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

delta/plugins/composite-views/src/main/scala/ch/epfl/bluebrain/nexus/delta/plugins/compositeviews/CompositeSink.scala

@@ -1,6 +1,7 @@
 package ch.epfl.bluebrain.nexus.delta.plugins.compositeviews
 
 import cats.implicits._
+import ch.epfl.bluebrain.nexus.delta.kernel.effect.migration._
 import ch.epfl.bluebrain.nexus.delta.kernel.kamon.KamonMetricComponent
 import ch.epfl.bluebrain.nexus.delta.kernel.syntax.kamonSyntax
 import ch.epfl.bluebrain.nexus.delta.plugins.blazegraph.client.BlazegraphClient
@@ -15,7 +16,7 @@ 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
@@ -25,7 +26,6 @@ import ch.epfl.bluebrain.nexus.delta.sourcing.state.GraphResource
 import ch.epfl.bluebrain.nexus.delta.sourcing.stream.Elem
 import ch.epfl.bluebrain.nexus.delta.sourcing.stream.Elem.{DroppedElem, FailedElem, SuccessElem}
 import ch.epfl.bluebrain.nexus.delta.sourcing.stream.Operation.Sink
-import ch.epfl.bluebrain.nexus.delta.kernel.effect.migration._
 import fs2.Chunk
 import monix.bio.Task
 import shapeless.Typeable
@@ -199,7 +199,8 @@ object CompositeSink {
       common: String,
       cfg: CompositeViewsConfig
   )(implicit rcr: RemoteContextResolution): ElasticSearchProjection => CompositeSink = { target =>
-    val esSink =
+    implicit val jsonLdOptions: JsonLdOptions = JsonLdOptions.AlwaysEmbed
+    val esSink                                =
       ElasticSearchSink.states(
         esClient,
         cfg.elasticsearchBatch.maxElements,

delta/plugins/elasticsearch/src/main/scala/ch/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._
@@ -19,7 +19,8 @@ import shapeless.Typeable
   *   a context to compute the compacted JSON-LD for of the [[GraphResource]]
   */
 final class GraphResourceToDocument(context: ContextValue, includeContext: Boolean)(implicit
-    cr: RemoteContextResolution
+    cr: RemoteContextResolution,
+    jsonLdOptions: JsonLdOptions
 ) extends Pipe {
   override type In  = GraphResource
   override type Out = Json

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")
 }

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 {

delta/sdk/src/main/scala/ch/epfl/bluebrain/nexus/delta/sdk/IndexingAction.scala

@@ -39,9 +39,7 @@ trait IndexingAction {
     */
   def projections(project: ProjectRef, elem: Elem[GraphResource]): ElemStream[CompiledProjection]
 
-  def apply(project: ProjectRef, elem: Elem[GraphResource])(implicit
-      contextShift: ContextShift[IO]
-  ): IO[List[FailedElem]] = {
+  def apply(project: ProjectRef, elem: Elem[GraphResource]): IO[List[FailedElem]] = {
     for {
       // To collect the errors
       errorsRef <- Ref.of[IO, List[FailedElem]](List.empty)

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
@@ -114,7 +114,7 @@ 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

delta/testkit/src/main/scala/ch/epfl/bluebrain/nexus/testkit/CirceEq.scala

@@ -3,10 +3,20 @@ package ch.epfl.bluebrain.nexus.testkit
 import ch.epfl.bluebrain.nexus.testkit.CirceEq.IgnoredArrayOrder
 import io.circe._
 import io.circe.syntax._
-import org.scalatest.matchers.{MatchResult, Matcher}
+import org.scalatest.matchers.{HavePropertyMatchResult, HavePropertyMatcher, MatchResult, Matcher}
 
 trait CirceEq {
   def equalIgnoreArrayOrder(json: Json): IgnoredArrayOrder = IgnoredArrayOrder(json)
+
+  def field(fieldName: String, expectedValue: Json): HavePropertyMatcher[Json, Json] = HavePropertyMatcher(left => {
+    val actualValue = left.hcursor.downField(fieldName).as[Json].getOrElse(Json.Null)
+    HavePropertyMatchResult(
+      actualValue == expectedValue,
+      fieldName,
+      expectedValue,
+      actualValue
+    )
+  })
 }
 
 object CirceEq {

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    . } .
+
+    } .
 }

tests/docker/config/search-context.json

@@ -30,6 +30,12 @@
   "protocol": {
     "@container": "@set"
   },
+  "preSynapticPathway": {
+    "@container": "@set"
+  },
+  "postSynapticPathway": {
+    "@container": "@set"
+  },
   "project": {
     "@type": "@id"
   },

tests/src/test/resources/kg/search/id-query-single-field.json

@@ -0,0 +1,16 @@
+{
+  "_source": [
+    "{{field}}"
+  ],
+  "query": {
+    "bool": {
+      "filter": [
+        {
+          "term": {
+            "@id.keyword": "{{id}}"
+          }
+        }
+      ]
+    }
+  }
+}

tests/src/test/resources/kg/search/id-query.json

@@ -1,7 +1,4 @@
 {
-  "_source": [
-    "{{field}}"
-  ],
   "query": {
     "bool": {
       "filter": [

tests/src/test/resources/kg/search/synapse-two-pathways.json

@@ -0,0 +1,31 @@
+{
+  "@context": "https://bbp.neuroshapes.org",
+  "@id": "https://bbp.epfl.ch/data/synapse-two-pathways",
+  "@type": [
+    "Entity",
+    "Parameter",
+    "SchafferCollateralAnatomyParameter",
+    "SynapsesPerConnection",
+    "ExperimentalSynapsesPerConnection"
+  ],
+  "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",
+  "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"
+      }
+    ]
+  }
+}

tests/src/test/resources/kg/search/synapse.json

@@ -0,0 +1,31 @@
+{
+  "@context": "https://bbp.neuroshapes.org",
+  "@id": "https://bbp.epfl.ch/data/synapse",
+  "@type": [
+    "Entity",
+    "Parameter",
+    "SchafferCollateralAnatomyParameter",
+    "SynapsesPerConnection",
+    "ExperimentalSynapsesPerConnection"
+  ],
+  "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",
+  "synapticPathway": {
+    "postSynaptic": [
+      {
+        "@id": "http://api.brain-map.org/api/v2/data/Structure/453",
+        "about": "BrainRegion",
+        "label": "Somatosensory areas",
+        "notation": "SS"
+      }
+    ],
+    "preSynaptic": [
+      {
+        "@id": "http://api.brain-map.org/api/v2/data/Structure/453",
+        "about": "BrainRegion",
+        "label": "Somatosensory areas",
+        "notation": "SS"
+      }
+    ]
+  }
+}