From b9e71b5bf576a1a19fa4c4b070cc53c6162104ba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Cristina=20E=2E=20Gonz=C3=A1lez-Espinoza?= Date: Thu, 22 Aug 2024 11:42:04 +0200 Subject: [PATCH 1/7] Make simulationReady property a construction from a quality metric annotation --- tests/docker/config/construct-query.sparql | 51 ++- .../data/morphology-quality-annotation.json | 356 ++++++++++++++++++ .../simulation-ready-neuron-morphology.json | 20 - .../tests/kg/SearchConfigIndexingSpec.scala | 3 +- 4 files changed, 399 insertions(+), 31 deletions(-) create mode 100644 tests/src/test/resources/kg/search/data/morphology-quality-annotation.json diff --git a/tests/docker/config/construct-query.sparql b/tests/docker/config/construct-query.sparql index 4d4c8a3a9b..80f0bdc790 100644 --- a/tests/docker/config/construct-query.sparql +++ b/tests/docker/config/construct-query.sparql @@ -333,16 +333,6 @@ CONSTRUCT { ) } - OPTIONAL { - BIND( - IF( - EXISTS {?id nsg:annotation / nsg:hasBody .}, - true, - false - ) AS ?simulationReady - ) - } - OPTIONAL { BIND( IF( @@ -628,6 +618,47 @@ CONSTRUCT { BIND( BNODE((CONCAT(STR(?id), '/neuronDensity'))) as ?neuronDensityBN ) . } . + # NeuronMorphologies + OPTIONAL { + ?id a nsg:NeuronMorphology ; + ^nsg:hasSource / ^nsg:hasTarget ?qualityMeasurementAnnotation . + + ?qualityMeasurementAnnotation a nsg:QualityMeasurementAnnotationAnnotation ; + nsg:hasBody ?canBeLoadedBody . + ?canBeLoadedBody nsg:isMeasurementOf bmo:CanBeLoadedWithMorphioMetric ; + schema:value ?canBeLoaded . + + ?qualityMeasurementAnnotation a nsg:QualityMeasurementAnnotationAnnotation ; + nsg:hasBody ?neuriteHasDiffDiameterBody . + ?neuriteHasDiffDiameterBody nsg:isMeasurementOf bmo:NeuriteHasDifferentDiametersMetric ; + schema:value ?neuriteHasDiffDiameter . + + ?qualityMeasurementAnnotation a nsg:QualityMeasurementAnnotationAnnotation ; + nsg:hasBody ?hasNonZeroNeuriteRadiiBody . + ?hasNonZeroNeuriteRadiiBody nsg:isMeasurementOf bmo:HasAllNonZeroNeuriteRadiiMetric ; + schema:value ?hasNonZeroNeuriteRadii . + + ?qualityMeasurementAnnotation a nsg:QualityMeasurementAnnotationAnnotation ; + nsg:hasBody ?hasNonZeroSecitonLengthBody . + ?canBeLoadedBody nsg:isMeasurementOf bmo:HasAllNonZeroSectionLengthsMetric ; + schema:value ?hasNonZeroSecitonLength . + + ?qualityMeasurementAnnotation a nsg:QualityMeasurementAnnotationAnnotation ; + nsg:hasBody ?hasNonZeroSomaBody . + ?canBeLoadedBody nsg:isMeasurementOf bmo:HasNoZeroSomaRadiusMetric ; + schema:value ?hasNonZeroSoma . + BIND( + IF (?canBeLoaded && + ?neuriteHasDiffDiameter && + ?hasNonZeroNeuriteRadii && + ?hasNonZeroSecitonLength && + ?hasNonZeroSoma, + true, + false + ) AS ?simulationReady + ) + } + # Simulation campaign configuration OPTIONAL { ?id a bmo:SimulationCampaignConfiguration . diff --git a/tests/src/test/resources/kg/search/data/morphology-quality-annotation.json b/tests/src/test/resources/kg/search/data/morphology-quality-annotation.json new file mode 100644 index 0000000000..fef656810b --- /dev/null +++ b/tests/src/test/resources/kg/search/data/morphology-quality-annotation.json @@ -0,0 +1,356 @@ +{ + "@context": "https://bbp.neuroshapes.org", + "@id": "https://bbp.epfl.ch/data/morphology-quality-annotation", + "@type": [ + "Annotation", + "QualityMeasurementAnnotation" + ], + "description": "This resources contains quality measurement annotations of the neuron morphology 18869_00253", + "distribution": [ + { + "@type": "DataDownload", + "atLocation": { + "@type": "Location", + "location": "file:///gpfs/bbp.cscs.ch/data/project/proj94/nexus/bbp-external/seu/8/1/d/7/9/6/3/2/18869_00253.json", + "store": { + "@id": "https://bbp.epfl.ch/neurosciencegraph/data/86b26915-1c4a-41ab-8865-0d6f4dfbdf72", + "@type": "RemoteDiskStorage", + "_rev": 1 + } + }, + "contentSize": { + "unitCode": "bytes", + "value": 1449 + }, + "contentUrl": "https://bbp.epfl.ch/nexus/v1/files/bbp-external/seu/https%3A%2F%2Fbbp.epfl.ch%2Fdata%2Fbbp-external%2Fseu%2Fab54853c-c3af-4993-b59e-c506d5d28767", + "digest": { + "algorithm": "SHA-256", + "value": "7c8c3cecd0da792fcb94c48ad2d54fae3f314ce8582847dfd4ea8c666c7b49d4" + }, + "encodingFormat": "application/json", + "name": "18869_00253.json" + }, + { + "@type": "DataDownload", + "atLocation": { + "@type": "Location", + "location": "file:///gpfs/bbp.cscs.ch/data/project/proj94/nexus/bbp-external/seu/d/1/6/5/5/4/b/d/18869_00253.tsv", + "store": { + "@id": "https://bbp.epfl.ch/neurosciencegraph/data/86b26915-1c4a-41ab-8865-0d6f4dfbdf72", + "@type": "RemoteDiskStorage", + "_rev": 1 + } + }, + "contentSize": { + "unitCode": "bytes", + "value": 958 + }, + "contentUrl": "https://bbp.epfl.ch/nexus/v1/files/bbp-external/seu/https%3A%2F%2Fbbp.epfl.ch%2Fdata%2Fbbp-external%2Fseu%2F117cd4c5-0d49-447c-b5a0-ec8368a3bd8a", + "digest": { + "algorithm": "SHA-256", + "value": "f9b9006c28519947fba6c75ce5c53266d4636e51f4884a0ef1078fa981da8715" + }, + "encodingFormat": "application/tsv", + "name": "18869_00253.tsv" + } + ], + "hasBody": [ + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/CanBeLoadedWithMorphioMetric", + "@type": "Metric", + "label": "Can be loaded with Morphio Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/ZThicknessMetric", + "@type": "Metric", + "label": "Z Thickness Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/NeuriteHasDifferentDiametersMetric", + "@type": "Metric", + "label": "Neurite Has Different Diameters Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://neuroshapes.org/danglingBranchMetric", + "@type": "Metric", + "label": "Dangling Branch Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://neuroshapes.org/rootNodeJumpMetric", + "@type": "Metric", + "label": "Root Node Jump Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://neuroshapes.org/zJumpMetric", + "@type": "Metric", + "label": "Z Jump Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://neuroshapes.org/narrowStartMetric", + "@type": "Metric", + "label": "Narrow Start Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://neuroshapes.org/fatEndMetric", + "@type": "Metric", + "label": "Fat End Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://neuroshapes.org/zeroLengthSegmentMetric", + "@type": "Metric", + "label": "Zero Length Segment Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/HasAllNonZeroNeuriteRadiiMetric", + "@type": "Metric", + "label": "Has all non-zero neurite radii Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/HasAllNonZeroSectionLengthsMetric", + "@type": "Metric", + "label": "Has all non-zero section lengths Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://neuroshapes.org/narrowNeuriteSectionMetric", + "@type": "Metric", + "label": "Narrow Neurite Section Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/HasNoFlatNeuritesMetric", + "@type": "Metric", + "label": "Has no flat neurites Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/HasUnifurcationMetric", + "@type": "Metric", + "label": "Has Unifurcation Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/HasMultifurcationMetric", + "@type": "Metric", + "label": "Has Multifurcation Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/HasNoZeroSomaRadiusMetric", + "@type": "Metric", + "label": "Has non-zero soma radius Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/HasApicalDendriteMetric", + "@type": "Metric", + "label": "Has Apical Dendrite Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/HasBasalDendrite", + "@type": "Metric", + "label": "Has Basal Dendrite Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://bbp.epfl.ch/ontologies/core/bmo/HasAxonMetric", + "@type": "Metric", + "label": "Has Axon Metric" + }, + "value": true + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://neuroshapes.org/dendriteStemmingFromSomaMetric", + "@type": "Metric", + "label": "Dendrite Stemming From Soma Metric" + }, + "value": "5" + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://neuroshapes.org/axonMetric", + "@type": "Metric", + "label": "Axon Metric" + }, + "value": "1" + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://neuroshapes.org/maximumBranchOrderMetric", + "@type": "Metric", + "label": "Maximum Branch Order Metric" + }, + "value": "22" + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://neuroshapes.org/totalSectionLengthMetric", + "@type": "Metric", + "label": "Total Section Length Metric" + }, + "value": "38094.47402250767" + }, + { + "@type": [ + "QualityMeasurement", + "AnnotationBody" + ], + "isMeasurementOf": { + "@id": "https://neuroshapes.org/maximumSectionLengthMetric", + "@type": "Metric", + "label": "Maximum Section Length Metric" + }, + "value": "4363.8212890625" + } + ], + "hasTarget": { + "@type": "AnnotationTarget", + "hasSource": { + "@id": "https://bbp.epfl.ch/data/simulation-ready-neuron-morphology", + "@type": "NeuronMorphology", + "_rev": 9 + } + }, + "name": "Quality Measurement Annotation of 18869_00253" + } \ No newline at end of file diff --git a/tests/src/test/resources/kg/search/data/simulation-ready-neuron-morphology.json b/tests/src/test/resources/kg/search/data/simulation-ready-neuron-morphology.json index e86f252cb3..791700fc8c 100644 --- a/tests/src/test/resources/kg/search/data/simulation-ready-neuron-morphology.json +++ b/tests/src/test/resources/kg/search/data/simulation-ready-neuron-morphology.json @@ -35,26 +35,6 @@ "@type": "ScholarlyArticle" } } - }, - { - "@type": [ - "QualityAnnotation", - "Annotation" - ], - "hasBody": { - "@id": "https://bbp.epfl.ch/ontologies/core/bmo/SimulationReady", - "@type": [ - "AnnotationBody", - "DataScope" - ], - "label": "Simulation Ready" - }, - "motivatedBy": { - "@id": "quality:Assessment", - "@type": "Motivation" - }, - "name": "Data usage scope annotation", - "note": "Dataset can be used to simulate single cell MEModels." } ], "brainLocation": { diff --git a/tests/src/test/scala/ch/epfl/bluebrain/nexus/tests/kg/SearchConfigIndexingSpec.scala b/tests/src/test/scala/ch/epfl/bluebrain/nexus/tests/kg/SearchConfigIndexingSpec.scala index ef353070a5..1acabba31f 100644 --- a/tests/src/test/scala/ch/epfl/bluebrain/nexus/tests/kg/SearchConfigIndexingSpec.scala +++ b/tests/src/test/scala/ch/epfl/bluebrain/nexus/tests/kg/SearchConfigIndexingSpec.scala @@ -77,7 +77,8 @@ class SearchConfigIndexingSpec extends BaseIntegrationSpec { "protocol.json", "person.json", "emodel/emodel-workflow.json", - "emodel/emodel-configuration.json" + "emodel/emodel-configuration.json", + "morphology-quality-annotation.json" ) private val allResources = otherResources ++ mainResources From 15c2a3f10ca04352127cf9cbc634dd4ff7f95474 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Cristina=20E=2E=20Gonz=C3=A1lez-Espinoza?= Date: Fri, 23 Aug 2024 13:47:48 +0200 Subject: [PATCH 2/7] added the quality measurement annotation type --- tests/docker/config/resource-types.json | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/docker/config/resource-types.json b/tests/docker/config/resource-types.json index afd0d84d19..23d7dd6d99 100644 --- a/tests/docker/config/resource-types.json +++ b/tests/docker/config/resource-types.json @@ -47,6 +47,7 @@ "https://neuroshapes.org/PSPamplitude", "https://neuroshapes.org/ReconstructedCell", "https://neuroshapes.org/ReconstructedPatchedCell", + "https://neuroshapes.org/QualityMeasurementAnnotation", "https://neuroshapes.org/Simulation", "https://neuroshapes.org/SimulationCampaign", "https://bbp.epfl.ch/ontologies/core/bmo/SimulationCampaignConfiguration", From 57c7110ea78d113d4a4cc63270cffdaa8a1b4e8f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Cristina=20E=2E=20Gonz=C3=A1lez-Espinoza?= Date: Fri, 23 Aug 2024 13:58:00 +0200 Subject: [PATCH 3/7] revert last change and some query fixes --- tests/docker/config/construct-query.sparql | 51 ++++++++++------------ tests/docker/config/resource-types.json | 1 - 2 files changed, 24 insertions(+), 28 deletions(-) diff --git a/tests/docker/config/construct-query.sparql b/tests/docker/config/construct-query.sparql index 5e05ab8053..c79fe522ab 100644 --- a/tests/docker/config/construct-query.sparql +++ b/tests/docker/config/construct-query.sparql @@ -649,39 +649,36 @@ CONSTRUCT { OPTIONAL { ?id a nsg:NeuronMorphology ; ^nsg:hasSource / ^nsg:hasTarget ?qualityMeasurementAnnotation . - - ?qualityMeasurementAnnotation a nsg:QualityMeasurementAnnotationAnnotation ; - nsg:hasBody ?canBeLoadedBody . - ?canBeLoadedBody nsg:isMeasurementOf bmo:CanBeLoadedWithMorphioMetric ; - schema:value ?canBeLoaded . - - ?qualityMeasurementAnnotation a nsg:QualityMeasurementAnnotationAnnotation ; - nsg:hasBody ?neuriteHasDiffDiameterBody . - ?neuriteHasDiffDiameterBody nsg:isMeasurementOf bmo:NeuriteHasDifferentDiametersMetric ; - schema:value ?neuriteHasDiffDiameter . - - ?qualityMeasurementAnnotation a nsg:QualityMeasurementAnnotationAnnotation ; - nsg:hasBody ?hasNonZeroNeuriteRadiiBody . - ?hasNonZeroNeuriteRadiiBody nsg:isMeasurementOf bmo:HasAllNonZeroNeuriteRadiiMetric ; - schema:value ?hasNonZeroNeuriteRadii . - - ?qualityMeasurementAnnotation a nsg:QualityMeasurementAnnotationAnnotation ; - nsg:hasBody ?hasNonZeroSecitonLengthBody . - ?canBeLoadedBody nsg:isMeasurementOf bmo:HasAllNonZeroSectionLengthsMetric ; - schema:value ?hasNonZeroSecitonLength . - - ?qualityMeasurementAnnotation a nsg:QualityMeasurementAnnotationAnnotation ; - nsg:hasBody ?hasNonZeroSomaBody . - ?canBeLoadedBody nsg:isMeasurementOf bmo:HasNoZeroSomaRadiusMetric ; - schema:value ?hasNonZeroSoma . + + ?qualityMeasurementAnnotation a nsg:QualityMeasurementAnnotationAnnotation . + + ?qualityMeasurementAnnotation nsg:hasBody ?canBeLoadedBody . + ?canBeLoadedBody nsg:isMeasurementOf bmo:CanBeLoadedWithMorphioMetric ; + schema:value ?canBeLoaded . + + ?qualityMeasurementAnnotation nsg:hasBody ?neuriteHasDiffDiameterBody . + ?neuriteHasDiffDiameterBody nsg:isMeasurementOf bmo:NeuriteHasDifferentDiametersMetric ; + schema:value ?neuriteHasDiffDiameter . + + ?qualityMeasurementAnnotation nsg:hasBody ?hasNonZeroNeuriteRadiiBody . + ?hasNonZeroNeuriteRadiiBody nsg:isMeasurementOf bmo:HasAllNonZeroNeuriteRadiiMetric ; + schema:value ?hasNonZeroNeuriteRadii . + + ?qualityMeasurementAnnotation nsg:hasBody ?hasNonZeroSectionLengthBody . + ?hasNonZeroSectionLengthBody nsg:isMeasurementOf bmo:HasAllNonZeroSectionLengthsMetric ; + schema:value ?hasNonZeroSectionLength . + + ?qualityMeasurementAnnotation nsg:hasBody ?hasNonZeroSomaBody . + ?hasNonZeroSomaBody nsg:isMeasurementOf bmo:HasNoZeroSomaRadiusMetric ; + schema:value ?hasNonZeroSoma . BIND( IF (?canBeLoaded && ?neuriteHasDiffDiameter && ?hasNonZeroNeuriteRadii && ?hasNonZeroSecitonLength && ?hasNonZeroSoma, - true, - false + true, + false ) AS ?simulationReady ) } diff --git a/tests/docker/config/resource-types.json b/tests/docker/config/resource-types.json index 23d7dd6d99..afd0d84d19 100644 --- a/tests/docker/config/resource-types.json +++ b/tests/docker/config/resource-types.json @@ -47,7 +47,6 @@ "https://neuroshapes.org/PSPamplitude", "https://neuroshapes.org/ReconstructedCell", "https://neuroshapes.org/ReconstructedPatchedCell", - "https://neuroshapes.org/QualityMeasurementAnnotation", "https://neuroshapes.org/Simulation", "https://neuroshapes.org/SimulationCampaign", "https://bbp.epfl.ch/ontologies/core/bmo/SimulationCampaignConfiguration", From fa50cba292f4beafa844977791061b0cf66f3812 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Cristina=20E=2E=20Gonz=C3=A1lez-Espinoza?= Date: Fri, 23 Aug 2024 14:15:11 +0200 Subject: [PATCH 4/7] fix typo in type of annotation --- tests/docker/config/construct-query.sparql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/docker/config/construct-query.sparql b/tests/docker/config/construct-query.sparql index c79fe522ab..74cd9b2318 100644 --- a/tests/docker/config/construct-query.sparql +++ b/tests/docker/config/construct-query.sparql @@ -650,7 +650,7 @@ CONSTRUCT { ?id a nsg:NeuronMorphology ; ^nsg:hasSource / ^nsg:hasTarget ?qualityMeasurementAnnotation . - ?qualityMeasurementAnnotation a nsg:QualityMeasurementAnnotationAnnotation . + ?qualityMeasurementAnnotation a nsg:QualityMeasurementAnnotation . ?qualityMeasurementAnnotation nsg:hasBody ?canBeLoadedBody . ?canBeLoadedBody nsg:isMeasurementOf bmo:CanBeLoadedWithMorphioMetric ; From 4cfc64972999c4a6143d98d04438b5a8b54dc891 Mon Sep 17 00:00:00 2001 From: Simon Date: Tue, 27 Aug 2024 11:31:40 +0200 Subject: [PATCH 5/7] Update dependencies for 1.10.0-M19 (#5121) Co-authored-by: Simon Dumas --- build.sbt | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/build.sbt b/build.sbt index 54cea8218a..cd29d37284 100755 --- a/build.sbt +++ b/build.sbt @@ -20,9 +20,9 @@ val akkaHttpCirceVersion = "1.39.2" val akkaCorsVersion = "1.2.0" val akkaVersion = "2.6.21" val alpakkaVersion = "3.0.4" -val apacheCompressVersion = "1.27.0" +val apacheCompressVersion = "1.27.1" val apacheIOVersion = "2.16.1" -val awsSdkVersion = "2.27.2" +val awsSdkVersion = "2.27.13" val betterMonadicForVersion = "0.3.1" val caffeineVersion = "3.1.8" val catsEffectVersion = "3.5.4" @@ -31,11 +31,11 @@ val catsVersion = "2.12.0" val circeVersion = "0.14.9" val circeOpticsVersion = "0.15.0" val circeExtrasVersions = "0.14.4" -val classgraphVersion = "4.8.174" +val classgraphVersion = "4.8.175" val declineVersion = "2.4.1" -val distageVersion = "1.2.11" +val distageVersion = "1.2.12" val doobieVersion = "1.0.0-RC5" -val fs2Version = "3.10.2" +val fs2Version = "3.11.0" val fs2AwsVersion = "6.1.3" val googleAuthClientVersion = "1.36.0" val handleBarsVersion = "4.4.0" @@ -46,13 +46,13 @@ val kamonVersion = "2.7.3" val kanelaAgentVersion = "1.0.18" val kindProjectorVersion = "0.13.3" val log4catsVersion = "2.7.0" -val logbackVersion = "1.5.6" +val logbackVersion = "1.5.7" val magnoliaVersion = "1.1.10" val mockitoVersion = "1.17.37" -val munitVersion = "1.0.0" +val munitVersion = "1.0.1" val munitCatsEffectVersion = "2.0.0" val nimbusJoseJwtVersion = "9.40" -val postgresJdbcVersion = "42.7.3" +val postgresJdbcVersion = "42.7.4" val pureconfigVersion = "0.17.7" val scalaTestVersion = "3.2.19" val scalaXmlVersion = "2.3.0" From 2183e0ebc3b4e88b2c04a8b5ce90d9c74218eeab Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Cristina=20E=2E=20Gonz=C3=A1lez-Espinoza?= Date: Tue, 27 Aug 2024 15:19:34 +0200 Subject: [PATCH 6/7] fix little typo --- tests/docker/config/construct-query.sparql | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/tests/docker/config/construct-query.sparql b/tests/docker/config/construct-query.sparql index 74cd9b2318..835c05db07 100644 --- a/tests/docker/config/construct-query.sparql +++ b/tests/docker/config/construct-query.sparql @@ -655,6 +655,9 @@ CONSTRUCT { ?qualityMeasurementAnnotation nsg:hasBody ?canBeLoadedBody . ?canBeLoadedBody nsg:isMeasurementOf bmo:CanBeLoadedWithMorphioMetric ; schema:value ?canBeLoaded . + BIND ( + IF (isLiteral(?canBeLoaded), + IF (?canBeLoaded)) ?qualityMeasurementAnnotation nsg:hasBody ?neuriteHasDiffDiameterBody . ?neuriteHasDiffDiameterBody nsg:isMeasurementOf bmo:NeuriteHasDifferentDiametersMetric ; @@ -675,7 +678,7 @@ CONSTRUCT { IF (?canBeLoaded && ?neuriteHasDiffDiameter && ?hasNonZeroNeuriteRadii && - ?hasNonZeroSecitonLength && + ?hasNonZeroSectionLength && ?hasNonZeroSoma, true, false From 9e0f592f420c2c78df8890b69d912dd45fcdee9b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Cristina=20E=2E=20Gonz=C3=A1lez-Espinoza?= Date: Tue, 27 Aug 2024 15:20:21 +0200 Subject: [PATCH 7/7] remove unused text --- tests/docker/config/construct-query.sparql | 3 --- 1 file changed, 3 deletions(-) diff --git a/tests/docker/config/construct-query.sparql b/tests/docker/config/construct-query.sparql index 835c05db07..dc48a777a3 100644 --- a/tests/docker/config/construct-query.sparql +++ b/tests/docker/config/construct-query.sparql @@ -655,9 +655,6 @@ CONSTRUCT { ?qualityMeasurementAnnotation nsg:hasBody ?canBeLoadedBody . ?canBeLoadedBody nsg:isMeasurementOf bmo:CanBeLoadedWithMorphioMetric ; schema:value ?canBeLoaded . - BIND ( - IF (isLiteral(?canBeLoaded), - IF (?canBeLoaded)) ?qualityMeasurementAnnotation nsg:hasBody ?neuriteHasDiffDiameterBody . ?neuriteHasDiffDiameterBody nsg:isMeasurementOf bmo:NeuriteHasDifferentDiametersMetric ;