diff --git a/tests/docker/config/construct-query.sparql b/tests/docker/config/construct-query.sparql index 579a0484eb..b41488c0d9 100644 --- a/tests/docker/config/construct-query.sparql +++ b/tests/docker/config/construct-query.sparql @@ -382,8 +382,8 @@ CONSTRUCT { ?protocolId schema:value ?protocolValue . } . } . - OPTIONAL { ?generation prov:startedAtTime / schema:value ?generationStartedAtTime . } . - OPTIONAL { ?generation prov:endedAtTime / schema:value ?generationEndedAtTime . } . + OPTIONAL { ?generation prov:startedAtTime ?generationStartedAtTime . } . + OPTIONAL { ?generation prov:endedAtTime ?generationEndedAtTime . } . } # Image diff --git a/tests/docker/config/mapping.json b/tests/docker/config/mapping.json index 01e68703f8..9ced4061f1 100644 --- a/tests/docker/config/mapping.json +++ b/tests/docker/config/mapping.json @@ -116,6 +116,21 @@ "properties": { "value": { "type": "double" } } + }, + "neuronDensity": { + "properties": { + "value": { "type": "double" } + } + }, + "layerThickness": { + "properties": { + "value": { "type": "double" } + } + }, + "boutonDensity": { + "properties": { + "value": { "type": "double" } + } } } } \ No newline at end of file diff --git a/tests/docker/config/search-context.json b/tests/docker/config/search-context.json index d8a6c6ea70..3b98c7416f 100644 --- a/tests/docker/config/search-context.json +++ b/tests/docker/config/search-context.json @@ -51,6 +51,12 @@ "updatedAt": { "@type": "http://www.w3.org/2001/XMLSchema#dateTime" }, + "startedAt": { + "@type": "http://www.w3.org/2001/XMLSchema#dateTime" + }, + "endedAt": { + "@type": "http://www.w3.org/2001/XMLSchema#dateTime" + }, "_self": { "@type": "@id", "@id": "https://bluebrain.github.io/nexus/field/self" diff --git a/tests/src/test/resources/kg/search/activity.json b/tests/src/test/resources/kg/search/activity.json index 89748c3164..9d5b060f80 100644 --- a/tests/src/test/resources/kg/search/activity.json +++ b/tests/src/test/resources/kg/search/activity.json @@ -7,7 +7,7 @@ ], "endedAtTime": { "@type": "xsd:dateTime", - "value": "2015-05-01T00:00:00" + "@value": "2015-05-01T00:00:00" }, "generated": { "@id": "https://bbp.epfl.ch/neurosciencegraph/data/neuronmorphologies/da3b1e42-5f7f-4065-8be3-d2132c219bc2", @@ -27,7 +27,7 @@ "reconstructionCompressionCorrected": "yes", "startedAtTime": { "@type": "xsd:dateTime", - "value": "2015-01-21T00:00:00" + "@value": "2015-01-21T00:00:00" }, "used": { "@id": "https://bbp.epfl.ch/neurosciencegraph/data/5d43d0ad-1edd-434d-9a08-907968ecdbc3", diff --git a/tests/src/test/resources/kg/search/neuroshapes.json b/tests/src/test/resources/kg/search/neuroshapes.json index fae7c0f4b9..360779e171 100644 --- a/tests/src/test/resources/kg/search/neuroshapes.json +++ b/tests/src/test/resources/kg/search/neuroshapes.json @@ -260,9 +260,6 @@ "BrainCellFeature": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/BrainCellFeature" }, - "BrainCellSynapticType": { - "@id": "https://bbp.epfl.ch/ontologies/core/bmo/BrainCellSynapticType" - }, "BrainCellTranscriptomeType": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/BrainCellTranscriptomeType" }, @@ -278,6 +275,15 @@ "BrainComponentType": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/BrainComponentType" }, + "BrainHemisphere": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/BrainHemisphere" + }, + "BrainHemisphereLeft": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/BrainHemisphereLeft" + }, + "BrainHemisphereRight": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/BrainHemisphereRight" + }, "BrainImaging": { "@id": "nsg:BrainImaging" }, @@ -426,6 +432,9 @@ "CellSurfaceArea": { "@id": "https://bbp.epfl.ch/ontologies/core/efeatures/CellSurfaceArea" }, + "CellTypeAssignmentAnnotation": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/CellTypeAssignmentAnnotation" + }, "CellTypeMapping": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/CellTypeMapping" }, @@ -435,6 +444,12 @@ "CheckAISInitiation": { "@id": "https://bbp.epfl.ch/ontologies/core/efeatures/CheckAISInitiation" }, + "ChemicalSynapse": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/ChemicalSynapse" + }, + "ChemicalSynapticConnection": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/ChemicalSynapticConnection" + }, "ChlorideChannel": { "@id": "https://neuroshapes.org/ChlorideChannel" }, @@ -528,6 +543,9 @@ "DeHyperPol": { "@id": "http://bbp.epfl.ch/neurosciencegraph/ontologies/stimulustypes/DeHyperPol" }, + "DecayTimeConstant": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/DecayTimeConstant" + }, "DecayTimeConstantAfterStim": { "@id": "https://bbp.epfl.ch/ontologies/core/efeatures/DecayTimeConstantAfterStim" }, @@ -576,21 +594,12 @@ "DynamicParametersCircuitProperty": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/DynamicParametersCircuitProperty" }, - "E1": { - "@id": "https://bbp.epfl.ch/ontologies/core/celltypes/E1" - }, "E1SynapseType": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/E1SynapseType" }, - "E2": { - "@id": "https://bbp.epfl.ch/ontologies/core/celltypes/E2" - }, "E2SynapseType": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/E2SynapseType" }, - "E3": { - "@id": "https://bbp.epfl.ch/ontologies/core/celltypes/E3" - }, "E3SynapseType": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/E3SynapseType" }, @@ -684,6 +693,12 @@ "ElectricalStimulus": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/ElectricalStimulus" }, + "ElectricalSynapse": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/ElectricalSynapse" + }, + "ElectricalSynapticConnection": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/ElectricalSynapticConnection" + }, "ElectrophysiologyFeature": { "@id": "nsg:ElectrophysiologyFeature" }, @@ -810,6 +825,9 @@ "GABA": { "@id": "https://neuroshapes.org/GABA" }, + "GABAB_ratio": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/GABAB_ratio" + }, "GO": "http://purl.obolibrary.org/obo/GO_", "GPFS": { "@id": "nsg:GPFS" @@ -889,21 +907,12 @@ "Hyperparameter": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/Hyperparameter" }, - "I1": { - "@id": "https://bbp.epfl.ch/ontologies/core/celltypes/I1" - }, "I1SynapseType": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/I1SynapseType" }, - "I2": { - "@id": "https://bbp.epfl.ch/ontologies/core/celltypes/I2" - }, "I2SynapseType": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/I2SynapseType" }, - "I3": { - "@id": "https://bbp.epfl.ch/ontologies/core/celltypes/I3" - }, "I3SynapseType": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/I3SynapseType" }, @@ -985,6 +994,9 @@ "InhibitoryTransmitter": { "@id": "https://neuroshapes.org/InhibitoryTransmitter" }, + "InitialConcentrationOfMg": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/InitialConcentrationOfMg" + }, "InputResistance": { "@id": "https://bbp.epfl.ch/ontologies/core/efeatures/InputResistance" }, @@ -1619,9 +1631,6 @@ "NeuronProjectionType": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/NeuronProjectionType" }, - "NeuronSynapticType": { - "@id": "https://bbp.epfl.ch/ontologies/core/bmo/NeuronSynapticType" - }, "NeuronSynthesisCategory": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/NeuronSynthesisCategory" }, @@ -2204,6 +2213,9 @@ "SoftwareAgent": { "@id": "prov:SoftwareAgent" }, + "SoftwareApplication": { + "@id": "schema:SoftwareApplication" + }, "SoftwareSourceCode": { "@id": "schema:SoftwareSourceCode" }, @@ -2396,6 +2408,9 @@ "SynapsePhenotypicFeature": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/SynapsePhenotypicFeature" }, + "SynapsePhysiologyModel": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/SynapsePhysiologyModel" + }, "SynapsePlasticityType": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/SynapsePlasticityType" }, @@ -2405,6 +2420,9 @@ "SynapseType": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/SynapseType" }, + "SynapticConductanceWeight": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/SynapticConductanceWeight" + }, "SynapticConnection": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/SynapticConnection" }, @@ -2417,6 +2435,15 @@ "SynapticConnectivityTrace": { "@id": "nsg:SynapticConnectivityTrace" }, + "SynapticParameter": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/SynapticParameter" + }, + "SynapticParameterAnnotation": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/SynapticParameterAnnotation" + }, + "SynapticParameterAssignment": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/SynapticParameteAssignment" + }, "SynapticPathway": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/SynapticPathway" }, @@ -2426,9 +2453,18 @@ "SynapticPathwayType": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/SynapticPathwayType" }, + "SynapticReversalPotential": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/SynapticReversalPotential" + }, "SynapticStrength": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/SynapticStrength" }, + "SynapticTypeAssignment": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/SynapticTypeAssignment" + }, + "SynapticTypeMapping": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/SynapticTypeMapping" + }, "SynthesizedAstrocyteMorphology": { "@id": "nsg:SynthesizedAstrocyteMorphology" }, @@ -2507,6 +2543,12 @@ "Threshold": { "@id": "nsg:Threshold" }, + "TimeConstantInMsForRecoveryFromDepression": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/TimeConstantInMsForRecoveryFromDepression" + }, + "TimeConstantInMsForRecoveryFromFacilitation": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/TimeConstantInMsForRecoveryFromFacilitation" + }, "TimeSeries": { "@id": "https://neuroshapes.org/TimeSeries" }, @@ -2534,6 +2576,9 @@ "TraceCollection": { "@id": "nsg:TraceCollection" }, + "TraceDataWebContainer": { + "@id": "bmo:TraceDataWebContainer" + }, "TraceFeature": { "@id": "nsg:TraceFeature" }, @@ -2710,6 +2755,9 @@ "annotatorComment": { "@id": "nsg:annotatorComment" }, + "application": { + "@id": "bmo:application" + }, "associatedIon": { "@id": "https://neuroshapes.org/associatedIon", "@type": "@id" @@ -3028,6 +3076,12 @@ "eType": { "@id": "nsg:eType" }, + "e_GABAA": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/e_GABAA" + }, + "e_GABAB": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/e_GABAB" + }, "edgeCollection": { "@id": "nsg:edgeCollection" }, @@ -3082,7 +3136,8 @@ "@id": "nsg:endTime" }, "endedAtTime": { - "@id": "prov:endedAtTime" + "@id": "prov:endedAtTime", + "@type": "xsd:dateTime" }, "endianness": { "@id": "nsg:endianness" @@ -3158,6 +3213,9 @@ "function": { "@id": "nsg:function" }, + "functionalizedWith": { + "@id": "bmo:functionilizedWith" + }, "gain": { "@id": "nsg:gain" }, @@ -3194,6 +3252,9 @@ "givenName": { "@id": "schema:givenName" }, + "gmax": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/gmax" + }, "gradient2D": { "@id": "nsg:gradient2D" }, @@ -3203,6 +3264,12 @@ "graph_order": { "@id": "mba:graph_order" }, + "gsyn": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/gsyn" + }, + "gsynSRSF": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/gsynSRSF" + }, "hadActivity": { "@id": "prov:hadActivity" }, @@ -3665,6 +3732,9 @@ "note": { "@id": "skos:note" }, + "nrrp": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/nrrp" + }, "nsg": "https://neuroshapes.org/", "numberOfProjections": { "@id": "nsg:numberOfProjections" @@ -3933,6 +4003,9 @@ "scale": { "@id": "nsg:scale" }, + "scale_mg": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/scale_mg" + }, "schema": "http://schema.org/", "score": { "@id": "nsg:score" @@ -4011,6 +4084,9 @@ "slicingPlane": { "@id": "nsg:slicingPlane" }, + "slope_mg": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/slope_mg" + }, "softwareSourceCode": { "@id": "nsg:softwareSourceCode" }, @@ -4066,7 +4142,8 @@ "@id": "nsg:startMembranePotential" }, "startedAtTime": { - "@id": "prov:startedAtTime" + "@id": "prov:startedAtTime", + "@type": "xsd:dateTime" }, "statistic": { "@id": "nsg:statistic" @@ -4132,6 +4209,12 @@ "synapseRelease": { "@id": "nsg:synapseRelease" }, + "synapticConnection": { + "@id": "bmo:synapticConnection" + }, + "synapticPathway": { + "@id": "bmo:synapticPathway" + }, "target": { "@id": "nsg:target" }, @@ -4148,12 +4231,24 @@ "tau_d_AMPA": { "@id": "https://bbp.epfl.ch/ontologies/core/parameters/tau_d_AMPA" }, + "tau_d_GABAA": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/tau_d_GABAA" + }, + "tau_d_GABAB": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/tau_d_GABAB" + }, "tau_d_NMDA": { "@id": "https://bbp.epfl.ch/ontologies/core/parameters/tau_d_NMDA" }, "tau_r_AMPA": { "@id": "https://bbp.epfl.ch/ontologies/core/parameters/tau_r_AMPA" }, + "tau_r_GABAA": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/tau_r_GABAA" + }, + "tau_r_GABAB": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/tau_r_GABAB" + }, "tau_r_NMDA": { "@id": "https://bbp.epfl.ch/ontologies/core/parameters/tau_r_NMDA" }, @@ -4219,6 +4314,15 @@ "type": { "@id": "rdf:type" }, + "u": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/u" + }, + "u0": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/u0" + }, + "uHillCoefficient": { + "@id": "https://bbp.epfl.ch/ontologies/core/parameters/uHillCoefficient" + }, "uberon": "http://purl.obolibrary.org/obo/UBERON_", "uniprotID": { "@id": "https://bbp.epfl.ch/ontologies/core/bmo/uniprotID" @@ -4249,6 +4353,9 @@ "value": { "@id": "schema:value" }, + "valuePattern": { + "@id": "schema:valuePattern" + }, "valueX": { "@id": "nsg:valueX" }, @@ -4343,7 +4450,53 @@ "@container": "@list" }, "xml": "http://www.w3.org/XML/1998/namespace/", - "xsd": "http://www.w3.org/2001/XMLSchema#" + "xsd": "http://www.w3.org/2001/XMLSchema#", + "_constrainedBy": { + "@id": "https://bluebrain.github.io/nexus/vocabulary/constrainedBy", + "@type": "@id" + }, + "_createdAt": { + "@id": "https://bluebrain.github.io/nexus/vocabulary/createdAt", + "@type": "http://www.w3.org/2001/XMLSchema#dateTime" + }, + "_createdBy": { + "@id": "https://bluebrain.github.io/nexus/vocabulary/createdBy", + "@type": "@id" + }, + "_deprecated": "https://bluebrain.github.io/nexus/vocabulary/deprecated", + "_incoming": { + "@id": "https://bluebrain.github.io/nexus/vocabulary/incoming", + "@type": "@id" + }, + "_instant": "https://bluebrain.github.io/nexus/vocabulary/instant", + "_outgoing": { + "@id": "https://bluebrain.github.io/nexus/vocabulary/outgoing", + "@type": "@id" + }, + "_project": { + "@id": "https://bluebrain.github.io/nexus/vocabulary/project", + "@type": "@id" + }, + "_rev": "https://bluebrain.github.io/nexus/vocabulary/rev", + "_schemaProject": { + "@id": "https://bluebrain.github.io/nexus/vocabulary/schemaProject", + "@type": "@id" + }, + "_self": { + "@id": "https://bluebrain.github.io/nexus/vocabulary/self", + "@type": "@id" + }, + "_source": "https://bluebrain.github.io/nexus/vocabulary/source", + "_subject": "https://bluebrain.github.io/nexus/vocabulary/metadata/subject", + "_updatedAt": { + "@id": "https://bluebrain.github.io/nexus/vocabulary/updatedAt", + "@type": "http://www.w3.org/2001/XMLSchema#dateTime" + }, + "_updatedBy": { + "@id": "https://bluebrain.github.io/nexus/vocabulary/updatedBy", + "@type": "@id" + } }, - "@id": "https://neuroshapes.org" + "@id": "https://neuroshapes.org", + "_self": "https://bbp.epfl.ch/nexus/v1/resources/neurosciencegraph/datamodels/_/https:%2F%2Fneuroshapes.org" } \ No newline at end of file diff --git a/tests/src/test/scala/ch/epfl/bluebrain/nexus/tests/kg/SearchConfigSpec.scala b/tests/src/test/scala/ch/epfl/bluebrain/nexus/tests/kg/SearchConfigSpec.scala index 8c3d2eb2f8..8e033d3fc1 100644 --- a/tests/src/test/scala/ch/epfl/bluebrain/nexus/tests/kg/SearchConfigSpec.scala +++ b/tests/src/test/scala/ch/epfl/bluebrain/nexus/tests/kg/SearchConfigSpec.scala @@ -279,8 +279,8 @@ class SearchConfigSpec extends BaseSpec { "value" : "https://doi.org/10.1016/j.cell.2015.09.029" } ], - "startedAt" : "2015-01-21T00:00:00", - "endedAt" : "2015-05-01T00:00:00" + "startedAt" : "2015-01-21T00:00:00.000Z", + "endedAt" : "2015-05-01T00:00:00.000Z" } } """ @@ -651,7 +651,7 @@ class SearchConfigSpec extends BaseSpec { "have the correct startedAt for a simulation" in { val query = queryField(simulationId, "startedAt") - val expected = json"""{ "startedAt" : "2023-07-05T11:00:00.000000" }""" + val expected = json"""{ "startedAt" : "2023-07-05T11:00:00.000Z" }""" assertOneSource(query) { json => json should equalIgnoreArrayOrder(expected) @@ -660,7 +660,7 @@ class SearchConfigSpec extends BaseSpec { "have the correct endedAt for a simulation" in { val query = queryField(simulationId, "endedAt") - val expected = json"""{ "endedAt" : "2023-07-12T15:00:00.000000" }""" + val expected = json"""{ "endedAt" : "2023-07-12T15:00:00.000Z" }""" assertOneSource(query) { json => json should equalIgnoreArrayOrder(expected)