Visulisations options windows wipes xml-file out when closing by close window button

[AxelWeber]

When something in the "visulisations options window" goes wrong or is not correctly assigned, the OK button is out of function. There is no hint given why the window behaves like this. I faced this problem after using a adopted xml file for visualisation settings from another expression data set. I simply closed the window by clicking the close button on the upper right corner of the window. After closing the window in this way, the content of the xml-file vanished (the file size was zero). This behavior can destroy the work of hours. I would therefore suggest not to touch the contents of the xml-file when closing the window without clicking the OK button.

[AxelWeber]

I used Pathvisio 2.0.3 via java webstart on a Ubuntu 8.04 linux machine.

[martijn]

Sorry to hear that you lost data. We'll do our best to fix this.

Is this problem reproducible? Is there a series of steps to take that make this error happen again?

Also, do you still have the log file (in C:\Documents Settings\<username>\.PathVisio\PathVisio.log or in /home/<username>/.PathVisio/PathVisio?.log ? If yes, could you attach that to this ticket?

If everything else fails, I'll at least add a feature that a backup of the xml file is saved somewhere.

[AxelWeber]

I reproduced it in a temporary folder. I provided a xml file that resulted in a visualisation with advanced color settings that had a missing color set assignment (<null>). Therefore the OK button was disabled in the visualisations window and I closed it by clicking on the close window button (upper right corner of the kde / java window). After that the xml file is empty. The attached logfile does not provide many information about that. Remark: We are working on a rather big map with a lot of nodes and literature references that we plan to put on wikipathways after publication.

[AxelWeber]

That means that after escaping the window by closing it all other color settings are lost because of one missing color assignment. It would be nice to have an error handling for that or a pop up message that tells the user which assignments are missing to complete the color settings in the visualisation window. A backup file solution will cause much less programing effort and is probably the fastest way to fix that bug. Many thanks in advance. - I really like your nice pathway editing tool!

[martijn]

Ok, I think I fixed this completely:

* A colorset with null assignment is handled gracefully, it's simply skipped during writing out * An error during saving the visualization will lead to a popup message * The current xml file should not be affected if there is an error during writing out.

If you can, please test the beta version at  http://www.pathvisio.org/webstart/daily/pathvisio.jnlp, and let us know if you're still having problems.

[AxelWeber]

As far as I see in the daily version, it works now correct without loss of data. I recognized a minor point that I recently added to the trac system ( http://www.pathvisio.org/ticket/1132). A second comment is as follows: It would be nice to have a CANCEL-button for the case that the OK button is out of function (or a pop up message, for click on disabled OK button).