improve three debug messages by bernt-matthias · Pull Request #11908 · galaxyproject/galaxy

bernt-matthias · 2021-04-28T11:36:47Z

What did you do?

Small change to ~~two~~ three (debug) messages

Why did you make this change?

tool evaluation: for tools with many outputs its helpful to know which datasets and collections have been created.

drmaa: for debugging its more convenient to see the command that could be copy pasted

filter errors: debug is not shown in planemo output where it would be really helpful.

actually I would like to reraise here .. the try except block is there from the beginning 89ff0ef ... maybe this is now a feature ..

How to test the changes?

(select the most appropriate option; if the latter, provide steps for testing below)

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 contributions under Galaxy's current license.
I agree to allow the Galaxy committers to license these and all my past contributions to the core galaxy codebase under the MIT license. If this condition is an issue, uncheck and just let us know why with an e-mail to galaxy-committers@lists.galaxyproject.org.

For UI Components

I've included a screenshot of the changes

tool evaluation: for tools with many outputs its helpful to know which datasets and collections have been created. drmaa: for debugging its more convenient to see the command that could be copy pasted

lib/galaxy/tools/actions/__init__.py

mvdbeek · 2021-04-29T08:50:53Z

lib/galaxy/tools/actions/__init__.py

                return True  # do not create this dataset
        except Exception as e:
-            log.debug('Tool %s output %s: dataset output filter (%s) failed: %s' % (tool.id, output.name, filter.text, e))
+            log.info(f'Tool {tool.id} output {output.name}: dataset output filter ({filter.text}) failed: {e}')


This should be at the debug level, that's going to spam the logs even if everything is alright. The log level for this module needs to be changed in planemo.

Alright, then I revert this. Can you tell me an example when this is triggered and you do not want to see the message?

Would this be done here: https://github.com/galaxyproject/planemo/blob/f5b2a4aa2d0f93c1152adddde0ac61f037fe64ad/planemo/galaxy/config.py#L130?

That's the rough idea, would be awesome if we can tune it there.

Maybe like so: galaxyproject/planemo#1165

debug messages are not shown in planemo output where the message can be really helpful. Co-authored-by: David López <46503462+davelopez@users.noreply.github.com>

This reverts commit 140ca74.

one could also pass `log_level="warning"` but this swallows some useful messages at startup and shutdown, ie. ``` INFO: Started server process [1394761] INFO: Waiting for application startup. INFO: Application startup complete. INFO: Uvicorn running on http://127.0.0.1:8296 (Press CTRL+C to quit) ... INFO: Shutting down INFO: Waiting for application shutdown. INFO: Application shutdown complete. INFO: Finished server process [1394761] ```

mvdbeek · 2021-04-29T11:43:46Z

lib/galaxy_test/driver/driver_util.py

    from uvicorn.server import Server
    from uvicorn.config import Config
-    config = Config(app, host=host, port=int(port))
+    config = Config(app, host=host, port=int(port), access_log=False)


Nice! But for Galaxy tests the access logs are useful sometimes. Maybe that could be controlled with an environment variable ? GALAXY_TEST_ACCESS_LOG ? Then planemo can set this but we keep the access logs in the CI.

sure. is there an example where an env var is used somewhere in the code base?

https://github.com/mvdbeek/galaxy/blob/20d92afc5cae22d22528bbfd84eeadc94939efc5/lib/galaxy_test/driver/driver_util.py#L983

bernt-matthias · 2021-04-29T14:35:02Z

Do you also have a tip where in Planemo I would set the environment variable?

mvdbeek · 2021-04-29T17:05:18Z

https://github.com/galaxyproject/planemo/blob/1b61aa1f75b6fad5ba14efc42e6746d1ade0f09a/planemo/galaxy/config.py#L501 seems like a good place

bernt-matthias · 2021-04-29T20:07:13Z

Is there some place in the docs where such environment variables are listed and explained? If not it might be good to add it somewhere?

will work with galaxyproject/galaxy#11908

lib/galaxy_test/driver/driver_util.py

mvdbeek · 2021-05-03T10:45:55Z

Is there some place in the docs where such environment variables are listed and explained? If not it might be good to add it somewhere?

There's a somewhat complete listing in https://github.com/mvdbeek/galaxy/blob/926268ce6e1acd3db4e51ceb72e689899c545b9c/run_tests.sh#L181.
If you add it there we can later pull that out into https://docs.galaxyproject.org/en/master/dev/index.html ?

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

run_tests.sh

lib/galaxy_test/driver/driver_util.py

- fix and simplify reading of env variable - shorten doc Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

github-actions · 2021-05-03T17:53:31Z

This PR was merged without a "kind/" label, please correct.

github-actions bot added area/jobs area/tool-framework labels Apr 28, 2021

github-actions bot added this to the 21.05 milestone Apr 28, 2021

improve two debug messages

7757006

tool evaluation: for tools with many outputs its helpful to know which datasets and collections have been created. drmaa: for debugging its more convenient to see the command that could be copy pasted

bernt-matthias force-pushed the topic/2debugmsg branch from c3278a6 to 7757006 Compare April 28, 2021 13:03

bernt-matthias changed the title ~~improve two debug messages~~ improve three debug messages Apr 28, 2021

davelopez reviewed Apr 29, 2021

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lib/galaxy/tools/actions/__init__.py Outdated Show resolved Hide resolved

mvdbeek reviewed Apr 29, 2021

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bernt-matthias and others added 2 commits April 29, 2021 13:21

promote filter faiure message

140ca74

debug messages are not shown in planemo output where the message can be really helpful. Co-authored-by: David López <46503462+davelopez@users.noreply.github.com>

Revert "promote filter faiure message"

8f22fa5

This reverts commit 140ca74.

bernt-matthias force-pushed the topic/2debugmsg branch from 99bce85 to 8f22fa5 Compare April 29, 2021 11:22

mvdbeek reviewed Apr 29, 2021

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control uvicorn access log with env variable

0167da6

bernt-matthias force-pushed the topic/2debugmsg branch from 6d796f0 to 0167da6 Compare April 29, 2021 14:34

bernt-matthias added a commit to bernt-matthias/planemo that referenced this pull request Apr 29, 2021

disable all access log messages from uvicorn

622379c

will work with galaxyproject/galaxy#11908

mvdbeek reviewed May 3, 2021

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lib/galaxy_test/driver/driver_util.py Outdated Show resolved Hide resolved

mvdbeek approved these changes May 3, 2021

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bernt-matthias and others added 2 commits May 3, 2021 12:53

rename environment variable

076231c

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

doc

4697281

mvdbeek reviewed May 3, 2021

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run_tests.sh Outdated Show resolved Hide resolved

lib/galaxy_test/driver/driver_util.py Outdated Show resolved Hide resolved

Apply suggestions from code review

f886978

- fix and simplify reading of env variable - shorten doc Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

mvdbeek approved these changes May 3, 2021

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mvdbeek merged commit 21796c3 into galaxyproject:dev May 3, 2021

nsoranzo added the kind/enhancement label May 3, 2021

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bernt-matthias commented Apr 29, 2021

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mvdbeek commented Apr 29, 2021

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bernt-matthias commented Apr 28, 2021 •

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