Improve inefficient SPARQL query template

[surchs]

Our current SPARQL query template has a couple of problems that make it slow:

Unnecessary nesting of OPTIONAL clauses https://github.com/neurobagel/api/blob/1e9ef34d54b89b824c42f1e6293a0ab9d5931c65/app/api/utility.py#L232-L237

and

https://github.com/neurobagel/api/blob/1e9ef34d54b89b824c42f1e6293a0ab9d5931c65/app/api/utility.py#L258-L264 (even worse)

in order of importance

• by not explicitly putting the desired session type in the triple pattern, we have to traverse the entire graph to see if there is anything that fits the pattern with nb:hasAcquisition/nb:hasContrastType -> very slow!
• the OPTIONAL statement is not necessary. If a subject does not have a phenotypic or imaging session, we don't need to look any further anyway
• we have access to ?subject from the outer scope, so no need to restate it here

also: https://github.com/neurobagel/api/blob/1e9ef34d54b89b824c42f1e6293a0ab9d5931c65/app/api/utility.py#L207-L211

is most likely not necessary - it would only help to capture those subjects who do not have any file system path associated and thus would not be datalad gettable.

TODOs:

• [x] explicitly state session types for pheno and imaging session in the triple patterns of the sub-queries
• [ ] remove superfluous OPTIONAL statements (they are expensive)
• [ ] remove repeated triple patterns in sub-queries

From initial testing, this will let us cut query execution time by an order of magnitude.

See also: https://github.com/neurobagel/planning/issues/142

[surchs]

Turns out the main thing was really just stating explicitly what session type we want for the imaging session. That cut the query execution time by ~ 90%

[surchs]

:rocket: Issue was released in v0.2.1 :rocket: