Adding SIGNOR provenance

README.md

@@ -21,6 +21,15 @@ CAMs (Causal Activity Models) are small knowledge graphs built using the [Web On
 - `sbt docker:stage docker:publishLocal`
 - `docker run -p 8080:8080 -it renciorg/cam-kp-api:0.1` (or detached mode: `docker run -p 8080:8080 -d renciorg/cam-kp-api:0.1`)
 
+## Testing
+
+Two types of tests are included in this repository:
+- Unit tests can be run by running `sbt test`
+- Integration tests require Docker. To run them:
+  1. Create the Docker image for cam-kp-api by running `sbt docker:stage docker:publishLocal`
+  2. Run the integration tests by running `sbt IntegrationTest/test`.
+     You can also run a single test by running e.g. `sbt "IntegrationTest/testOnly org.renci.cam.it.BiolinkTest"`
+
 ## Issue Management
 
 Anyone can create new issues by clicking on "New issue" button on the [issues](https://github.com/NCATS-Tangerine/cam-kp-api/issues) page of this repository. Click here for the [current issues](https://github.com/NCATS-Tangerine/cam-kp-api/issues).

src/test/scala/org/renci/cam/test/KnowledgeSourceTest.scala

@@ -0,0 +1,111 @@
+package org.renci.cam.test
+
+import com.typesafe.scalalogging.LazyLogging
+import org.renci.cam._
+import org.renci.cam.domain._
+import zio.Layer
+import zio.config.ZConfig
+import zio.config.typesafe.TypesafeConfig
+import zio.test._
+
+/** Tests whether we return the correct knowledge sources on queries.
+  */
+object KnowledgeSourceTest extends DefaultRunnableSpec with LazyLogging {
+
+  /** This query asks: "what is positively regulated by GO:0004709 [MAP3K activity]?" One of the sources from original knowledge source
+    * infores:go-cam should be http://model.geneontology.org/568b0f9600000284
+    */
+  val testPositivelyRegulatedByMAP3K = {
+    val trapiQueryGraph = TRAPIQueryGraph(
+      Map(
+        "n0" -> TRAPIQueryNode(Some(List(IRI("http://purl.obolibrary.org/obo/GO_0004709"))), None, None),
+        "n1" -> TRAPIQueryNode(None, Some(List(BiolinkClass("NamedThing"))), None)
+      ),
+      Map("e0" -> TRAPIQueryEdge(Some(List(BiolinkPredicate("positively_regulates"))), "n0", "n1", None))
+    )
+    logger.info(s"Querying with TRAPI query: ${trapiQueryGraph}")
+    val query = QueryService.run(1000, trapiQueryGraph)
+
+    suite("testPositivelyRegulatedByMAP3K")(
+      testM("Received GO-CAM results, including model http://model.geneontology.org/568b0f9600000284") {
+        for {
+          response <- query
+          kgraph = response.message.knowledge_graph.getOrElse(TRAPIKnowledgeGraph(Map(), Map()))
+          attrsById = kgraph.edges.transform((_, value) => value.attributes.getOrElse(List()))
+
+          // Sources
+          sourcesById = attrsById.transform((_, value) => value.map(_.attribute_source.get))
+
+          // Original knowledge sources
+          originalKnowledgeSourcesById = attrsById.transform((_, value) =>
+            value.filter(_.attribute_type_id == BiolinkPredicate("original_knowledge_source").iri))
+          originalKnowledgeSources = originalKnowledgeSourcesById.values.flatten
+
+          // Find edges from a particular entry of GeneOntology model http://model.geneontology.org/568b0f9600000284
+          selectedAttribs = originalKnowledgeSources.filter(_.value_url.getOrElse("") == "http://model.geneontology.org/568b0f9600000284")
+          selectedSources = selectedAttribs.flatMap(_.attribute_source)
+          selectedOKGs = selectedAttribs.filter(_.attribute_type_id == BiolinkPredicate("original_knowledge_source").iri).flatMap(_.value)
+
+        } yield assert(response.message.results)(Assertion.isSome(Assertion.isNonEmpty)) &&
+          assert(sourcesById.values.flatten)(Assertion.contains("infores:cam-kp")) &&
+          assert(selectedAttribs)(Assertion.isNonEmpty) &&
+          assert(selectedSources)(Assertion.forall(Assertion.equalTo("infores:cam-kp"))) &&
+          assert(selectedOKGs)(Assertion.forall(Assertion.equalTo("infores:go-cam")))
+      }
+    )
+  }
+
+  /** This query asks: "list all named things related to valproic acid (CHEBI:39867)" The original knowledge source should include:
+    * infores:ctd
+    */
+  val testRelatedToValproicAcid = {
+    val trapiQueryGraph = TRAPIQueryGraph(
+      Map(
+        "n0" -> TRAPIQueryNode(Some(List(IRI("http://purl.obolibrary.org/obo/CHEBI_39867"))), None, None),
+        "n1" -> TRAPIQueryNode(None, Some(List(BiolinkClass("NamedThing"))), None)
+      ),
+      Map("e0" -> TRAPIQueryEdge(Some(List(BiolinkPredicate("related_to"))), "n0", "n1", None))
+    )
+    logger.info(s"Querying with TRAPI query: ${trapiQueryGraph}")
+    val query = QueryService.run(1000, trapiQueryGraph)
+
+    suite("testRelatedToValproicAcid")(
+      testM("Received CTD results, including model http://ctdbase.org/detail.go?type=relationship&ixnId=3203039#inferred") {
+
+        for {
+          response <- query
+          kgraph = response.message.knowledge_graph.getOrElse(TRAPIKnowledgeGraph(Map(), Map()))
+          attrsById = kgraph.edges.transform((_, value) => value.attributes.getOrElse(List()))
+
+          // Sources
+          sourcesById = attrsById.transform((_, value) => value.map(_.attribute_source.get))
+
+          // Original knowledge sources
+          originalKnowledgeSourcesById = attrsById.transform((_, value) =>
+            value.filter(_.attribute_type_id == BiolinkPredicate("original_knowledge_source").iri))
+          originalKnowledgeSources = originalKnowledgeSourcesById.values.flatten
+
+          // Find edges from a particular entry of CTD model http://ctdbase.org/detail.go?type=relationship&ixnId=3203039#inferred
+          selectedAttribs = originalKnowledgeSources.filter(
+            _.value_url.getOrElse("") == "http://ctdbase.org/detail.go?type=relationship&ixnId=3203039#inferred")
+          selectedSources = selectedAttribs.flatMap(_.attribute_source)
+          selectedOKGs = selectedAttribs.filter(_.attribute_type_id == BiolinkPredicate("original_knowledge_source").iri).flatMap(_.value)
+
+        } yield assert(response.message.results)(Assertion.isSome(Assertion.isNonEmpty)) &&
+          assert(sourcesById.values.flatten)(Assertion.contains("infores:cam-kp")) &&
+          assert(selectedAttribs)(Assertion.isNonEmpty) &&
+          assert(selectedSources)(Assertion.forall(Assertion.equalTo("infores:cam-kp"))) &&
+          assert(selectedOKGs)(Assertion.forall(Assertion.equalTo("infores:ctd")))
+      }
+    )
+  }
+
+  val configLayer: Layer[Throwable, ZConfig[AppConfig]] = TypesafeConfig.fromDefaultLoader(AppConfig.config)
+  val testLayer = HttpClient.makeHttpClientLayer ++ Biolink.makeUtilitiesLayer ++ configLayer >+> SPARQLQueryExecutor.makeCache.toLayer
+
+  def spec: Spec[environment.TestEnvironment, TestFailure[Throwable], TestSuccess] = suite("Knowledge source tests")(
+    testPositivelyRegulatedByMAP3K,
+    testRelatedToValproicAcid
+  ).provideCustomLayer(testLayer.mapError(TestFailure.die))
+
+}