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Update knowledge sources #638

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Update knowledge sources #638

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c294136
Replaced original_knowledge_source with primary_knowledge_source.
gaurav Mar 28, 2023
226ecfc
Replaced originalKS with primaryKS for clarity.
gaurav Mar 31, 2023
faadb31
Incremented version to 0.3 for release.
gaurav Mar 31, 2023
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2 changes: 1 addition & 1 deletion build.sbt
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ organization := "org.renci"

name := "cam-kp-api"

version := "0.3-pre4"
version := "0.3"

licenses := Seq("MIT license" -> url("https://opensource.org/licenses/MIT"))

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2 changes: 1 addition & 1 deletion src/main/resources/application.conf
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@@ -1,5 +1,5 @@
{
version = "0.3-pre4"
version = "0.3"
host = 0.0.0.0
port = 8080
port = ${?PORT}
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34 changes: 17 additions & 17 deletions src/main/scala/org/renci/cam/QueryService.scala
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Expand Up @@ -199,9 +199,9 @@ object QueryService extends LazyLogging {
appConfig <- getConfig[AppConfig]

// Generate the attributes we will need to produce the edge output.
originalKS <- ZIO
.fromOption(biolinkData.predicates.find(p => p.shorthand == "original_knowledge_source"))
.orElseFail(new Exception("could not get biolink:original_knowledge_source"))
primaryKS <- ZIO
.fromOption(biolinkData.predicates.find(p => p.shorthand == "primary_knowledge_source"))
.orElseFail(new Exception("could not get biolink:primary_knowledge_source"))
aggregatorKS <- ZIO
.fromOption(biolinkData.predicates.find(p => p.shorthand == "aggregator_knowledge_source"))
.orElseFail(new Exception("could not get biolink:aggregator_knowledge_source"))
Expand Down Expand Up @@ -237,7 +237,7 @@ object QueryService extends LazyLogging {
}
originalKSAttributes = originalKnowledgeSources.map { case (derivedFrom, inforesKS) =>
TRAPIAttribute(Some("infores:cam-kp"),
originalKS.iri,
primaryKS.iri,
None,
List(inforesKS),
Some(infoResBiolinkClass.iri),
Expand Down Expand Up @@ -674,9 +674,9 @@ object QueryService extends LazyLogging {
predicate = querySolution.getResource(queryEdgeID).getURI
predicateIRI = IRI(predicate)
tripleString = TripleString(source, predicate, target)
originalKS <- ZIO
.fromOption(biolinkData.predicates.find(p => p.shorthand == "original_knowledge_source"))
.orElseFail(new Exception("could not get biolink:original_knowledge_source"))
primaryKS <- ZIO
.fromOption(biolinkData.predicates.find(p => p.shorthand == "primary_knowledge_source"))
.orElseFail(new Exception("could not get biolink:primary_knowledge_source"))
aggregatorKS <- ZIO
.fromOption(biolinkData.predicates.find(p => p.shorthand == "aggregator_knowledge_source"))
.orElseFail(new Exception("could not get biolink:aggregator_knowledge_source"))
Expand All @@ -693,19 +693,19 @@ object QueryService extends LazyLogging {
Some(appConfig.location),
None,
None)
originalKSstr = provValue match {
primaryKSstr = provValue match {
case ctd if provValue.contains("ctdbase.org") => "infores:ctd"
case _ => "infores:go-cam"
}
originalKSAttribute = TRAPIAttribute(Some("infores:cam-kp"),
originalKS.iri,
None,
List(originalKSstr),
Some(infoResBiolinkClass.iri),
Some(provValue),
None,
None)
attributes = List(aggregatorKSAttribute, originalKSAttribute)
primaryKSAttribute = TRAPIAttribute(Some("infores:cam-kp"),
primaryKS.iri,
None,
List(primaryKSstr),
Some(infoResBiolinkClass.iri),
Some(provValue),
None,
None)
attributes = List(aggregatorKSAttribute, primaryKSAttribute)
relationLabelAndBiolinkPredicate <- ZIO
.fromOption(relationsMap.get(predicateIRI))
.orElseFail(new Exception("Unexpected edge relation"))
Expand Down