Import data from cytoscape sif and graphml

dondi / GRNsight

Web app and service for modeling and visualizing gene regulatory networks.

http://dondi.github.io/GRNsight

BSD 3-Clause "New" or "Revised" License

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Import data from cytoscape sif and graphml #288

Closed kdahlquist closed 8 years ago

kdahlquist commented 8 years ago

Related to issue #287, but importing is a different task.

kdahlquist commented 8 years ago

We decided that the File > Open menu item will refer to the native .xlsx format and that we will have a separate menu item File > Import > Cytoscape SIF, etc.

kdahlquist commented 8 years ago

Tasks for @kdahlquist:

Convert demo files 1-4 to SIF, GraphML, GML.
Once converted, load into Cytoscape

dondi commented 8 years ago

The v1.15 beta on the website now implements SIF import also. This gives SIF a full-cycle implementation now, allowing both import and export.

To save time, I think we'll have to stay light on the detail with error checking for imports. I implemented a generalized import error dialog in case something comes up, but it will take more effort to go to the level of reporting seen in the native .xlsx opening.

That said, upon looking at this issue, I observed that many of the error checks we perform on .xlsx would apply to any other imported file, regardless of the format. However, applying those checks without redundantly copying code will take some refactoring. I will write that up as a separate issue, likely feasible only after we have merged the current beta branch into master.

dondi commented 8 years ago

That refactoring issue has been written up as #300.

dondi commented 8 years ago

Current work-in-progress is import from GraphML. This one will require some documentation when we are done because GraphML captures a superset of what GRNsight can display. My current intent is to allow the successful import of any GraphML file, but the import will ignore features that GRNsight does not support (e.g., "hyperedges," nested graphs). Again my point of reference is http://graphml.graphdrawing.org/primer/graphml-primer.html. I aim to have GRNsight successfully import all of the sample .graphml files that are posted there, ignoring the portions of those files that do not have an equivalent in GRNsight.

In summary, the intent is to support importing of the following GraphML entities:

nodes (ID'ed by gene/node name)
edges (directed only)
edge weights All other features and attributes will be ignored (for now).

dondi commented 8 years ago

OK, GraphML import is now live on the beta 1.15 page. I was on that track already so I decided to finish that first, prior to looking at the testing results from the pre-existing functionality.

kdahlquist commented 8 years ago

We are not going to import from GML right now so that we can prioritize other issues.

kdahlquist commented 8 years ago

I am going to close this because the basic implementation is done and more discussion has been shifted over to #309 and #314.