Marius van den Beek
36a9d131ed
Merge pull request #18247 from itisAliRH/workflow-allow-bookmark-public
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[24.1] Allow bookmarking public workflows
2024-05-29 11:23:01 +02:00
Marius van den Beek
a2b03ac42b
Merge pull request #18234 from davelopez/24.0_drop_restriction_switch_immutable_histories
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[24.1] Drop restriction to switch to immutable histories
2024-05-29 11:22:29 +02:00
Marius van den Beek
f0d4f52f3e
Merge pull request #18204 from martenson/tight-axt
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[24.1] Tighten axt sniffer
2024-05-29 10:39:01 +02:00
Marius van den Beek
8ed752a0a0
Merge pull request #18239 from mvdbeek/release_24.1
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Merge 24.0 into 24.1
2024-05-28 19:25:24 +02:00
Alireza Heidari
067f6df3ef
✨ : allow bookmarking public workflows
2024-05-28 18:38:34 +02:00
mvdbeek
16cb72703a
Fix up loading failed error state in Dataset Attributes component
2024-05-28 14:37:15 +02:00
mvdbeek
093dcc8d3d
Merge branch 'release_24.0' into release_24.1
2024-05-28 14:34:20 +02:00
davelopez
9d662f5e49
Adapt History SelectorModal test
2024-05-28 14:30:19 +02:00
davelopez
6f38f5b7fe
Fix conditions for userOwnsHistory and isRegisteredUser
2024-05-28 13:34:56 +02:00
Marius van den Beek
316eb5bf81
Merge pull request #18233 from mvdbeek/reset_content_length_if_no_error_handling
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[24.0] Reset content-length for unhandled exceptions
2024-05-27 20:00:39 +02:00
davelopez
562129f561
Adapt HistoryView tests
2024-05-27 19:07:22 +02:00
davelopez
e41293de00
Display archived message only to the owner
2024-05-27 18:46:18 +02:00
davelopez
3bcc1717d0
Restore back condition to set current history in backend
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The effect of this is that we can switch to any owned history in the UI, but if the history has been deleted it will not change the current history in the backend and a browser refresh will bring back the real current history.
2024-05-27 17:57:42 +02:00
davelopez
a9de12285a
Support extract workflow from any history in client controller
2024-05-27 17:55:39 +02:00
davelopez
0b4c0b23bb
Avoid upload data to immutable histories
2024-05-27 16:57:27 +02:00
davelopez
31e14a9f58
Avoid workflow run on immutable histories
2024-05-27 16:38:29 +02:00
John Chilton
98d8ae99b4
Merge pull request #18223 from mvdbeek/discriminate_inputs_deleted_job_files
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[24.0] Raise appropriate exception if accessing deleted input file
2024-05-27 09:49:09 -04:00
John Chilton
82a54a5f62
Merge pull request #18229 from mvdbeek/decrease_visualization_log_level
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[24.0] Decrease log level for expected visualization errors
2024-05-27 09:44:54 -04:00
John Chilton
62b53c5e2a
Merge pull request #18231 from mvdbeek/set_peek_on_success_only
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[24.0] Don't set dataset peek for errored jobs
2024-05-27 09:42:56 -04:00
John Chilton
fef8341023
Merge pull request #18230 from mvdbeek/exception_handling_fetch_invalid_url
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[24.0] Raise ``RequestParameterInvalidException`` if url can't be verified
2024-05-27 09:41:24 -04:00
davelopez
c3d9974076
Restrict some more options in history menu
2024-05-27 14:33:46 +02:00
davelopez
3aa4db55d1
Avoid running tools on immutable histories
2024-05-27 14:33:30 +02:00
davelopez
28015972de
Inform users why some actions for histories might be disabled
2024-05-27 14:33:19 +02:00
davelopez
9ae4870e5b
Disable unavailable elements in History menu for immutable histories
2024-05-27 14:33:03 +02:00
davelopez
fbf7b5d99d
Allow to go to storage overview for immutable histories
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And handle the controls visibility to avoid history mutation by deleting datasets, etc.
2024-05-27 14:32:36 +02:00
davelopez
58fbd25aab
Disable collection editing for immutable histories
2024-05-27 14:21:07 +02:00
davelopez
c3ab818768
Allow to set any owned history as current
2024-05-27 14:13:21 +02:00
davelopez
0f8d412843
Drop redundant history state info in HistoryView
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The state will be displayed in all history panels
2024-05-27 14:12:57 +02:00
davelopez
0cd4ef17c6
Add button to set archived histories as current
2024-05-27 14:12:19 +02:00
davelopez
ade613ab5d
Display history status in Panel
2024-05-27 14:04:46 +02:00
davelopez
ead71fd8b4
Move immutability restriction check from HistoryView to HistoryPanel
2024-05-27 14:04:06 +02:00
davelopez
cdbd5e32ce
Drop backend restrictions to switch to immutable histories
2024-05-27 14:01:15 +02:00
mvdbeek
3c6a9a8eaf
Reset content-length for unhandled exceptions
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This prevents `ProtocolError` caused by the error middleware not being
able to reset the content length. Only affects routes that explicitly
set the content-length and don't have a default response handler.
This is effectively the case when using `web.expose`. To test this,
make sure you get Galaxy's error middleware output in the browser
and your console.
```
diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index c95d9df788..92b04684d3 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -456,6 +456,8 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
def imp(self, trans, dataset_id=None, **kwd):
"""Import another user's dataset via a shared URL; dataset is added to user's current history."""
# Set referer message.
+ trans.response.headers["content-length"] = 0
+ trans = None
referer = trans.request.referer
if referer and not referer.startswith(f"{trans.request.application_url}{url_for('/login')}"):
referer_message = f"<a href='{escape(referer)}'>return to the previous page</a>"
```
2024-05-27 11:37:54 +02:00
mvdbeek
54db4e9a7a
Don't fail set_peek if file does not look like GRO file
2024-05-27 10:23:59 +02:00
mvdbeek
3cd64e7861
Refactor set_peek and move exception handling
2024-05-27 10:15:54 +02:00
mvdbeek
11ae179c9a
Don't set dataset peek for errored jobs
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This is consistent with the extended metadata logic, and prevents:
```
Message
Job wrapper finish method failed
Stack Trace
Newest
IndexError
list index out of range
```
which only makes it harder to diagnose the actual error, which in the
case of https://sentry.galaxyproject.org/share/issue/831261683ce642a4976efa20a9a0e55c/
is `\nslurmstepd: error: *** JOB 1910486 ON js2-gpu-small0 CANCELLED AT 2024-05-26T23:30:00 DUE TO TIME LIMIT ***\n`
2024-05-27 10:06:46 +02:00
mvdbeek
30b1f4b2f9
Raise RequestParameterInvalidException if url can't be verified
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Kind of a followup to
https://github.com/galaxyproject/galaxy/pull/18155 .
Fixes:
```
ValueError
invalid literal for int() with base 10: 'sequences'
```
For the attempted url `"http://emp-single-end-sequences:sequences "`.
2024-05-27 09:54:09 +02:00
mvdbeek
ed70432254
Decrease visualization log level
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Minor followup to https://github.com/galaxyproject/galaxy/pull/18211 .
If we've got a MessageException I don't think we need to log this as an
error, since we're also showing a reasonable message to the user.
2024-05-27 09:09:59 +02:00
Marius van den Beek
d8b827f50e
Merge pull request #17818 from martenson/noexpand-private
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[24.0] do not expand datasets that are known to be inaccessible
2024-05-25 15:53:03 +02:00
Martin Cech
706ae5fab1
sorty sort
2024-05-24 14:17:57 -07:00
Martin Cech
cae34c843a
refactor chain and ucsc.net sniffing
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properly ignore comments
do not read the dataset unbounded, I think we have enough info from the headers and the first data line
2024-05-24 10:50:47 -07:00
Martin Cech
7819c9a3e9
switch to isdecimal
2024-05-24 10:14:49 -07:00
mvdbeek
cc2f83dac0
Raise appropriate exception if accessing deleted input file
2024-05-24 18:26:18 +02:00
Marius van den Beek
ae9ea865e1
Merge pull request #18214 from mvdbeek/error_messages_when_accessing_datasets_we_cannot_access
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[24.0] Check dataset state when attempting to acces dataset contents
2024-05-24 16:02:33 +02:00
davelopez
0104764bb8
Make accessible optional in HDAObject
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It is probably enough to serialize the `accessible` property only when requesting collection contents displayed in the UI.
2024-05-24 13:43:33 +02:00
davelopez
810b246fbf
Avoid requesting details for inaccessible datasets
2024-05-24 11:09:59 +02:00
davelopez
a0adf7e76b
Add missing event declaration
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Fixes typescript error:
Argument of type '"edit"' is not assignable to parameter of type '"toggleHighlights"'
2024-05-24 10:53:00 +02:00
davelopez
afac2afa24
Serialize accessible field for collection elements
2024-05-24 10:50:08 +02:00
davelopez
7961b475bb
Fix bool const OpenAPI TS schema conversion
2024-05-24 10:47:32 +02:00
Marius van den Beek
21a427213d
Merge pull request #18217 from mvdbeek/tighten_job_access
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[24.0] Restrict job_files access to jobs that are not terminal
2024-05-24 09:00:56 +02:00
Marius van den Beek