeek
3c0c5a9205
Complemntary changes to suggestions
2021-09-20 18:10:03 +02:00
davelopez
57b9e9a103
Explicitly return an empty response with 204
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See https://github.com/tiangolo/fastapi/issues/2832
2021-09-20 17:28:35 +02:00
Marius van den Beek
9538c18deb
Merge pull request #11309 from bernt-matthias/topic/build-collection-identifiers
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build list: list identifiers
2021-09-20 16:19:25 +02:00
Marius van den Beek
2f3942b47e
Merge pull request #12489 from jmchilton/fix_restart_selenium
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Fix bug when restarting Galaxy in selenium integration tests.
2021-09-20 15:46:55 +02:00
John Chilton
4d63e9830a
Merge pull request #12441 from davelopez/send_file_middleware
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FastAPI: add middelware to deal with file downloads
2021-09-20 09:43:11 -04:00
mvdbeek
4555ca5053
Fix logic for replacing tools in workflows with compatible versions
2021-09-20 14:17:14 +02:00
mvdbeek
ed9f46f757
Add two versions of build_list tool
2021-09-20 14:17:14 +02:00
Marius van den Beek
db6a91552f
Merge pull request #12501 from bernt-matthias/topic/lint-error-invalid-profile
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let invalid profile trigger linter error
2021-09-20 14:15:43 +02:00
Matthias Bernt
3e2773b145
use element_identifier if possible
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for collection input
2021-09-20 13:30:20 +02:00
Matthias Bernt
8c58a072c1
add buildlist 1.1.0 to workflow safe updates
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and try to use element_identifier
2021-09-20 13:30:19 +02:00
Matthias Bernt
4c25e96d28
remove test case with list input
2021-09-20 13:30:19 +02:00
Matthias Bernt
e45a913eef
fix
2021-09-20 13:30:19 +02:00
Matthias Bernt
82f258ccb6
add tests and use name instead of element_identifier
2021-09-20 13:30:19 +02:00
Matthias Bernt
7cf4085360
add tests
2021-09-20 13:30:19 +02:00
Matthias Bernt
8a5c02cd73
build list: list identifiers
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allow also element_identifiers or a manually specified name
2021-09-20 13:30:18 +02:00
Matthias Bernt
69692b830c
let invalid profile trigger linter error
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see https://github.com/galaxyproject/tools-iuc/pull/3969#issuecomment-922756692
2021-09-20 11:20:47 +02:00
Dannon
5ea0c5120d
Merge pull request #12466 from natefoo/tool-test-history-reuse
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Add options to override the history name and reuse histories in the tool test script
2021-09-19 19:49:13 -04:00
Dannon
4cfd44d4f9
Merge pull request #12488 from jmchilton/handle_deleted_panel_views
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Handle deleted panel views in the UI.
2021-09-19 19:27:07 -04:00
mvdbeek
8bc3e9f983
Expose job traceback
2021-09-19 18:40:59 +02:00
mvdbeek
2eba5b31e1
Use JobWrapper fail method to set dataset states
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This correctly sets the dataset and job state to error, but should be
refactored to not attempt to move outputs if that was already done.
2021-09-19 18:40:40 +02:00
Matthias Bernt
3a2e357cb0
revert a change to xsd
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https://github.com/galaxyproject/galaxy/pull/11026 extended the
description on how parameters in sections are referenced.
this already included syntax that is not merged yet:
https://github.com/galaxyproject/galaxy/pull/9493
this PR reverts this, see https://github.com/galaxyproject/galaxy/pull/9493#issuecomment-912588302
2021-09-17 18:49:22 +02:00
mvdbeek
3b13e9a11a
Raise exception if entry couldn't be added to loc file
2021-09-17 18:32:34 +02:00
mvdbeek
b65107eb83
Drop unused persist_on_error option
2021-09-17 18:31:52 +02:00
Oleg Zharkov
e4f0542bad
wait for error to appear
2021-09-17 18:27:09 +02:00
John Chilton
97f019e51b
Fix bug when restarting Galaxy in selenium integration tests.
2021-09-17 11:57:19 -04:00
John Chilton
66d8803fab
Handle deleted panel views.
2021-09-17 11:40:15 -04:00
Oleg Zharkov
31c4cc3893
check that contains is not None
2021-09-17 16:41:59 +02:00
davelopez
77f0140fc3
Join paths using pathlib
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FileResponse.path could return a relative path in some cases.
2021-09-17 16:31:38 +02:00
Oleg Zharkov
679486f388
add error message
2021-09-17 16:29:27 +02:00
Oleg Zharkov
234731632b
refactor test
2021-09-17 16:18:34 +02:00
Oleg Zharkov
3f0a7633c8
fix selenium
2021-09-17 15:32:15 +02:00
Marius van den Beek
386ab809fa
Merge pull request #11085 from astrovsky01/new_user_welcome
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New User Welcome page
2021-09-17 12:48:49 +02:00
davelopez
ee75fd490e
Remove getattr to access config values
2021-09-17 12:15:03 +02:00
David López and Sergey Golitsynskiy
c13294ed4a
Update lib/galaxy/webapps/galaxy/fast_app.py
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Co-authored-by: Sergey Golitsynskiy <sgolitsynskiy@gmail.com >
2021-09-17 11:00:42 +02:00
David López and Marius van den Beek
ad5dac31a3
Update lib/galaxy/webapps/galaxy/fast_app.py
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2021-09-17 11:00:42 +02:00
davelopez
7055a6c7a9
Add middelware to deal with file downloads
2021-09-17 11:00:42 +02:00
Oleg Zharkov
7001c9f8a5
fix HistorySharingTestCase::test_unsharing
2021-09-17 10:18:38 +02:00
Oleg Zharkov
bd157ead1d
fix selenium test_sharing_valid_by_id
2021-09-17 10:18:38 +02:00
davelopez
32adf91e56
Remove unused code
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This is efectively no longer used now so it can be removed as Marius suggested.
2021-09-17 10:18:38 +02:00
davelopez
673cd6a4cd
Fix FastAPI route in visualizations
2021-09-17 10:18:38 +02:00
Oleg Zharkov
af30274afc
fix cornercase, when only one dataset available, but user is able to make it public
2021-09-17 10:18:38 +02:00
davelopez
d98f3346de
Use unique resource name in tests
2021-09-17 10:18:37 +02:00
davelopez
c724f6ba93
Remove test assert no longer applicable
2021-09-17 10:18:37 +02:00
davelopez
13235d4981
Rename set_sharing_with_users to share_with_users
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- Fix legacy routes in buildapp.py
2021-09-17 10:18:37 +02:00
davelopez
cf1fa74ce5
Merge share and unshare in the same request
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Instead of having two different requests for adding or removing users from a shared resource now a simple list of users is sent in the request.
The resource will be shared with new users and unshared with users that are no more on that list.
2021-09-17 10:18:37 +02:00
davelopez
6d224447c9
Adapt tests to use JSON payload
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See https://github.com/galaxyproject/galaxy/pull/12152
2021-09-17 10:18:37 +02:00
Marius van den Beek