ExecutePipeline may crash with uninformative Qt error

hendrikweisser commented 10 years ago

If ExecutePipeline tries to use the same mechanism as TOPPAS for showing an error (a GUI dialog box), it will crash and only give an uninformative Qt error message:

"QWidget: Cannot create a QWidget when no GUI is being used"

This can happen if parameters of a tool in a pipeline cannot be read, e.g. due to problems with GenericWrapper.

BioComSoftware commented 7 years ago

Hey,

Did this ever get fixed and merged into a branch?

I ask because we're wanting to use the develop branch (for the feature in "First version of SpectraST search adapter util #2359") however when I try to run a known-good pipeline from "ExecutePipeline" i get the qwidget error again...

root@ubuntu:/usr/local/OpenMS-build/bin/ExecutePipeline -in /home/mikes/Assay-Workflows-Mikes/protein_lfq/smallchaintest.toppas -out_dir /home/mikes/OUTDATA/tmp/
QWidget: Cannot create a QWidget when no GUI is being used
Aborted (core dumped)

The weirdness THIS time is; normally this issue comes up when the piepline has an error and tries to pop a GUI window to display the error.

HOWEVER, when I run this pipeline through the GUI...it run OK.

The ExecutePipeline also works when run from the Master branch install of openms.

:/

jpfeuffer commented 7 years ago

Hi,

I do not know about a fix unfortunately but are the installations on the same or different machines? If they are on the same, there might be errors due to sharing the OPENMS_DATA_PATH that only occur in one installation.

BioComSoftware commented 7 years ago

Hi J,

Well, its the same box..but I replaced the branch-master install with a branch-devel install.

I had this error before using branch-devel, which is why I changed to the master branch. But now a feature that we want([FEATURE] First version of SpectraST search adapter util #2359) appears to only be available on the develop branch...and it seems the develop branch still has the issue(?)

Thanks!

jpfeuffer mailto:notifications@github.com 26 January 2017 at 16:15

Hi,

I do not know about a fix unfortunately but are the installations on the same or different machines? If they are on the same, there might be errors due to sharing the OPENMS_DATA_PATH that only occur in one installation.

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BioComSoftware commented 7 years ago

So, I'm wondering if - when running ExecutePipeline from the develop branch - it is still asking what tmp directory to use (and thus it tries to create the ppoup asking what tmp directory, thus triggering the QWidget error.)

I did NOT get this issue when running the master branch...but I'm wondering (as a workaround) if there's a way to designate what tmp directory to use in either the TOPPAS file, the OPEN.ini or the trf file...so that it doesn't ask.

HISTORY:

I've installed the 'develop' branch.
I try to run a known good TOPPAS pipeline (that runs fine in the GUI) with the "ExecutePipeline" command...and it fails with a 'Canot open a QWidget in non-GUI" error
The QWidget error does not specify WHAT window it is trying to open (I have seen this before when it tries to pop an error window).
So I'm ASSUMING that its (maybe) trying to pop the 'what tmp directory window)

Mike Rightmire mailto:mike.rightmire@biocomsoftware.com 26 January 2017 at 16:23 Hi J,

Well, its the same box..but I replaced the branch-master install with a branch-devel install.

I had this error before using branch-devel, which is why I changed to the master branch. But now a feature that we want([FEATURE] First version of SpectraST search adapter util #2359) appears to only be available on the develop branch...and it seems the develop branch still has the issue(?)

Thanks!

jpfeuffer mailto:notifications@github.com 26 January 2017 at 16:15

Hi,

I do not know about a fix unfortunately but are the installations on the same or different machines? If they are on the same, there might be errors due to sharing the OPENMS_DATA_PATH that only occur in one installation.

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BioComSoftware commented 7 years ago

Any word on this?

BioComSoftware commented 7 years ago

@hendrikweisser @jpfeuffer

Hi All,

So update.

If I create a new Pipeline from scratch, containing only a PPHR node, I can run it from ExecutePipeline just fine.

My understanding is, the QWidget error happens because the command line executable is trying to create a GUI window, which it can't from the command line (obviously).The Pipelines in question also run fine at a GUI windows (within TOPPAS) WITHOUT popping any additional windows whatsoever...however, when I try to run them with the ExecutePipeline command line, I get the QWidget error...I assume because they are trying to pop an informational message or directory request that doesn't pop when run at the command line.

It looks like this issue wasn't resolved, just buried somewhere in the code. This has become a block to my entire project. Hopefully, we can take a peek at it?

Thanks!

cbielow commented 7 years ago

Hi Mike, can you attach the pipeline here please. It should be self sufficient if possible, i.e. use nodes which are available in the standard OpenMS installation. If thats not possible, please attach the tdds for GW as well. I'll look into it.

BioComSoftware commented 7 years ago

Hi Chris,

Thanks so much for looking into this!

I'll send you the pipelines - let me get that assembled for you.

In the meantime, I wonder if we should look at the larger issue of the QTWidget again. I may be wrong, but isn't this error because the ExecutePipeline command is trying to pop a GUI window when it's not being called by the GUI?

Is it possible to track down what's calling this GUI window, and convert it to a text output instead?

Or is that what you need the pipelines to find? :D

Thanks again!

Chris Bielow mailto:notifications@github.com 2 February 2017 at 10:00

Hi Mike, can you attach the pipeline here please. It should be self sufficient if possible, i.e. use nodes which are available in the standard OpenMS installation. If thats not possible, please attach the tdds for GW as well. I'll look into it.

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BioComSoftware commented 7 years ago

Hi Chris,

I know it's a bit improper, but may I send this info to you privately (instead of over the OpenMS channel). I need to check with my project leader if he is comfortable sharing these pieplines publicly. But for the sake of your time, and the issue urgency, I don't mind sharing directly with you :)

Thanks! Mike

Chris Bielow mailto:notifications@github.com 2 February 2017 at 10:00

Hi Mike, can you attach the pipeline here please. It should be self sufficient if possible, i.e. use nodes which are available in the standard OpenMS installation. If thats not possible, please attach the tdds for GW as well. I'll look into it.

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cbielow commented 7 years ago

Or is that what you need the pipelines to find? :D

exactly.

You should have me one skype for file transfer or mail adress exchange

BioComSoftware commented 7 years ago

OK. When I open SOME of the offending pipelines IN THE TOPPAS GUI, I get this message (NOTE: at open NOT at run).

Perhaps this is the message thats causing the QWidget error?

This may relate to another issue I started in the maillist, about TOPPAs being unable to write to the system /tmp dir.

I worked around this issue, by changing the tmp dir in the openms.ini file.

Perhaps thats not reflected in these piepline saves?

BioComSoftware commented 7 years ago

Hi Chris,

I dont think I currently have you on Skype...but my skype is RightmireM if you'd be willing to make a contact request.

Searching for you on skype pulls up a LOT of people :D

Thanks!

Chris Bielow wrote:

Chris Bielow

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BioComSoftware commented 7 years ago

Hi Chris,

I'm 90% confident it's the tmp issue...

Anytime I open a pipeline in the GUI, and it creates that message, the pipeline fails at the command line ExecutePipeline with eh QWidget error.

Any pipeline I can open in the GUI, that DOES NOT create that message, runs.

The "Cannot write to tmp" error seems to be restricted to GW nodes.

=== Can we fix either the issue writing to tmp...or the QWidget error?

As far as tmp, I have...

Ensured /tmp is root:root rwxrwxrwx
Changed all the OpenMS.ini tmp_dir to "home/tmp" (a dir I created)
Ensured /home/tmp is rwxrwxrwx
Tried changing ownership of /home/tmp to the user calling ExecutePipeline, root, and a generic user that owns all of the OpenMS binaries in /usr/local/OpenMS/bin (biop:biop)

THANKS!

BioComSoftware commented 7 years ago

The QWidget error also appears if the pipeline tries to warn of nodes without output file locations...

cbielow commented 7 years ago

Hey Mike, this should be fixed now:

You can give it a try with all your pipelines on my branch

https://github.com/cbielow/OpenMS/tree/fix-Messagebox

hroest commented 7 years ago

@cbielow can we close this?

BioComSoftware commented 7 years ago

YA. I think so. Thx :)

Hannes Roest mailto:notifications@github.com 28 April 2017 at 21:17

@cbielow https://github.com/cbielow can we close this?

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ExecutePipeline may crash with uninformative Qt error #954