Mapping an IRI based lookup to ODGI

[JervenBolleman]

For example in the current vg models in RDF. All nodes have a {SOMEBASE}/node/{ID} iri as identifier. These can be used as hack to identify which methods to call.

Consider the sparql query.

PREFIX node:<http://example.org/node/>
PREFIX vg:<http://biohackathon.org/resource/vg#>

SELECT 
   ?node ?sequenceLength
WHERE {
  BIND(node:25 as ?node)
  ?node a vg:Node ; 
     rdf:value ?sequence .
 BIND(strlen(?sequence) AS ?sequenceLength)

Statically analysing the query AST we should be able to determine that this requires a call to odgi.get_handle as that will give us the handle for the node id.

ASK
node:25 a vg:Node .

Can return true as we can look into the IRI string to see it is a node.

SELECT
?sequence
WHERE
{
node:25 rdf:value ?sequence .
}

Can be mapped to odgi.get_handle on which we can ask for the sequence string.

Then the engine can do a classic translation to sequence length by just calling the python method.

[JervenBolleman]

Longer term we will want an index of node IRIs and an index of path IRIs instead of assuming they are all in the same namespace.