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Fix query stalling #621

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Fix query stalling #621

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b33af5a
Added an INNER_LIMIT to prevent queries from stalling.
gaurav Feb 7, 2023
7785a9f
Increased the inner limit based on the outer limit value.
gaurav Feb 7, 2023
9cf65d9
Fixed inner limit.
gaurav Feb 7, 2023
c872342
Reduced the inner limit multiplier to 1000.
gaurav Feb 7, 2023
045d509
Improved SPARQL code.
gaurav Feb 7, 2023
28f4b96
Removed ?*_class from projection and GROUP BY.
gaurav Mar 26, 2023
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13 changes: 8 additions & 5 deletions src/main/scala/org/renci/cam/QueryService.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -6,13 +6,13 @@ import io.circe.syntax._
import org.apache.jena.query.QuerySolution
import org.apache.jena.rdf.model.Resource
import org.phenoscape.sparql.SPARQLInterpolation._
import org.renci.cam.Biolink.{biolinkData, BiolinkData}
import org.renci.cam.Biolink.{BiolinkData, biolinkData}
import org.renci.cam.HttpClient.HttpClient
import org.renci.cam.SPARQLQueryExecutor.SPARQLCache
import org.renci.cam.Util.IterableSPARQLOps
import org.renci.cam.domain.{TRAPIAttribute, _}
import zio.config.{getConfig, ZConfig}
import zio.{config => _, Has, RIO, Task, UIO, ZIO}
import zio.config.{ZConfig, getConfig}
import zio.{Has, RIO, Task, UIO, ZIO, config => _}

import java.math.BigInteger
import java.nio.charset.StandardCharsets
Expand All @@ -21,6 +21,8 @@ import scala.jdk.CollectionConverters._

object QueryService extends LazyLogging {

val INNER_LIMIT_MULTIPLIER = 100

val ProvWasDerivedFrom: IRI = IRI("http://www.w3.org/ns/prov#wasDerivedFrom")

val RDFSSubClassOf: IRI = IRI("http://www.w3.org/2000/01/rdf-schema#subClassOf")
Expand Down Expand Up @@ -483,6 +485,8 @@ object QueryService extends LazyLogging {
val nodesToDirectTypes = getNodesToDirectTypes(queryGraph.nodes)
val edgePatterns = queryEdgeSparql.fold(sparql"")(_ + _)
val limitSparql = if (limit > 0) sparql" LIMIT $limit" else sparql""
val innerLimit = INNER_LIMIT_MULTIPLIER * limit
val innerLimitSparql = if (limit > 0) sparql" LIMIT $innerLimit" else sparql""
val queryString =
sparql"""SELECT DISTINCT $typeProjections
(GROUP_CONCAT(DISTINCT ?g; SEPARATOR='|') AS ?graphs)
Expand All @@ -494,7 +498,7 @@ object QueryService extends LazyLogging {
SELECT $nodeProjections ?g
WHERE {
$edgePatterns
}
} ${innerLimitSparql}
}
$BigDataQueryHintPrior $BigDataQueryHintRunFirst true .
}
Expand Down Expand Up @@ -565,7 +569,6 @@ object QueryService extends LazyLogging {
def getProjections(queryGraph: TRAPIQueryGraph, typesInsteadOfNodes: Boolean = false): QueryText = {
val projectionVariableNames =
queryGraph.edges.keys ++
queryGraph.nodes.keys.map(queryNodeID => s"${queryNodeID}_class") ++
(if (typesInsteadOfNodes) queryGraph.nodes.keys.map(queryNodeID => s"${queryNodeID}_type")
else queryGraph.edges.flatMap(e => List(e._2.subject, e._2.`object`)))
projectionVariableNames.map(Var(_)).map(v => sparql" $v ").fold(sparql"")(_ + _)
Expand Down