Agenda and Notes

Dev updates (Urie)

Server

• parseTree returns a 202 response with the URL in location header and in the body (requested by Andy Muir)
• Bad requests (no newick, invalid newick, etc.) get a 400 response and an appropriate error message
• Each tree is hashed when importing, and if a tree with the same hash is uploaded later, the URL for the existing tree is returned.
• Uploaded newick strings are saved to the filesystem, in case they need to be imported again later.
• Reset database on portnoy. Currently just the Smith tree and the NCBI taxonomy. Development server on estraven.iplantcollaborative.org is available for test uploads.
• Tried dedicated database server for estraven and performance was significantly worse:
  • importing the NCBI taxonomy to a local db: about 3 min.
  • importing the NCBI taxonomy to the db on euryale: about 9 min.

Client

• JSON now accepted in paste-style box.
  • Updated to allow name->style mappings (in addition to existing id->style mappings)
  • added a branchLabels element to json, to display text labels in the tr-standalone app
• Can now zoom out to parent node. Currently, this is done with the left-drag gesture.
• Labels in SVG output are now hidden if overlapping

BSA Updates from Naim

• went very well, no specific feedback from viewer
• one failure during live demo when sending tree, repeat worked fine
• used to view tree only, not tree + annotations
• current DB issue with View Tree link in DE (going to estraven)
• Naim hacked an alternate solution that sends as an analysis (yay!); but issues with opening URL automatically and cache clearing

Questions / Other notes

• how to we deal with the (possibly) large number of trees that might end up in that pull-down menu on the treeviewer?
  • should we remove the open menu item altogether?
  • or keep a short list of good demo trees
• plans for usability testing of DE after August
• what is next for the visualizer?
  • small fixes, UI improvements, help, etc.
  • documentation for standalone installation
  • need to connect with other viz needs within iPlant
  • probably not going to be any Core Software attention to viz until the end of the year
  • publication!
• Let's focus on the publication in the short term