scala model - Gene Ontology

[alberskib]

Implement scala model for GO. Please take into account experience and suggestion taken from actual java model (https://github.com/bio4j/bio4j/tree/master/src/main/java/com/bio4j/model/go) as well as new (bio4j/bio4j#40).

[alberskib]

@bio4j/dynamograph I think that GO model will be layered - there will be dynamoDB layer, scarph layer, as well as high level layer which will be provide clients with easy in use API. (layers could be expressed ie by class hierarchy, composition etc). Bio4j implementations based on neo4j and titanDb offers high level API written in java. As mentioned projects is used by some clients that could have some opinions regarding API (feedback) it will be great to gather such opinions in order to provide great model in scala.

[alberskib]

I am not sure whether I correctly used scarph lib so please take a look into it. The way I see how mentioned lib should be integrated is more or less like:

• model will be divided into 3 layers:
  • dynamoDB access layer
  • scarph layer
  • high level API layer
• dynamoDB access layer reflects database structure i.e. GOTermImpl, IsAImpl
• scaprh layer provide functionality to replace foreign ids into real values: i.e IsA with sourceGetter and targetGetter
• high level API layer provide easy in use client interface (not present in PR)

Actually there are couple of things that need to be discussed:

• each of GO relationships is abstracted by seperate type - as a result there is need to create lots of boilerplate code - sourceGetter, targetGetter which implementation are the same (different type hierarchy), maybe it should be replaced by single relationship type with some kind of additional field?
• current model is prepared specially for GO. Maybe it will be possible to replace the dynamoDB access layer by some kind of generic object i.e instead of GOTermImpl there will be some kind of DynamoDb Generic Object with Map<String, Object>. As result it scarph layer will consist of some kind of special GetPropertyObject which just get value from the map and return it.

[laughedelic]

You say the right thing in your last point. Scarph-DynamoDB binding shouldn't be mixed with the GO scarph model. See my comment and take a look at the titan example again:

• here is scarph titan implementation
• here is scarph model for the gods graph

they are completely independent. And they are connected only in one place:

• gods-graph model binding to the scarph titan implementation

[alberskib]

Next commit still needs some improvements i.e Handling GOTermNamespace enum by AnyDynamoVertex#unsafeGetProperty etc. Those change will be in next commits

[laughedelic]

@alberskib cool :+1: for the last commit. looking forward for the next one ")

[alberskib]

@bio4j/dynamograph Can I merge this branch?

[eparejatobes]

OK @alberskib LGTM