bio4j / bio4j-titan

Titan-specific bio4j implementation
https://github.com/bio4j/bio4j
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update to angulilos-titan 0.2 #41

Closed eparejatobes closed 9 years ago

eparejatobes commented 9 years ago

once bio4j/angulillos-titan#1 is ready

eparejatobes commented 9 years ago

@pablopareja I did this for the Enzyme module, is pretty straightforward

eparejatobes commented 9 years ago

it is actually nice, how we have things now I should say. :clap: :tophat:

eparejatobes commented 9 years ago

@pablopareja put this on hold, I'm taking a different route

pablopareja commented 9 years ago

Ok...

eparejatobes commented 9 years ago

@pablopareja I added a Scala test running EnzymeDB. Everything works fine but for the type definition part; they radically changed the behavior here in 0.5, and now VertexLabel, EdgeLabel etc are useless if you close the transaction from where you get them. This is just crazy. See

So basically we are left with only one option: use Strings everywhere when interfacing with Titan, and as types the corresponding xxxMakers; we will only call getName() on them, using the overloaded addVertex(String label), addEdge(String label), ... methods.

I think I can finish this tomorrow.

pablopareja commented 9 years ago

OK :wink:

eparejatobes commented 9 years ago

@pablopareja I did that change in bio4j/angulillos-titan#1 (moving to xxxMakers for types) and everything works smoothly now for EnzymeDB; run test here inside sbt. :+1:

pablopareja commented 9 years ago

Cool ! I just checked it out after pulling the changes and it's true :smiley: Should we then keep on updating the rest of modules to this new way of initialize the properties and labels?

pablopareja commented 9 years ago

@eparejatobes :question:

eparejatobes commented 9 years ago

yes!

pablopareja commented 9 years ago

Ok! I'm getting to work on it then :space_invader:

eparejatobes commented 9 years ago

@pablopareja let me check this

pablopareja commented 9 years ago

ok! :wink:

eparejatobes commented 9 years ago

tests pass, LGTM