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Use Jena and Topbraid versions #4837

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merged 7 commits into from
Apr 5, 2024

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imsdu
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@imsdu imsdu commented Apr 4, 2024

Fixes #4683

Before:

[info] NeuroMorphologySampleSpec:
[info] Creating a morphology
[info] - should succeed provisionning the mandatory schemas (5 seconds, 863 milliseconds)
[info] - should succeed creating the morphology without a schema (174 milliseconds)
[info] - should succeed creating the morphology with a schema (3 seconds, 227 milliseconds)
[info] - should succeed updating the morphology with a schema (3 seconds, 24 milliseconds)

After:

[info] NeuroMorphologySampleSpec:
[info] Creating a morphology
[info] - should succeed provisionning the mandatory schemas (2 seconds, 990 milliseconds)
[info] - should succeed creating the morphology without a schema (105 milliseconds)
[info] - should succeed creating the morphology with a schema (2 seconds, 203 milliseconds)
[info] - should succeed updating the morphology with a schema (2 seconds, 187 milliseconds)

@@ -109,7 +109,7 @@ lazy val fs2Aws = "io.laserdisc" %% "fs2-
lazy val fs2AwsS3 = "io.laserdisc" %% "fs2-aws-s3" % fs2AwsVersion
lazy val googleAuthClient = "com.google.oauth-client" % "google-oauth-client" % googleAuthClientVersion
lazy val handleBars = "com.github.jknack" % "handlebars" % handleBarsVersion
lazy val jenaArq = "org.apache.jena" % "jena-arq" % jenaVersion
lazy val jenaArq = "org.apache.jena" % "jena-arq" % jenaVersion exclude ("com.apicatalog", "titanium-json-ld")
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To make sure we don't use Json-LD 1.1 for now

import java.util.regex.Pattern.quote
import scala.concurrent.duration._

class SearchSparqlQuerySpec
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Failing useless test

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To me it would be great if you could also check the validation of something of type Dataset, as it is also a complex shape, and most of our models will inherit it, including neuron morphologies. So using for example this resource as dataset would do.

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Ok, I will write a ticket about it as it can help defuse some regressions early.
If we integrate more of those in our tests, we will have to update those to follow the changes so some help will be appreciated :)

@@ -21,6 +21,6 @@
},
"value": "nxv:42"
},
"targetedNodes": 417
"targetedNodes": 412
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why is this changing?

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@imsdu imsdu Apr 5, 2024

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Not totally sure but we don't load the dash/tosh extensions provided by Topbraid anymore so my guess is there are fewer constraints and fewer nodes can get validated in the end.
targetedNodes is also a Nexus thing and if a node validated by several constraints will be accounted several times.

@@ -57,7 +57,7 @@ val postgresJdbcVersion = "42.7.3"
val pureconfigVersion = "0.17.6"
val scalaTestVersion = "3.2.18"
val scalaXmlVersion = "2.2.0"
val topBraidVersion = "1.3.2" // 1.4.1 fails to validate some test schemas
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Did you encounter any particular issues with validation for some schemas?

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@imsdu imsdu Apr 5, 2024

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Only when loading the extensions from topbraid where they added more constraints in 1.4.x and some were breaking.
As we don't rely on them, I made the change to only rely on those from shacl core.
There are still a few tests to be done though (via the validate endpoints) to make sure things are ok

@imsdu imsdu merged commit 58c751f into BlueBrain:master Apr 5, 2024
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@imsdu imsdu deleted the 4683-update-jena-library branch April 5, 2024 11:25
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Update the version of the Jena library
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