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Merge 24.0 into 24.1 #18239

Merged
merged 85 commits into from
May 28, 2024
Merged

Merge 24.0 into 24.1 #18239

merged 85 commits into from
May 28, 2024

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mvdbeek
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@mvdbeek mvdbeek commented May 28, 2024

(Please replace this header with a description of your pull request. Please include BOTH what you did and why you made the changes. The "why" may simply be citing a relevant Galaxy issue.)
(If fixing a bug, please add any relevant error or traceback)
(For UI components, it is recommended to include screenshots or screencasts)

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.

martenson and others added 30 commits March 27, 2024 17:25
I assume the union_mode does not trickle down...

type accessible as literal False
that does not fetch dataset details or allow other interactions

minor adjustments
The data is either present in the store if a user has actually submitted
or job,  or it is not. That includes both `jobDef` and `jobResponse`.
Followup to galaxyproject#18141.
This eliminates the code path that failed in
galaxyproject#18189, and should
generally be a nice performance improvement.
…ataset_on_error

[24.0] Fix Edit Dataset UI when there is an error retrieving the dataset
…update

[24.0] Avoid object store path lookup when constructing JobState object
Can be string or array
This now matched the filter in formattedOptions, so that upon first
rendering there's no discrepancy with currentValue.
mvdbeek and others added 8 commits May 27, 2024 10:15
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>"

```
…g_fetch_invalid_url

[24.0] Raise ``RequestParameterInvalidException`` if url can't be verified
…ss_only

[24.0] Don't set dataset peek for errored jobs
…ation_log_level

[24.0] Decrease log level for expected visualization errors
…ts_deleted_job_files

[24.0] Raise appropriate exception if accessing deleted input file
…gth_if_no_error_handling

[24.0] Reset content-length for unhandled exceptions
@davelopez
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I can take a look at the merge failures if you are not already on it

@mvdbeek
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mvdbeek commented May 28, 2024

I was :). Can you take a look at 0f9eab7 ? My thinking is that we need to separate the two error conditions, if submitting the value failed we shouldn't disable the rest of the interface

@@ -26,7 +26,8 @@ const props = defineProps<Props>();
const historyStore = useHistoryStore();

const loading = ref(false);
const messageText = ref("");
const loadingFailed = ref(false);
const messageText = ref<string | null>(null);
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My thinking is that we need to separate the two error conditions, if submitting the value failed we shouldn't disable the rest of the interface

Yeah! That looks way better! Thank you!

Minor thing, undefined can serve here as well no need for extra null handling.

Suggested change
const messageText = ref<string | null>(null);
const messageText = ref<string>();

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don't we need to include undefined then in the type hint ?

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@davelopez davelopez May 28, 2024

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It should be inferred by leaving the value empty

image

Unless you want to use the more verbose type definition that imports Ref from vue:

const messageText: Ref<string | undefined> = ref();

@mvdbeek mvdbeek merged commit 8ed752a into galaxyproject:release_24.1 May 28, 2024
53 of 55 checks passed
@jdavcs jdavcs added this to the 24.1 milestone Jun 19, 2024
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8 participants