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Check for unsupported constraints (#566)
This PR adds TRAPI Tests to ensure that CAM-KP-API responds correctly to: - An attribute constraint it does not understand - A qualifier constraint it does not understand (as per PR NCATSTranslator/ReasonerAPI#364) Closes #565
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| package org.renci.cam.test | ||
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| import com.typesafe.scalalogging.LazyLogging | ||
| import io.circe._ | ||
| import io.circe.generic.auto._ | ||
| import io.circe.generic.semiauto._ | ||
| import org.apache.jena.query.{Query, QuerySolution} | ||
| import org.http4s.headers.{`Content-Type`, Accept} | ||
| import org.http4s.{EntityDecoder, MediaType, Method, Request, Uri} | ||
| import org.renci.cam.Biolink.biolinkData | ||
| import org.renci.cam.HttpClient.HttpClient | ||
| import org.renci.cam.Server.EndpointEnv | ||
| import org.renci.cam._ | ||
| import org.renci.cam.domain.{BiolinkClass, BiolinkPredicate, IRI, LogEntry, TRAPIAttribute, TRAPIResponse} | ||
| import zio.cache.Cache | ||
| import zio.config.ZConfig | ||
| import zio.config.typesafe.TypesafeConfig | ||
| import zio.interop.catz.concurrentInstance | ||
| import zio.test._ | ||
| import zio.{Layer, ZIO, ZLayer} | ||
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| object TRAPITest extends DefaultRunnableSpec with LazyLogging { | ||
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| /** If CAM-KP-API receives a attribute constraint that it does not support, it MUST respond with an error Code | ||
| * "UnsupportedAttributeConstraint". | ||
| */ | ||
| val testUnsupportedAttributeConstraints: Spec[EndpointEnv, TestFailure[Throwable], TestSuccess] = | ||
| suite("testUnsupportedAttributeConstraints") { | ||
| // Examples taken from https://github.com/NCATSTranslator/ReasonerAPI/blob/1e0795a1c4ff5bcac3ccd5f188fdc09ec6bd27c3/ImplementationRules.md#specifying-permitted-and-excluded-kps-to-an-ara | ||
| val query = """{ | ||
| "message": { | ||
| "query_graph": { | ||
| "nodes": { | ||
| "n0": { | ||
| "categories": ["biolink:GeneOrGeneProduct"] | ||
| }, | ||
| "n1": { "categories": ["biolink:AnatomicalEntity"], "ids": ["GO:0005634"] } | ||
| }, | ||
| "edges": { | ||
| "e0": { | ||
| "subject": "n0", | ||
| "object": "n1", | ||
| "predicates": ["biolink:part_of"], | ||
| "attribute_constraints": [{ | ||
| "id": "biolink:knowledge_source", | ||
| "name": "knowledge source", | ||
| "value": "infores:semmeddb", | ||
| "not": true, | ||
| "operator": "==" | ||
| }] | ||
| } | ||
| } | ||
| } | ||
| } | ||
| }""" | ||
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| testM("test unsupported attribute constraint") { | ||
| for { | ||
| biolinkData <- biolinkData | ||
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| server <- Server.httpApp | ||
| response <- server( | ||
| Request( | ||
| method = Method.POST, | ||
| uri = Uri.unsafeFromString("/query") | ||
| ) | ||
| .withHeaders(Accept(MediaType.application.json), `Content-Type`(MediaType.application.json)) | ||
| .withEntity(query) | ||
| ) | ||
| content <- EntityDecoder.decodeText(response) | ||
| trapiResponseJson <- ZIO.fromEither(io.circe.parser.parse(content)) | ||
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| trapiResponse <- ZIO.fromEither( | ||
| { | ||
| implicit val decoderIRI: Decoder[IRI] = Implicits.iriDecoder(biolinkData.prefixes) | ||
| implicit val keyDecoderIRI: KeyDecoder[IRI] = Implicits.iriKeyDecoder(biolinkData.prefixes) | ||
| implicit val decoderBiolinkClass: Decoder[BiolinkClass] = Implicits.biolinkClassDecoder(biolinkData.classes) | ||
| implicit val decoderBiolinkPredicate: Decoder[BiolinkPredicate] = | ||
| Implicits.biolinkPredicateDecoder(biolinkData.predicates) | ||
| implicit lazy val decoderTRAPIAttribute: Decoder[TRAPIAttribute] = deriveDecoder[TRAPIAttribute] | ||
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| trapiResponseJson.as[TRAPIResponse] | ||
| } | ||
| ) | ||
|
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| logs = trapiResponse.logs | ||
| logsWithUnsupportedAttributeConstraint = logs.getOrElse(List()).filter { | ||
| case LogEntry(_, Some("ERROR"), Some("UnsupportedAttributeConstraint"), _) => true | ||
| case _ => false | ||
| } | ||
| } yield assert(response.status)(Assertion.hasField("isSuccess", _.isSuccess, Assertion.isTrue)) && | ||
| assert(content)(Assertion.isNonEmptyString) && | ||
| // Should return an UnsupportedAttributeConstraint as the status ... | ||
| assert(trapiResponse.status)(Assertion.isSome(Assertion.equalTo("UnsupportedAttributeConstraint"))) && | ||
| // ... and in the logs. | ||
| assert(logs)(Assertion.isSome(Assertion.isNonEmpty)) && | ||
| assert(logsWithUnsupportedAttributeConstraint)(Assertion.isNonEmpty) | ||
| } | ||
| } | ||
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| /** If CAM-KP-API receives a qualifier constraint that it does not support, it MUST return an empty response (since no edges meet the | ||
| * constraint). | ||
| * | ||
| * (This is still in development at https://github.com/NCATSTranslator/ReasonerAPI/pull/364) | ||
| */ | ||
| val testUnsupportedQualifierConstraints = suite("testUnsupportedConstraints") { | ||
| // Examples taken from https://github.com/NCATSTranslator/ReasonerAPI/blob/7520ac564e63289dffe092d4c7affd6db4ba22f1/examples/Message/subject_and_object_qualifiers.json | ||
| val query = """{ | ||
| "message": { | ||
| "query_graph": { | ||
| "nodes": { | ||
| "n0": { | ||
| "categories": ["biolink:GeneOrGeneProduct"] | ||
| }, | ||
| "n1": { "categories": ["biolink:AnatomicalEntity"], "ids": ["GO:0005634"] } | ||
| }, | ||
| "edges": { | ||
| "e0": { | ||
| "subject": "n0", | ||
| "object": "n1", | ||
| "predicates": ["biolink:part_of"], | ||
| "qualifier_constraints": [{ | ||
| "qualifier_set": [{ | ||
| "qualifier_type_id": "biolink:subject_aspect_qualifier", | ||
| "qualifier_value": "abundance" | ||
| }, { | ||
| "qualifier_type_id": "biolink:subject_direction_qualifier", | ||
| "qualifier_value": "decreased" | ||
| }] | ||
| }] | ||
| } | ||
| } | ||
| } | ||
| } | ||
| }""" | ||
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| testM("test unsupported qualifier constraint on QEdge") { | ||
| for { | ||
| biolinkData <- biolinkData | ||
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| server <- Server.httpApp | ||
| response <- server( | ||
| Request( | ||
| method = Method.POST, | ||
| uri = Uri.unsafeFromString("/query") | ||
| ) | ||
| .withHeaders(Accept(MediaType.application.json), `Content-Type`(MediaType.application.json)) | ||
| .withEntity(query) | ||
| ) | ||
| content <- EntityDecoder.decodeText(response) | ||
| trapiResponseJson <- ZIO.fromEither(io.circe.parser.parse(content)) | ||
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| trapiResponse <- ZIO.fromEither( | ||
| { | ||
| implicit val decoderIRI: Decoder[IRI] = Implicits.iriDecoder(biolinkData.prefixes) | ||
| implicit val keyDecoderIRI: KeyDecoder[IRI] = Implicits.iriKeyDecoder(biolinkData.prefixes) | ||
| implicit val decoderBiolinkClass: Decoder[BiolinkClass] = Implicits.biolinkClassDecoder(biolinkData.classes) | ||
| implicit val decoderBiolinkPredicate: Decoder[BiolinkPredicate] = | ||
| Implicits.biolinkPredicateDecoder(biolinkData.predicates) | ||
| implicit lazy val decoderTRAPIAttribute: Decoder[TRAPIAttribute] = deriveDecoder[TRAPIAttribute] | ||
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| trapiResponseJson.as[TRAPIResponse] | ||
| } | ||
| ) | ||
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| logs = trapiResponse.logs | ||
| logWarningOfQualifierConstraints = logs.getOrElse(List()).filter { | ||
| // We've made this up ourselves. | ||
| case LogEntry(_, Some("WARNING"), Some("UnsupportedQualifierConstraint"), _) => true | ||
| case _ => false | ||
| } | ||
| } yield assert(response.status)(Assertion.hasField("isSuccess", _.isSuccess, Assertion.isTrue)) && | ||
| assert(content)(Assertion.isNonEmptyString) && | ||
| // Should return an overall status of Success | ||
| assert(trapiResponse.status)(Assertion.isSome(Assertion.equalTo("Success"))) && | ||
| // ... and in the logs | ||
| assert(logs)(Assertion.isSome(Assertion.isNonEmpty)) && | ||
| assert(logWarningOfQualifierConstraints)(Assertion.isNonEmpty) && | ||
| // ... and with no results. | ||
| assert(trapiResponse.message.results)(Assertion.isSome(Assertion.isEmpty)) | ||
| } | ||
| } | ||
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| val configLayer: Layer[Throwable, ZConfig[AppConfig]] = TypesafeConfig.fromDefaultLoader(AppConfig.config) | ||
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| val testLayer: ZLayer[ | ||
| Any, | ||
| Throwable, | ||
| HttpClient with ZConfig[Biolink.BiolinkData] with ZConfig[AppConfig] with ZConfig[Cache[Query, Throwable, List[QuerySolution]]]] = | ||
| HttpClient.makeHttpClientLayer ++ Biolink.makeUtilitiesLayer ++ configLayer >+> SPARQLQueryExecutor.makeCache.toLayer | ||
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| def spec: Spec[environment.TestEnvironment, TestFailure[Throwable], TestSuccess] = suite("TRAPI tests")( | ||
| testUnsupportedAttributeConstraints, | ||
| testUnsupportedQualifierConstraints | ||
| ).provideCustomLayer(testLayer.mapError(TestFailure.die)) | ||
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| } |