This week was broadly used to address the comments of my mentors and improving the code. The first major comment was regarding using source and targets while drawing edges. We were using dummy nodes to show edges, by using the start and end coordinates of the given interactions. Now GPML uploader uses the GraphRef attribute to find the source and target nodes. Again there are some problems with this approach as there are files like http://www.wikipathways.org/index.php/Pathway:WP109 which don’t specify the GraphRef for source and target nodes. Currently we are thinking of throwing an error if GraphRefs aren’t present. To test this further I am writing to script to scrape through the wikipathways file and test the GPML uploader for all the files listed there, using http://webservice.wikipathways.org/listPathways and the API http://webservice.wikipathways.org/getPathwayAs?fileType=gpml&pwId=WP4&revision=0 and count the errors we encounter with our GPML uploader.
To use the graphspace interface I did a pretty naive thing, copying the file itself to the folder (dumb I know). I did this beacause the normal way of importing wasn’t working for some reason. To debug this I started looking for namespace collisions, couldn’t find any (technically good for the code, bad for me :/). The solution turns out to be pretty simple, delete the .pyc files because they are still present after you delete the original files and my import was importing the old .pyc file hence wasn’t able to debug.
More to come, thinking of blogging twice a week!