Transfer files to host so EM can find them locally.

[mikekucera]

This pull request changes the Protocol2_createEM.Rmd script to use two CyREST endpoints have been added to EnrichmentMap.

• /enrichmentmap/textfileupload - CyREST POST endpoint
  • Allows a text file to be uploaded to the host using a standard http multipart file upload. The endpoint returns the absolute path to the copy of the file on the host. This path can then be given to the enrichmentmap build command so that enrichmentmap can find the file locally. The script no longer requires host_machine_dir to be set.
• "enrichmentmap export png" command
  • Near the end of the script an image of the network is exported, but without host_machine_dir this can't be done anymore. I added a command to EM that exports the network image to the users home directory instead.

Refs https://github.com/BaderLab/EnrichmentMapApp/issues/385

[risserlin]

Thanks Mike! Do I need to use the updated EM jar to use this function? Will it work with the current release as well (because it is transferring the files to the CytoscapeConfiguration directory according to the path associated with the uploaded files? I am going to put a feature request in to get the upload File to the RCy3. Can it be a generic method for any app that needs files? How is it handled differently from the EM side? (basically I am asking the same question in multiple ways :) )

[mikekucera]

I added the upload function to the EM app, its not part of CyREST. You need the latest EM build that I sent you. If it works for you then it can be part of the next EM release. By putting it in the EM app it will work with the current version of Cytoscape. It could be made a generic feature in CyREST/RCy3, but you would have to wait for new releases of both.