Add pre and post synaptic pathways to BG -> ES projection

BlueBrain · Oct 25, 2023 · 7d63947 · 7d63947
1 parent 66113f4
commit 7d63947
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Showing 9 changed files with 201 additions and 17 deletions.
diff --git a/...s/src/main/scala/ch/epfl/bluebrain/nexus/delta/plugins/compositeviews/CompositeSink.scala b/...s/src/main/scala/ch/epfl/bluebrain/nexus/delta/plugins/compositeviews/CompositeSink.scala
@@ -15,7 +15,7 @@ import ch.epfl.bluebrain.nexus.delta.plugins.elasticsearch.client.{ElasticSearch
 import ch.epfl.bluebrain.nexus.delta.plugins.elasticsearch.indexing.{ElasticSearchSink, GraphResourceToDocument}
 import ch.epfl.bluebrain.nexus.delta.rdf.RdfError
 import ch.epfl.bluebrain.nexus.delta.rdf.graph.Graph
-import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.api.{JsonLdApi, JsonLdJavaApi}
+import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.api.{JsonLdApi, JsonLdJavaApi, JsonLdOptions}
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.{ContextValue, RemoteContextResolution}
 import ch.epfl.bluebrain.nexus.delta.rdf.query.SparqlQuery.SparqlConstructQuery
 import ch.epfl.bluebrain.nexus.delta.rdf.syntax.iriStringContextSyntax
@@ -123,6 +123,7 @@ final class Batch[SinkFormat](
   /** Replaces the graph of a provided [[GraphResource]] by extracting its new graph from the provided (full) graph. */
   private def replaceGraph(gr: GraphResource, fullGraph: Graph) = {
     implicit val api: JsonLdApi = JsonLdJavaApi.lenient
+    implicit val options        = JsonLdOptions.AlwaysEmbed
     fullGraph
       .replaceRootNode(iri"${gr.id}/alias")
       .toCompactedJsonLd(ContextValue.empty)

diff --git a/...h/epfl/bluebrain/nexus/delta/plugins/elasticsearch/indexing/GraphResourceToDocument.scala b/...h/epfl/bluebrain/nexus/delta/plugins/elasticsearch/indexing/GraphResourceToDocument.scala
@@ -1,6 +1,6 @@
 package ch.epfl.bluebrain.nexus.delta.plugins.elasticsearch.indexing
 
-import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.api.{JsonLdApi, JsonLdJavaApi}
+import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.api.{JsonLdApi, JsonLdJavaApi, JsonLdOptions}
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.JsonLdContext.keywords
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.{ContextValue, RemoteContextResolution}
 import ch.epfl.bluebrain.nexus.delta.sdk.implicits._
@@ -33,6 +33,7 @@ final class GraphResourceToDocument(context: ContextValue, includeContext: Boole
 
   /** Given a [[GraphResource]] returns a JSON-LD created from the merged graph and metadata graph */
   def graphToDocument(element: GraphResource): Task[Option[Json]] = {
+    implicit val jsonLdOptions = JsonLdOptions.AlwaysEmbed
     val graph = element.graph ++ element.metadataGraph
     val json  =
       if (element.source.isEmpty())

diff --git a/delta/rdf/src/main/scala/ch/epfl/bluebrain/nexus/delta/rdf/jsonld/api/JsonLdOptions.scala b/delta/rdf/src/main/scala/ch/epfl/bluebrain/nexus/delta/rdf/jsonld/api/JsonLdOptions.scala
@@ -29,4 +29,5 @@ final case class JsonLdOptions(
 
 object JsonLdOptions {
   implicit val defaults: JsonLdOptions = JsonLdOptions()
+  val AlwaysEmbed: JsonLdOptions = defaults.copy(embed = "@always")
 }
diff --git a/delta/rdf/src/test/scala/ch/epfl/bluebrain/nexus/delta/rdf/jsonld/CompactedJsonLdSpec.scala b/delta/rdf/src/test/scala/ch/epfl/bluebrain/nexus/delta/rdf/jsonld/CompactedJsonLdSpec.scala
@@ -1,10 +1,10 @@
 package ch.epfl.bluebrain.nexus.delta.rdf.jsonld
 
-import ch.epfl.bluebrain.nexus.delta.rdf.{Fixtures, GraphHelpers}
 import ch.epfl.bluebrain.nexus.delta.rdf.IriOrBNode.BNode
 import ch.epfl.bluebrain.nexus.delta.rdf.implicits._
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.ContextValue
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.JsonLdContext.keywords
+import ch.epfl.bluebrain.nexus.delta.rdf.{Fixtures, GraphHelpers}
 import ch.epfl.bluebrain.nexus.testkit.scalatest.ce.CatsEffectSpec
 
 class CompactedJsonLdSpec extends CatsEffectSpec with Fixtures with GraphHelpers {

diff --git a/delta/sdk/src/main/scala/ch/epfl/bluebrain/nexus/delta/sdk/ResourceShift.scala b/delta/sdk/src/main/scala/ch/epfl/bluebrain/nexus/delta/sdk/ResourceShift.scala
@@ -2,15 +2,15 @@ package ch.epfl.bluebrain.nexus.delta.sdk
 
 import cats.effect.IO
 import cats.syntax.all._
+import ch.epfl.bluebrain.nexus.delta.kernel.effect.migration._
 import ch.epfl.bluebrain.nexus.delta.rdf.IriOrBNode.Iri
-import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.api.{JsonLdApi, JsonLdJavaApi}
+import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.api.{JsonLdApi, JsonLdJavaApi, JsonLdOptions}
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.JsonLdContext.keywords
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.RemoteContextResolution
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.encoder.JsonLdEncoder
 import ch.epfl.bluebrain.nexus.delta.sdk.jsonld.JsonLdContent
 import ch.epfl.bluebrain.nexus.delta.sdk.model.{BaseUri, ResourceF}
 import ch.epfl.bluebrain.nexus.delta.sdk.syntax._
-import ch.epfl.bluebrain.nexus.delta.kernel.effect.migration._
 import ch.epfl.bluebrain.nexus.delta.sourcing.Serializer
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.{EntityType, ProjectRef, ResourceRef}
 import ch.epfl.bluebrain.nexus.delta.sourcing.offset.Offset
@@ -89,9 +89,10 @@ abstract class ResourceShift[State <: ScopedState, A, M](
   private def toGraphResource(project: ProjectRef, resource: ResourceF[A])(implicit
       cr: RemoteContextResolution
   ): IO[GraphResource] = {
-    val content  = resourceToContent(resource)
-    val metadata = content.metadata
-    val id       = resource.resolvedId
+    implicit val jsonLdOptions = JsonLdOptions.AlwaysEmbed
+    val content                = resourceToContent(resource)
+    val metadata               = content.metadata
+    val id                     = resource.resolvedId
     for {
       graph             <- valueJsonLdEncoder.graph(resource.value).toCatsIO
       rootGraph          = graph.replaceRootNode(id)
@@ -114,7 +115,7 @@ abstract class ResourceShift[State <: ScopedState, A, M](
     )
   }
 
-  private def encodeMetadata(id: Iri, metadata: Option[M])(implicit cr: RemoteContextResolution) =
+  private def encodeMetadata(id: Iri, metadata: Option[M])(implicit cr: RemoteContextResolution, opts: JsonLdOptions) =
     (metadata, metadataEncoder) match {
       case (Some(m), Some(e)) => e.graph(m).toCatsIO.map { g => Some(g.replaceRootNode(id)) }
       case (_, _)             => IO.none

diff --git a/tests/docker/config/construct-query.sparql b/tests/docker/config/construct-query.sparql
@@ -183,6 +183,18 @@ CONSTRUCT {
   ?alias  :campaign            ?campaignId              .
                                ?campaignId              :identifier      ?campaignId   ;
                                                         :name           ?campaignName .
+
+  ## Synapses
+  ?alias  :postSynapticPathway  ?postSynaptic   .
+                            ?postSynaptic   :about      ?postSynapticAbout      ;
+                                              :label      ?postSynapticLabel      ;
+                                              :notation   ?postSynapticNotation   .
+
+  ?alias  :preSynapticPathway  ?preSynaptic .
+                            ?preSynaptic       :about      ?preSynapticAbout       ;
+                                              :label      ?preSynapticLabel       ;
+                                              :notation   ?preSynapticNotation    .
+
 } WHERE {
   VALUES ?id { {resource_id} } .
   BIND( IRI(concat(str(?id), '/', 'alias')) AS ?alias ) .
@@ -633,4 +645,16 @@ CONSTRUCT {
     } .
   } .
 
+  # Synapses
+  OPTIONAL {
+    ?id bmo:synapticPathway / nsg:postSynaptic  ?postSynaptic   .
+                                                ?postSynaptic   schema:about    ?postSynapticAbout      ;
+                                                                rdfs:label      ?postSynapticLabel      .
+                                                OPTIONAL {      ?postSynaptic   skos:notation           ?postSynapticNotation   . } .
+    ?id bmo:synapticPathway / nsg:preSynaptic     ?preSynaptic .
+                                                  ?preSynaptic    schema:about     ?preSynapticAbout       ;
+                                                                  rdfs:label       ?preSynapticLabel       .
+                                                  OPTIONAL { ?preSynaptic     skos:notation   ?preSynapticNotation    . } .
+
+    } .
 }
diff --git a/tests/docker/config/search-context.json b/tests/docker/config/search-context.json
@@ -30,6 +30,12 @@
   "protocol": {
     "@container": "@set"
   },
+  "preSynapticPathway": {
+    "@container": "@set"
+  },
+  "postSynapticPathway": {
+    "@container": "@set"
+  },
   "project": {
     "@type": "@id"
   },

diff --git a/tests/src/test/resources/kg/search/synapse.json b/tests/src/test/resources/kg/search/synapse.json
@@ -0,0 +1,93 @@
+{
+  "@context": "https://bbp.neuroshapes.org",
+  "@id": "https://bbp.epfl.ch/data/synapse",
+  "@type": [
+    "Entity",
+    "Parameter",
+    "SchafferCollateralAnatomyParameter",
+    "SynapsesPerConnection",
+    "ExperimentalSynapsesPerConnection"
+  ],
+  "brainLocation": {
+    "brainRegion": {
+      "@id": "http://purl.obolibrary.org/obo/UBERON_0003883",
+      "label": "CA3"
+    }
+  },
+  "comment": "inferred from Sik et al (1993) but unclear exactly how ",
+  "contribution": {
+    "@type": "Contribution",
+    "agent": {
+      "@id": "https://bbp.epfl.ch/nexus/v1/realms/bbp/users/aantonie",
+      "@type": "Agent"
+    }
+  },
+  "description": "SynapseDensity parameter from Schaffer axon collateral (pre-synaptic) to PV+ (post-synaptic) neurons. These data are part of the Schaffer collateral anatomy data.",
+  "name": "SynapseDensity parameter from Schaffer axon collateral (pre-synaptic) to PV+ (post-synaptic) neurons",
+  "series": [
+    {
+      "statistic": "mean",
+      "unitCode": "synapses/connection",
+      "value": 1.19
+    },
+    {
+      "statistic": "N synapses",
+      "unitCode": "dimensionless",
+      "value": 274
+    },
+    {
+      "statistic": "standard deviation",
+      "unitCode": "synapses/connection",
+      "value": 0.48
+    },
+    {
+      "statistic": "standard error of the mean",
+      "unitCode": "synapses/connection",
+      "value": 0.028997860479848495
+    },
+    {
+      "statistic": "minimum",
+      "unitCode": "synapses/connection",
+      "value": 1
+    },
+    {
+      "statistic": "maximum",
+      "unitCode": "synapses/connection",
+      "value": 3
+    }
+  ],
+  "subject": {
+    "@type": "Subject",
+    "species": {
+      "@id": "http://purl.obolibrary.org/obo/NCBITaxon_10116",
+      "label": "Rattus norvegicus"
+    },
+    "strain": {
+      "@id": "http://www.ebi.ac.uk/efo/EFO_0001352",
+      "label": "Sprague Dawley"
+    },
+    "weight": {
+      "maxValue": 300,
+      "minValue": 200,
+      "unitCode": "grams"
+    }
+  },
+  "synapticPathway": {
+    "postSynaptic": [
+      {
+        "@id": "http://api.brain-map.org/api/v2/data/Structure/454",
+        "about": "OtherBrainRegion",
+        "label": "Other somatosensory areas",
+        "notation": "OSS"
+      }
+    ],
+    "preSynaptic": [
+      {
+        "@id": "http://api.brain-map.org/api/v2/data/Structure/453",
+        "about": "BrainRegion",
+        "label": "Somatosensory areas",
+        "notation": "SS"
+      }
+    ]
+  }
+}
diff --git a/...ain/nexus/tests/kg/SearchConfigSpec.scala → ...s/tests/kg/SearchConfigIndexingSpec.scala b/...ain/nexus/tests/kg/SearchConfigSpec.scala → ...s/tests/kg/SearchConfigIndexingSpec.scala
@@ -7,12 +7,13 @@ import ch.epfl.bluebrain.nexus.tests.BaseIntegrationSpec
 import ch.epfl.bluebrain.nexus.tests.Identity.resources.Rick
 import ch.epfl.bluebrain.nexus.tests.iam.types.Permission.{Organizations, Resources}
 import io.circe.Json
+import org.scalactic.source.Position
 import org.scalatest.Assertion
 
 import java.time.Instant
 import concurrent.duration._
 
-class SearchConfigSpec extends BaseIntegrationSpec {
+class SearchConfigIndexingSpec extends BaseIntegrationSpec {
 
   implicit override def patienceConfig: PatienceConfig = PatienceConfig(config.patience * 2, 300.millis)
 
@@ -30,6 +31,7 @@ class SearchConfigSpec extends BaseIntegrationSpec {
   private val boutonDensityId      = "https://bbp.epfl.ch/data/bouton-density"
   private val simulationCampaignId = "https://bbp.epfl.ch/data/simulation-campaign"
   private val simulationId         = "https://bbp.epfl.ch/data/simulation"
+  private val synapseId            = "https://bbp.epfl.ch/data/synapse"
   private val detailedCircuitId    = "https://bbp.epfl.ch/data/detailed-circuit"
 
   // the resources that should appear in the search index
@@ -40,6 +42,7 @@ class SearchConfigSpec extends BaseIntegrationSpec {
     "/kg/search/unassessed-trace.json",
     "/kg/search/neuron-morphology.json",
     "/kg/search/neuron-density.json",
+//    "/kg/search/synapse.json",
     "/kg/search/layer-thickness.json",
     "/kg/search/bouton-density.json",
     "/kg/search/detailed-circuit.json",
@@ -784,6 +787,45 @@ class SearchConfigSpec extends BaseIntegrationSpec {
       }
     }
 
+    "have the correct pre synaptic pathway" in {
+      val query    = queryField(synapseId, "preSynapticPathway")
+      val expected =
+        json"""{
+          "preSynapticPathway": [
+            {
+              "@id": "http://api.brain-map.org/api/v2/data/Structure/453",
+              "about": "https://bbp.epfl.ch/neurosciencegraph/data/BrainRegion",
+              "label": "Somatosensory areas",
+              "notation": "SS"
+            }
+          ]
+        }
+      """
+
+      assertOneSource(query) { json =>
+        json should equalIgnoreArrayOrder(expected)
+      }
+    }
+
+    "have the correct post synaptic pathway" in {
+      val query    = queryField(synapseId, "postSynapticPathway")
+      val expected =
+        json"""{
+          "postSynapticPathway": [
+              {
+                "@id": "http://api.brain-map.org/api/v2/data/Structure/454",
+                "about": "https://bbp.epfl.ch/neurosciencegraph/data/OtherBrainRegion",
+                "label": "Other somatosensory areas",
+                "notation": "OSS"
+              }
+            ]
+        }
+      """
+
+      assertOneSource(query) { json =>
+        json should equalIgnoreArrayOrder(expected)
+      }
+    }
   }
 
   /**
@@ -809,20 +851,35 @@ class SearchConfigSpec extends BaseIntegrationSpec {
     * Queries ES using the provided query. Asserts that there is only on result in _source. Runs the provided assertion
     * on the _source.
     */
-  private def assertOneSource(query: Json)(assertion: Json => Assertion): IO[Assertion] =
+  private def assertOneSource(query: Json)(assertion: Json => Assertion)(implicit pos: Position): IO[Assertion] =
     eventually {
       deltaClient.post[Json]("/search/query", query, Rick) { (body, response) =>
         response.status shouldEqual StatusCodes.OK
-        val sources = Json.fromValues(body.findAllByKey("_source"))
-        val source  = sources.hcursor.downArray.as[Json]
-        val actual  = source.getOrElse(Json.Null)
 
-        sources.asArray.value.size shouldBe 1
-        assertion(actual)
+        val results = Json
+          .fromValues(body.findAllByKey("_source"))
+          .hcursor
+          .as[List[Json]]
+          .getOrElse(Nil)
+
+        results match {
+          case single :: Nil => assertion(single)
+          case Nil           =>
+            fail(
+              s"Expected exactly 1 source to match query, got 0.\n " +
+                s"Query was ${query.spaces2}"
+            )
+          case many          =>
+            fail(
+              s"Expected exactly 1 source to match query, got ${many.size}.\n" +
+                s"Query was: ${query.spaces2}\n" +
+                s"Results were: $results"
+            )
+        }
       }
     }
 
-  private def assertEmpty(query: Json): IO[Assertion] =
+  private def assertEmpty(query: Json)(implicit pos: Position): IO[Assertion] =
     assertOneSource(query)(j => assert(j == json"""{ }"""))
 
   /** Check that a given field in the json can be parsed as [[Instant]] */