Add emodel fields to search (#4720)

* Add emodel fields to search --------- Co-authored-by: Simon Dumas <[email protected]>
BlueBrain · Feb 8, 2024 · d8b76a1 · d8b76a1
1 parent f940f65
commit d8b76a1
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Showing 31 changed files with 244 additions and 146 deletions.
diff --git a/tests/docker/config/construct-query.sparql b/tests/docker/config/construct-query.sparql
@@ -57,7 +57,7 @@ CONSTRUCT {
                                                   :idLabel     ?layerIdLabel .
 
   ## Contributors
-  ?alias  :contributors    ?contributorId              .
+  ?alias  :contributors    ?contributorId         .
                            ?contributorId         rdf:type     ?contributorType   ;
                                                   :label       ?contributorName   ;
                                                   :idLabel     ?contributorIdName ;
@@ -78,10 +78,11 @@ CONSTRUCT {
 
   ## Generation
   ?alias  :generation      ?generation            .
-                           ?generation            :protocol        ?protocol                ;
-                                                  :startedAt       ?generationStartedAtTime ;
-                                                  :endedAt         ?generationEndedAtTime   .
-                                                                   ?protocol                :label      ?protocolName       ;
+                           ?generation            :protocol         ?protocol                ;
+                                                  :startedAt        ?generationStartedAtTime ;
+                                                  :endedAt          ?generationEndedAtTime   ;
+                                                  :followedWorkflow ?followedWorkflow        .
+                                                                    ?protocol               :label      ?protocolName       ;
                                                                                             :propertyID ?protocolPropertyId ;
                                                                                             :value      ?protocolValue      .
 
@@ -118,8 +119,8 @@ CONSTRUCT {
 
   ## Start / end / status
   ?alias  :startedAt         ?startedAt           ;
-       :endedAt              ?endedAt             ;
-       :status               ?status              .
+          :endedAt           ?endedAt             ;
+          :status            ?status              .
 
   ## Subject
   ?alias  :subjectAge        ?age                 .
@@ -198,13 +199,20 @@ CONSTRUCT {
   ## Morphology features
   ?alias :compartment          ?featureCompartment .
   ?alias :neuronMorphology     ?neuronMorphologyId .
+                               ?neuronMorphologyId :name ?neuronMorphologyName .
+
   ?alias :featureSeries        ?featureSeries    .
                                ?featureSeries    :value       ?featureValue         ;
                                                  :unit        ?featureUnit          ;
                                                  :label       ?featureLabel         ;
                                                  :statistic   ?featureStat          ;
                                                  :compartment ?featureCompartment   .
-
+
+  ## EModels
+  ?alias :emodel               ?emodel  .
+                               ?emodel  :score            ?emodelScore ;
+                                        :neuronMorphology ?emodelMorphologyId .
+                                                          ?emodelMorphologyId :name ?emodelMorphologyName .
 } WHERE {
   VALUES ?id { {resource_id} } .
   BIND( IRI(concat(str(?id), '/', 'alias')) AS ?alias ) .
@@ -391,8 +399,9 @@ CONSTRUCT {
         ?protocolId  schema:value       ?protocolValue      .
       } .
     } .
-    OPTIONAL { ?generation  prov:startedAtTime  ?generationStartedAtTime . } .
-    OPTIONAL { ?generation  prov:endedAtTime    ?generationEndedAtTime   . } .
+    OPTIONAL { ?generation  prov:startedAtTime   ?generationStartedAtTime . } .
+    OPTIONAL { ?generation  prov:endedAtTime     ?generationEndedAtTime   . } .
+    OPTIONAL { ?generation  nsg:followedWorkflow ?followedWorkflow        . } .
   }
 
   # Image
@@ -673,16 +682,36 @@ CONSTRUCT {
     ?id a bmo:NeuronMorphologyFeatureAnnotation .
 
     OPTIONAL {
-      ?id                   nsg:hasTarget / nsg:hasSource      ?neuronMorphologyId ;
-                            bmo:compartment                    ?featureCompartment ;
-                            nsg:hasBody                        ?featureBody        .
-
-      ?featureBody          nsg:isMeasurementOf / rdfs:label   ?featureLabel       ;
-                            schema:value / nsg:series          ?featureSeries      .
-      ?featureSeries        nsg:statistic                      ?featureStat        ;
-                            schema:value                       ?featureValue       ;
+      ?id                   nsg:hasTarget / nsg:hasSource      ?neuronMorphologyId   ;
+                            bmo:compartment                    ?featureCompartment   ;
+                            nsg:hasBody                        ?featureBody          .
+      ?neuronMorphologyId   schema:name                        ?neuronMorphologyName .
+
+      ?featureBody          nsg:isMeasurementOf / rdfs:label   ?featureLabel         ;
+                            schema:value / nsg:series          ?featureSeries        .
+      ?featureSeries        nsg:statistic                      ?featureStat          ;
+                            schema:value                       ?featureValue         ;
                             schema:unitCode                    ?featureUnit
 
     }.
   } .
+
+   # EModels
+   OPTIONAL {
+      ?id a nsg:EModel .
+
+      BIND(BNODE() AS ?emodel ) .
+
+      OPTIONAL { ?id  nsg:score ?emodelScore   . } .
+
+      OPTIONAL {
+        ?followedWorkflow schema:hasPart ?emodelConfig .
+
+        ?emodelConfig a bmo:EModelConfiguration   ;
+                      bmo:uses ?emodelMorphologyId    .
+                      # info about the morphology
+                      ?emodelMorphologyId  a nsg:NeuronMorphology            ;
+                                           schema:name ?emodelMorphologyName .
+      } .
+   }
 }
diff --git a/tests/docker/config/search-context.json b/tests/docker/config/search-context.json
@@ -39,8 +39,9 @@
   "featureSeries": {
     "@container": "@set"
   },
-  "neuronMorphology": {
-    "@type": "@id"
+  "followedWorkflow": {
+    "@type": "@id",
+    "@id": "https://bluebrain.github.io/nexus/field/followedWorkflow"
   },
   "project": {
     "@type": "@id"

diff --git a/.../resources/kg/search/bbp-neuroshapes.json → ...es/kg/search/context/bbp-neuroshapes.json b/.../resources/kg/search/bbp-neuroshapes.json → ...es/kg/search/context/bbp-neuroshapes.json
diff --git a/...test/resources/kg/search/neuroshapes.json → ...ources/kg/search/context/neuroshapes.json b/...test/resources/kg/search/neuroshapes.json → ...ources/kg/search/context/neuroshapes.json
diff --git a/...rc/test/resources/kg/search/activity.json → ...st/resources/kg/search/data/activity.json b/...rc/test/resources/kg/search/activity.json → ...st/resources/kg/search/data/activity.json
diff --git a/...src/test/resources/kg/search/article.json → ...est/resources/kg/search/data/article.json b/...src/test/resources/kg/search/article.json → ...est/resources/kg/search/data/article.json
diff --git a/...t/resources/kg/search/bouton-density.json → ...ources/kg/search/data/bouton-density.json b/...t/resources/kg/search/bouton-density.json → ...ources/kg/search/data/bouton-density.json
diff --git a/...st/resources/kg/search/curated-trace.json → ...sources/kg/search/data/curated-trace.json b/...st/resources/kg/search/curated-trace.json → ...sources/kg/search/data/curated-trace.json
diff --git a/...resources/kg/search/detailed-circuit.json → ...rces/kg/search/data/detailed-circuit.json b/...resources/kg/search/detailed-circuit.json → ...rces/kg/search/data/detailed-circuit.json
diff --git a/tests/src/test/resources/kg/search/data/emodel/emodel-configuration.json b/tests/src/test/resources/kg/search/data/emodel/emodel-configuration.json
@@ -0,0 +1,18 @@
+{
+  "@context": "https://bbp.neuroshapes.org",
+  "@type": [
+    "Entity",
+    "EModelConfiguration"
+  ],
+  "@id": "https://bbp.epfl.ch/data/emodel-configuration",
+  "uses": [
+    {
+      "@id": "https://bbp.epfl.ch/data/neuron-morphology",
+      "@type": "NeuronMorphology"
+    },
+    {
+      "@id": "https://bbp.epfl.ch/data/subcellular-model-script",
+      "@type": "SubCellularModelScript"
+    }
+  ]
+}
diff --git a/tests/src/test/resources/kg/search/data/emodel/emodel-workflow.json b/tests/src/test/resources/kg/search/data/emodel/emodel-workflow.json
@@ -0,0 +1,36 @@
+{
+  "@context": "https://bbp.neuroshapes.org",
+  "@type": [
+    "Entity",
+    "EModelWorkflow"
+  ],
+  "@id": "https://bbp.epfl.ch/data/emodel-workflow",
+  "generates": [
+    {
+      "@id": "https://bbp.epfl.ch/data/emodel",
+      "@type": "EModel"
+    },
+    {
+      "@id": "https://bbp.epfl.ch/data/emodel-script",
+      "@type": "EModelScript"
+    },
+    {
+      "@id": "https://bbp.epfl.ch/data/fitness-calculator-config",
+      "@type": "FitnessCalculatorConfiguration"
+    }
+  ],
+  "hasPart": [
+    {
+      "@id": "https://bbp.epfl.ch/data/extraction-targets-configuration",
+      "@type": "ExtractionTargetsConfiguration"
+    },
+    {
+      "@id": "https://bbp.epfl.ch/data/extraction-targets-configuration",
+      "@type": "EModelPipelineSettings"
+    },
+    {
+      "@id": "https://bbp.epfl.ch/data/emodel-configuration",
+      "@type": "EModelConfiguration"
+    }
+  ]
+}
diff --git a/tests/src/test/resources/kg/search/data/emodel/emodel.json b/tests/src/test/resources/kg/search/data/emodel/emodel.json
@@ -0,0 +1,21 @@
+{
+  "@context": "https://bbp.neuroshapes.org",
+  "@type": [
+    "Entity",
+    "EModel"
+  ],
+  "@id": "https://bbp.epfl.ch/data/emodel",
+  "generation": {
+    "@type": "Generation",
+    "activity": {
+      "@type": "Activity",
+      "followedWorkflow": {
+        "@id": "https://bbp.epfl.ch/data/emodel-workflow",
+        "@type": "EModelWorkflow"
+      }
+    }
+  },
+  "name": "EM__fa285b7__dSTUT__15",
+  "score": 47.566230109706076,
+  "seed": 15
+}
diff --git a/.../features/apical-dendrite-annotation.json → .../features/apical-dendrite-annotation.json b/.../features/apical-dendrite-annotation.json → .../features/apical-dendrite-annotation.json
diff --git a/...s/kg/search/features/axon-annotation.json → ...search/data/features/axon-annotation.json b/...s/kg/search/features/axon-annotation.json → ...search/data/features/axon-annotation.json
diff --git a/...h/features/basal-dendrite-annotation.json → ...a/features/basal-dendrite-annotation.json b/...h/features/basal-dendrite-annotation.json → ...a/features/basal-dendrite-annotation.json
diff --git a/...earch/features/morphology-annotation.json → .../data/features/morphology-annotation.json b/...earch/features/morphology-annotation.json → .../data/features/morphology-annotation.json
diff --git a/...s/kg/search/features/soma-annotation.json → ...search/data/features/soma-annotation.json b/...s/kg/search/features/soma-annotation.json → ...search/data/features/soma-annotation.json
diff --git a/.../resources/kg/search/layer-thickness.json → ...urces/kg/search/data/layer-thickness.json b/.../resources/kg/search/layer-thickness.json → ...urces/kg/search/data/layer-thickness.json
diff --git a/...src/test/resources/kg/search/license.json → ...est/resources/kg/search/data/license.json b/...src/test/resources/kg/search/license.json → ...est/resources/kg/search/data/license.json
diff --git a/...t/resources/kg/search/neuron-density.json → ...ources/kg/search/data/neuron-density.json b/...t/resources/kg/search/neuron-density.json → ...ources/kg/search/data/neuron-density.json
diff --git a/...esources/kg/search/neuron-morphology.json → ...ces/kg/search/data/neuron-morphology.json b/...esources/kg/search/neuron-morphology.json → ...ces/kg/search/data/neuron-morphology.json
diff --git a/tests/src/test/resources/kg/search/org.json → ...rc/test/resources/kg/search/data/org.json b/tests/src/test/resources/kg/search/org.json → ...rc/test/resources/kg/search/data/org.json
diff --git a/...est/resources/kg/search/patched-cell.json → ...esources/kg/search/data/patched-cell.json b/...est/resources/kg/search/patched-cell.json → ...esources/kg/search/data/patched-cell.json
diff --git a/.../src/test/resources/kg/search/person.json → ...test/resources/kg/search/data/person.json b/.../src/test/resources/kg/search/person.json → ...test/resources/kg/search/data/person.json
diff --git a/...rc/test/resources/kg/search/protocol.json → ...st/resources/kg/search/data/protocol.json b/...rc/test/resources/kg/search/protocol.json → ...st/resources/kg/search/data/protocol.json
diff --git a/...urces/kg/search/synapse-two-pathways.json → .../kg/search/data/synapse-two-pathways.json b/...urces/kg/search/synapse-two-pathways.json → .../kg/search/data/synapse-two-pathways.json
diff --git a/...src/test/resources/kg/search/synapse.json → ...est/resources/kg/search/data/synapse.json b/...src/test/resources/kg/search/synapse.json → ...est/resources/kg/search/data/synapse.json
diff --git a/...s/src/test/resources/kg/search/trace.json → .../test/resources/kg/search/data/trace.json b/...s/src/test/resources/kg/search/trace.json → .../test/resources/kg/search/data/trace.json
diff --git a/...resources/kg/search/unassessed-trace.json → ...rces/kg/search/data/unassessed-trace.json b/...resources/kg/search/unassessed-trace.json → ...rces/kg/search/data/unassessed-trace.json
diff --git a/tests/src/test/scala/ch/epfl/bluebrain/nexus/tests/kg/SearchAccessSpec.scala b/tests/src/test/scala/ch/epfl/bluebrain/nexus/tests/kg/SearchAccessSpec.scala
@@ -33,9 +33,9 @@ class SearchAccessSpec extends BaseIntegrationSpec {
       _ <- aclDsl.addPermission(s"/$orgId/$projId1", Rick, Resources.Read)
       _ <- aclDsl.addPermission(s"/$orgId/$projId2", Rick, Resources.Read)
 
-      _ <- postResource("kg/search/neuroshapes.json")
-      _ <- postResource("kg/search/bbp-neuroshapes.json")
-      _ <- postResource("kg/search/trace.json")
+      _ <- postResource("kg/search/context/neuroshapes.json")
+      _ <- postResource("kg/search/context/bbp-neuroshapes.json")
+      _ <- postResource("kg/search/data/trace.json")
     } yield ()
 
     setup.accepted