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Programatically created file cannot be opened: exception

0 votes


I am currently working with automatically assigning groups for the elements in the graph. I wrote a small script in python for assigning nested subgroups. The structure of the final xml files seems to be correct, I repeated the process manually in yEd and have got a very similar file.  

However, I cannot open the files generated by my script, the error message with the exception is attached. I had also tried to open it in the web version and it works fine. But on the web version I cannot use layout functionality.

Can you please give me a tip what is wrong and how to make the files open in a desktop  app as well?

Thanks for the nice app and for your help,




My files: 



in Help by

1 Answer

0 votes

Your GraphML files are not well-formed.

E.g in CCR4-dependent immune cell chemotaxis in asthma and atopic dermatitis.graphml there is a <node> element with id="extracellular::membrane" and a <graph> element with id="extracellular::membrane".
This is not allowed in XML - the values of id attributes have to be unique.

Moreover, the aforementioned "extracellular::membrane" node is a group node with a <graph> child element and a <node> child element.
This is not allowed in GraphML. A <node> element may not have other <node> elements as (direct) children. (Instead there has to be exactly one <graph> child element holding all the required <node> descendants.)
See the Structural View in the GraphML Specification for information on valid GraphML structure.

by [yWorks] (144k points)
Hi Thomas,

Thanks for your fast and proper reply. I reworked my script and my files and was able to upload them to yEd.
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