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    Marius
    @mvdbeek:matrix.org
    [m]
    also have a look if you don't want to implement this as a pulsar job runner, with the EmbeddedPulsarJobRunner you can use it just like a regular job runner (and you can get optional staging / rewriting etc "for free")
    Simon Bray
    @simonbray:matrix.org
    [m]
    Ahh, thanks Marius
    I had return job_state for successful jobs where I should have had return None
    Mahendra Paipuri
    @mahendrapaipuri
    Hello, this is some diagnosis of the question I posted in admins channel about watch_tools functionality. I managed to read the source code and I am missing something. So, the tool_watcher is initialised here and set it as property here (between there is duplication of self.tool_watcher) and eventually the watchers are started in start method. But I do not find where the "important" attribute monitored_dirs to the ToolWatcher class is being set? Certainly, not here. From my understanding, tool_watcher is running but not monitoring any files or directories. Maybe its a bug? When I add a new tool to the tools directory, nothing happens? Maybe I am misunderstanding the usage of watch_tools? Can someone please shed some light into it? Cheers!
    Mahendra Paipuri
    @mahendrapaipuri
    I have printed the self.tool_watcher at the end of start method in the ConfigWatchers class and I got this
    {'observer': <InotifyObserver(Thread-3, started daemon 140611877312256)>, 'observer_class': <class 'watchdog.observers.inotify.InotifyObserver'>, 'event_handler': <galaxy.tool_util.toolbox.watcher.ToolFileEventHandler object at 0x7fe328fdccd0>, 'monitored_dirs': {}, 'toolbox': <galaxy.config_watchers.ConfigWatchers object at 0x7fe328fdcfd0>, 'tool_file_ids': {}, 'tool_dir_callbacks': {}}
    Mahendra Paipuri
    @mahendrapaipuri
    Hello, did anyone try modifying the default log_format of Galaxy. We would like to add the current Galaxy user (the user that logged into Galaxy) to the log format to trace the actions of each user (our security team is quite paranoid). Is it possible? Cheers!
    bernt-matthias
    @bernt-matthias:matrix.org
    [m]
    Struggling to find the code that sets the value of tool parameter that is used in the command's cheetah and output filters (specifically a select that uses the default of the param in a test)
    Could someone point me to the sources?
    M Bernt
    @bernt-matthias:matrix.org
    [m]
    Needed to fix this: galaxyproject/galaxy#14998 ...
    M Bernt
    @bernt-matthias:matrix.org
    [m]
    Thanks Nate Coraor
    Jochen Bick
    @bimbam23
    how can I fix this outdated issue:
    Browserslist: caniuse-lite is outdated. Please run: npx browserslist@latest --update-db Why you should do it regularly: https://github.com/browserslist/browserslist#browsers-data-updating
    dannon
    @dannon:matrix.org
    [m]
    You shouldn't need to do that, it's just a warning.
    Are you seeing an actual error somewhere in the client build?
    (we/I periodically do update browserslist as a part of regular dependency upgrades -- this isn't saying you need to do something special in your local galaxy)
    Jochen Bick
    @bimbam23
    Hi Dannon, it's not a real problem but it comes when starting the local instance
    dannon
    @dannon:matrix.org
    [m]
    What galaxy version out of curiosity?
    Jochen Bick
    @bimbam23
    22.05
    a new setup from 3 days ago :-)
    dannon
    @dannon:matrix.org
    [m]
    Well. If you can, ignore it for now and with any luck releases won't have to build the client anymore with 23.0 and you won't see this anymore :)
    Jochen Bick
    @bimbam23
    ok, thanks for the quick help
    Nate Coraor
    @natefoo:matrix.org
    [m]
    👋 @bimbam23 welcome back
    Qiang Gu
    @qiagu:matrix.org
    [m]

    Planemo lint with galaxy-tool-util v22.1 raises an error:

    Applying linter inputs... FAIL
    .. ERROR: Select parameter [metrics] has multiple options with the same value
    .. INFO: Found 61 input parameters.

    galaxyproject/planemo#1324

    Nate Coraor
    @natefoo:matrix.org
    [m]
    Presumably the answer is "not really" since we haven't already done it, but is there any way we can modify the test output so that the actual errors aren't buried thousands of lines up in the test output? e.g. https://github.com/galaxyproject/galaxy/actions/runs/3493313117/jobs/5860927967#step:15:907
    Qiang Gu
    @qiagu:matrix.org
    [m]
    @natefoo:matrix.org I met a similar issue. Luke (@luke-c-sargent ) solved the issue yesterday. Click the left part on the summary page and scroll down, there are artifacts for people to check out. Hope this info helps your issue as well.
    Nate Coraor
    @natefoo:matrix.org
    [m]
    Thanks! It's certainly much easier to find there, although you still have to download, unzip, and open the contents rather than viewing it online.
    Qiang Gu
    @qiagu
    Agreed on the inconvenience. My tool test error messages only exit in the artifacts.
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    We don't really enforce coverage, so maybe we don't need that. Although most of the output is warnings, from SQLAlchemy in particular
    Nate Coraor
    @natefoo:matrix.org
    [m]
    Right - a few of those might actually be relevant deprecation warnings and the like, especially for cpython or the standard lib, but you'd never see them anyway through all the noise.
    John Davis
    @ic4f:matrix.org
    [m]
    SQLAlchemy warnings will go away soon enough (we have lots of "removed in 2.0" warnings - that's intentional: it keeps track of stuff that must be fixed before we can upgrade to 2.0
    claudiofr
    @claudiofr
    I am new here and am interested in contributing to the galaxy project. I'm a retired software developer with experience using a wide variety of software development tools and environments but I am relatively new to python. My only experience has been in developing a few jupyter notebooks. No python based web applications. Earlier in my career I worked a lot with Java and unix. In the later part it was windows and C#. I have a windows 11 laptop and from what I gather reading the docs linux would be the preferred development platform, correct? If so, does anybody have any experience running ubuntu on windows 11 using the WSL (windows subsystem for linux) for galaxy development? I'm in the middle of reading the Galaxy Code Architecture Slides but any advice on where to start would also be appreciated.
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    Running Galaxy in Ubuntu under WSL worked fine, in my limited experience.
    John Davis
    @ic4f:matrix.org
    [m]
    Hey, @claudiofr , welcome to the community! With a background in unix and Java (and C#), I think you'll pick up Python in no time. Galaxy is a nontrivial system, but you absolutely don't need to understand all of its parts to make (significant) contributions to the code base. The code architecture slides are a good place to start. If you are not quite comfortable with Python, a good Python language tutorial might be helpful (I'd look for one for experienced programmers - I think you'll be able to find Python tutorials for Java programmers - those would be the most relevant, I think). Then, definitely, get galaxy to start on your local system (WSL or a VM, etc.), then maybe take a look at some of the introductory tutorials on training.galaxyproject.org, maybe this one at some point, and then it's, more or less, choose your own adventure. Hope this helps :)
    Viktoria Isabel Schwarz
    @kciy:matrix.org
    [m]
    Hi, I have a question regarding Workflow reports: how can I refer to elements inside a collection? E.g. if I want to display the pngs in the report that are inside a collection in my history
    Jochen Bick
    @bimbam23
    I have another quick question: Are labels set in the tool_config.yml that are inside a section actually working? I just get an empty space holder https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/tool_conf.xml.sample#L86
    Mahendra Paipuri
    @mahendrapaipuri
    Hello @dannon:matrix.org , I have noticed that this galaxyproject/galaxy@7bc1559 is broken in case if this.chart.plugin.specs is an empty object. In my case I was using openlayers plugin to visualize shapefiles and seems like plugin does not set specs attribute.
    dannon
    @dannon:matrix.org
    [m]
    @mahendrapaipuri: Ahh, interesting -- I'll take a look
    M Bernt
    @bernt-matthias:matrix.org
    [m]
    I remember that there was a "rule" regarding set_meta raising exceptions .. but I can't remember what it was.
    Was it to just write something to log and return None?
    Marius
    @mvdbeek:matrix.org
    [m]
    Nothing special there, are you thinking of the sniffer ?
    If there's an exception in a datatype's sniffer we treat that as no match. In set_meta the dataset enters the metadata_failed state
    M Bernt
    @bernt-matthias:matrix.org
    [m]
    Thanks Marius must have mixed this up. Then I'm wondering why this https://github.com/galaxyproject/tools-iuc/issues/4936#issuecomment-1329186687 just popped up
    Marius
    @mvdbeek:matrix.org
    [m]
    I don't know, but that is what should happen
    M Bernt
    @bernt-matthias:matrix.org
    [m]
    Agree .. Ideally tool_test_output.html would contain this as well. Will open an issue at planemo for this.
    Marius
    @mvdbeek:matrix.org
    [m]
    If it is already in the structured data json you only need to add it to the template
    Something like
    diff --git a/planemo/reports/report_markdown.tpl b/planemo/reports/report_markdown.tpl
    index f44cd247d9..e9f1049506 100644
    --- a/planemo/reports/report_markdown.tpl
    +++ b/planemo/reports/report_markdown.tpl
    @@ -30,7 +30,7 @@
     | Skipped    | {{ state.skipped }} |
    
    
    -{% set display_job_attributes = {'command_line': 'Command Line', 'exit_code': 'Exit Code', 'stderr': 'Standard Error', 'stdout': 'Standard Output'} %}
    +{% set display_job_attributes = {'command_line': 'Command Line', 'exit_code': 'Exit Code', 'stderr': 'Standard Error', 'stdout': 'Standard Output', 'traceback': 'Traceback'} %}
     {% for status, desc in {'error': 'Errored', 'failure': 'Failed', 'success': 'Passed'}.items() if state[status]%}
     <details><summary>{{ desc }} {{ execution_type }}s</summary>
     {%   for test in raw_data.tests %}
    (the html is generated from the markdown, so that should fix both)
    M Bernt
    @bernt-matthias:matrix.org
    [m]

    Thanks. Can open a PR if you like.

    Just checked: planemo '<0.75' did not report such errors.

    Marius
    @mvdbeek:matrix.org
    [m]
    while I got you here, can you take a look at galaxyproject/planemo#1327 ? With that and the other recent fixes we should get a pretty good handle on the weekly test failures