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ProtProtocols / IsoProt

Protocol of the analysis of iTRAQ/TMT proteomics data including quantification, statistical analysis and maybe clustering
https://protprotocols.github.io
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Regain original functionality #31

Closed veitveit closed 6 years ago

veitveit commented 6 years ago

After the large changes of the python scripts, nothing works anymore. Default parameters are wrongly set (#29 ) and not updated when changed (#30). I also don't find the file with the experimental design anymore. The button to run the R scripts does not work either.

@jgriss @gvinterhalter Please take a look

jgriss commented 6 years ago

Hi @gvinterhalter,

I'll have this done within the next hour.

jgriss commented 6 years ago

Hi @veitveit and @gvinterhalter ,

I think that all bugs should now be fixed. One remaining issue is that when the user clicks the button to execute the next R cells, the output of the cell to process the id data is not displayed immediately. Therefore, the user doesn't get any output and might think that something broke.

I believe this was working before but I can't really figure out why it changed. It is a known old bug of the RKernel but I'm not aware that we changed any versions?

Once this is resolved in some way, I'd consider this issue done.

veitveit commented 6 years ago

Thanks! I don't recall that we already got live R output. The R code is run through the R magic and not the kernel and I don't think we can do anything about this. Hence we need to notify the user or have a listener that checks the cell for its state.

Actually, the R code is still not triggered by the button. I can take a look as soon as I find time (hopefully end of the week).

2018-06-23 22:07 GMT+02:00 Johannes Griss notifications@github.com:

Hi @veitveit https://github.com/veitveit and @gvinterhalter https://github.com/gvinterhalter ,

I think that all bugs should now be fixed. One remaining issue is that when the user clicks the button to execute the next R cells, the output of the cell to process the id data is not displayed immediately. Therefore, the user doesn't get any output and might think that something broke.

I believe this was working before but I can't really figure out why it changed. It is a known old bug of the RKernel but I'm not aware that we changed any versions?

Once this is resolved in some way, I'd consider this issue done.

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gvinterhalter commented 6 years ago

I think @veitveit is right. Rkernel had this issue https://github.com/IRkernel/IRkernel/issues/3 but not anymore. This, I believe is rpy2 problem and deserves a separate issue.

@veitveit, for me the button works up until "## Further Analysis".

veitveit commented 6 years ago

Cool, working now with me, too. Thanks!