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molgenis / molgenis

MOLGENIS - for scientific data: management, exploration, integration and analysis.
https://molgenis.org
GNU Lesser General Public License v3.0
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MOLGENIS (Docker) crash on data upload #6612

Closed esthervanenckevort closed 6 years ago

esthervanenckevort commented 7 years ago

How to Reproduce

Expected behavior

The data is loaded

Observed behavior

I get the message: '51_app_1 exited with code 137' on the console

LuukDijkhuis commented 7 years ago

some info: in the quick importer I get "Import failed; Header was found, but no data is present in sheet". When I add dummy data to the empty header I get an infinite spinner, but the data gets loaded. When I try the same (add dummy data to the empty headers) and upload it in the "advanced" importer I still get "51_app_1 exited with code 137"

dennishendriksen commented 7 years ago

The exit code is from a process in the Docker container: http://tldp.org/LDP/abs/html/exitcodes.html

ConnorStroomberg commented 6 years ago

As the current version of molgenis is 5.2 i have tried to reproduce the bug by uploading the emx file ( GeniHeart_final.xlsx ) using the molgenis 5.2 docker ( using docker compose ). I was unable to reproduce the error. However i was not able to successfully import the files. I have tried the same steps using the 5.1 molgenis docker, and get the same results.

@LuukDijkhuis the file is a emx format, the format is not supported by the 'quick importer' as the emx format defines the meta-data as well as the data, while the 'quick importer' is used to import data without meta data ( the quick importer guesses the meta data based on the data )

The error suggests a error in the GeniHeart_final.xlsx file. Looking at the file it seems row 56 in the attribute sheet contains a error, the 'refEntity' column has a non null value but the 'dataType' column contains the value 'text'.

@djvanenckevort i am not sure what the correct values should be, could you fix the emx file and send me the updated file, i will then try to reproduce the issue again using the updated file.

screen shot 2017-10-26 at 09 46 40

esthervanenckevort commented 6 years ago

The issue is that it crashes on this file, even though the file is invalid it should not crash the MOLGENIS docker, but provide an error.

ConnorStroomberg commented 6 years ago

@djvanenckevort in that case i am not able to reproduce the issue.

LuukDijkhuis commented 6 years ago

this is starting to pingpong. The file has an error, which stops the upload process. Possibly the file should be fixed and then it might fail. But since the errorcode points to a memory problem it can be very dependent on the local situation whether or not it occurs. So the point is: if this is the exact version of the EMX file that triggers the error at the customer site, then we cannot reproduce it as-is. If it isn't then please get us the exact one that fails. We can also put in a dummy value so that it would load in principle but that would be rather random and doesn't guarantee a correct fix.

mark-de-haan commented 6 years ago

See this PR in the docker repository for a workable scenario