Started checking issue623

Author: labra

build.sbt

@@ -1,13 +1,13 @@
-lazy val scala212 = "2.12.17"
-lazy val scala213 = "2.13.10"
-lazy val scala3 = "3.2.1"
+lazy val scala212 = "2.12.20"
+lazy val scala213 = "2.13.15"
+lazy val scala3 = "3.6.3"
 lazy val supportedScalaVersions = List(
-  scala3,
   scala213,
+  scala3,
   scala212
 )
 
-val Java11 = JavaSpec.temurin("11") 
+val Java11 = JavaSpec.temurin("11")
 
 lazy val srdfVersion = "0.1.125"
 lazy val utilsVersion = "0.2.25"
@@ -19,7 +19,7 @@ lazy val catsVersion = "2.9.0"
 lazy val catsEffectVersion = "3.4.4"
 lazy val circeVersion = "0.14.2"
 lazy val commonsTextVersion = "1.8"
-lazy val declineVersion = "2.4.1"
+lazy val declineVersion = "2.5.0"
 lazy val fansiVersion = "0.3.0"
 lazy val fs2Version = "3.4.0"
 lazy val jenaVersion = "4.3.2"
@@ -73,7 +73,6 @@ lazy val wdtkUtil = "org.wikidata.wdtk" % "wdtk-util" % wikidataToolkitVersion
 lazy val scalacheck = "org.scalacheck" %% "scalacheck" % scalacheckVersion
 lazy val typesafeConfig = "com.typesafe" % "config" % typesafeConfigVersion
 
-
 lazy val logbackClassic = "ch.qos.logback" % "logback-classic" % logbackVersion
 lazy val scalaLogging =
   "com.typesafe.scala-logging" %% "scala-logging" % scalaLoggingVersion
@@ -142,8 +141,8 @@ lazy val shexs = project
       catsEffect,
       decline,
       declineEffect,
-      slf4jAPI,
-      slf4jSimple,
+      // slf4jAPI,
+      // slf4jSimple,
       srdf,
       srdf4j,
       srdfJena,
@@ -252,7 +251,7 @@ lazy val wshex = project
   .settings(
     crossScalaVersions := supportedScalaVersions,
     libraryDependencies ++= Seq(
-      utils, 
+      utils,
       catsCore,
       catsKernel,
       circeCore,
@@ -269,7 +268,7 @@ lazy val wshex = project
       scalaCollCompat,
       srdfJena,
       munit % Test,
-      munitEffect % Test,
+      munitEffect % Test
     ),
     testFrameworks += new TestFramework("munit.Framework")
   )
@@ -580,6 +579,8 @@ lazy val commonSettings = compilationSettings ++ sharedDependencies ++ Seq(
       email = "jelabra@gmail.com",
       url = url("https://weso.labra.es")
     )
-  ),
-  libraryDependencies += compilerPlugin("com.github.ghik" % "zerowaste" % "0.2.1" cross CrossVersion.full)
+  )
+  /*libraryDependencies += compilerPlugin(
+    ("com.github.ghik" % "zerowaste" % "1.0.0").cross(CrossVersion.full)
+  )*/
 ) ++ warnUnusedImport

examples/separation.shex

@@ -0,0 +1,8 @@
+prefix :       <http://example.org/> 
+
+# Separation test 
+:S {
+    :p @:S +
+}
+
+:S1 NOT @:S 

modules/shex/src/main/scala/es/weso/shex/Dependencies.scala

@@ -25,11 +25,12 @@ object Dependencies {
     depGraph(schema).map(_.negCycles)
 
   def oddNegCycles(schema: Schema): ES[Set[Set[(ShapeLabel, ShapeLabel)]]] =
-    depGraph(schema).map(_.oddNegCycles)
-    /*    for {
+    // depGraph(schema).map(_.oddNegCycles)
+    for {
       dg <- depGraph(schema)
-      negCycles = dg.negCycles.filter { nc => dg.countNegLinks(nc) % 2 == 1 }
-    } yield negCycles */
+      _ <- { println(s"Dependency graph: $dg"); Right(()) }
+      negCycles = dg.negCycles.filter(nc => dg.countNegLinks(nc) % 2 == 1)
+    } yield negCycles
 
   /** Returns the dependency graph of a schema
     *
@@ -42,7 +43,7 @@ object Dependencies {
       case None         => emptyGraph
       case Some(shapes) => shapes.foldRight(emptyGraph)(addDependency(schema))
     }
-//    println(s"Dependency graph: $r")
+    println(s"Dependency graph: $r")
     r
   }
 
@@ -65,8 +66,15 @@ object Dependencies {
   def getLabel(se: ShapeExpr): ES[ShapeLabel] =
     Either.fromOption(se.id, s"Shape $se has no label")
 
-  def dependencies(schema: Schema, shape: ShapeExpr, source: ShapeLabel, posNeg: PosNeg): ES[Deps] =
-    // println(s"Calculating dependencies of shape $shape with source label $source and posNeg $posNeg")
+  def dependencies(
+      schema: Schema,
+      shape: ShapeExpr,
+      source: ShapeLabel,
+      posNeg: PosNeg
+  ): ES[Deps] = {
+    println(
+      s"Calculating dependencies of shape $shape with source label $source and posNeg $posNeg"
+    )
     shape match {
       case s: ShapeAnd =>
         s.shapeExprs.map(dependencies(schema, _, source, posNeg)).sequence[ES, Deps].map(_.flatten)
@@ -101,6 +109,7 @@ object Dependencies {
       case _: ShapeExternal => noDeps
       case sd: ShapeDecl    => dependencies(schema, sd.shapeExpr, source, posNeg)
     }
+  }
 
   def dependenciesTripleExpr(
       schema: Schema,

modules/shex/src/main/scala/es/weso/shex/Schema.scala

@@ -130,21 +130,22 @@ case class Schema(
     _ <- shapesMap.keySet.toList.map(lbl => checkShapeLabel(lbl)).sequence
   } yield (())
 
-  private lazy val checkOddNegCycles: Either[String, Unit] =
-    // println(s"OddNegCycles: $oddNegCycles")
+  private lazy val checkOddNegCycles: Either[String, Unit] = {
+    println(s"OddNegCycles: $oddNegCycles")
     oddNegCycles match {
       case Left(e) => Left(e)
       case Right(cs) =>
         if (cs.isEmpty) Right(())
         else
           Left(s"Negative cycles: ${showCycles(oddNegCycles)}")
     }
+  }
 
   lazy val wellFormed: Either[String, Unit] = for {
     _ <- checkOddNegCycles
-    // _ <- { println(s"Passed checkOddNegCycles..."); Right(())}
+    _ <- { println(s"Passed checkOddNegCycles..."); Right(()) }
     _ <- checkBadShapeLabels
-    // _ <- { println(s"Passed checkBadShapeLabels..."); Right(())}
+    _ <- { println(s"Passed checkBadShapeLabels..."); Right(()) }
   } yield (())
 
   def relativize(maybeBase: Option[IRI]): Schema = maybeBase match {
@@ -161,7 +162,7 @@ case class Schema(
   def resolve(base: Option[IRI], verbose: VerboseLevel): IO[ResolvedSchema] =
     ResolvedSchema.resolve(this, base, verbose)
 
-  def withId(iri: IRI): Schema = this.copy(id = iri)  
+  def withId(iri: IRI): Schema = this.copy(id = iri)
 
   def withShapes(ses: ShapeExpr*): Schema = this.copy(shapes = ses.toList.some)
 
@@ -177,7 +178,6 @@ object Schema {
   def emptyWithId(iri: IRI): Schema =
     Schema.empty.withId(iri)
 
-
   def fromIRI(
       i: IRI,
       base: Option[IRI],

project/build.properties

@@ -1 +1 @@
-sbt.version=1.8.0
+sbt.version=1.10.11

project/metals.sbt

@@ -3,6 +3,6 @@
 
 // This file enables sbt-bloop to create bloop config files.
 
-addSbtPlugin("ch.epfl.scala" % "sbt-bloop" % "1.5.17")
+addSbtPlugin("ch.epfl.scala" % "sbt-bloop" % "2.0.9")
 
 // format: on

project/plugins.sbt

@@ -1,13 +1,13 @@
-addSbtPlugin("com.codecommit" % "sbt-github-actions" % "0.14.2")
-addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.2.0")
+addSbtPlugin("com.github.sbt" % "sbt-github-actions" % "0.25.0")
+addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "2.3.0")
 addSbtPlugin("com.eed3si9n" % "sbt-buildinfo" % "0.11.0")
 addSbtPlugin("com.github.sbt" % "sbt-unidoc" % "0.5.0")
-addSbtPlugin("com.github.sbt" % "sbt-ci-release" % "1.5.10")
-// addSbtPlugin("com.github.sbt"    % "sbt-git"             % "2.0.0")
-addSbtPlugin("com.github.sbt" % "sbt-native-packager" % "1.9.9")
+addSbtPlugin("com.github.sbt" % "sbt-ci-release" % "1.5.12")
+addSbtPlugin("com.github.sbt" % "sbt-git" % "2.1.0")
+addSbtPlugin("com.github.sbt" % "sbt-native-packager" % "1.11.1")
 addSbtPlugin("org.lyranthe.sbt" % "partial-unification" % "1.1.2")
 addSbtPlugin("org.scalameta" % "sbt-mdoc" % "2.3.5")
-addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.0")
+addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.3.1")
 addSbtPlugin("com.simplytyped" % "sbt-antlr4" % "0.8.3")
-addSbtPlugin("com.typesafe.sbt" % "sbt-site" % "1.4.1")
+addSbtPlugin("com.github.sbt" % "sbt-site-asciidoctor" % "1.5.0")
 addCompilerPlugin("com.olegpy" %% "better-monadic-for" % "0.3.1")

project/project/metals.sbt

@@ -3,6 +3,6 @@
 
 // This file enables sbt-bloop to create bloop config files.
 
-addSbtPlugin("ch.epfl.scala" % "sbt-bloop" % "1.5.17")
+addSbtPlugin("ch.epfl.scala" % "sbt-bloop" % "2.0.9")
 
 // format: on

project/project/project/metals.sbt

@@ -3,6 +3,6 @@
 
 // This file enables sbt-bloop to create bloop config files.
 
-addSbtPlugin("ch.epfl.scala" % "sbt-bloop" % "1.5.17")
+addSbtPlugin("ch.epfl.scala" % "sbt-bloop" % "2.0.9")
 
 // format: on

src/main/scala/es/weso/shexs/Main.scala

@@ -10,6 +10,8 @@ import es.weso.shex.validator.Validator
 import es.weso.shextest.manifest.{Validate => _, _}
 import com.monovore.decline._
 import com.monovore.decline.effect._
+import com.typesafe.scalalogging.LazyLogging
+
 // import buildinfo._
 import java.nio.file.Path
 import es.weso.shapepath.schemamappings.SchemaMappings
@@ -45,7 +47,8 @@ object Main
       name = "shex-s",
       header = "ShEx-Scala command line tool",
       version = "0.2.2" // BuildInfo.version
-    ) {
+    )
+    with LazyLogging {
 
   lazy val mappingOpt = Opts.option[Path](
     "mapping",
@@ -72,7 +75,31 @@ object Main
     if (verbose) IO.println(msg)
     else IO(())
 
-  override def main: Opts[IO[ExitCode]] =
+  private def disable_logs(): Unit = {
+    // The following code is needed to remove extra logging from Jena
+    import org.apache.jena.riot.system.stream.JenaIOEnvironment
+    import org.apache.jena.riot.system.stream.LocationMapper
+    val mapper: LocationMapper = new LocationMapper()
+    JenaIOEnvironment.setGlobalLocationMapper(mapper)
+
+    // Force logging level to None
+    val log: ch.qos.logback.classic.Logger =
+      logger.underlying.asInstanceOf[ch.qos.logback.classic.Logger]
+    log.getName()
+    import org.slf4j.LoggerFactory
+    import ch.qos.logback.classic._
+    val es_weso_log: ch.qos.logback.classic.Logger =
+      LoggerFactory.getLogger("es.weso").asInstanceOf[ch.qos.logback.classic.Logger]
+    val org_log: ch.qos.logback.classic.Logger =
+      LoggerFactory.getLogger("org").asInstanceOf[ch.qos.logback.classic.Logger]
+    org_log.setLevel(Level.OFF)
+    es_weso_log.setLevel(Level.OFF)
+    log.setLevel(Level.OFF)
+
+  }
+
+  override def main: Opts[IO[ExitCode]] = {
+    disable_logs()
     schemaMappingCommand
       .orElse(Validate.validateCommand)
       .orElse(shapePathValidateCommand)
@@ -90,6 +117,7 @@ object Main
       .map(
         _.handleErrorWith(infoError)
       )
+  }
 
   def infoError(err: Throwable): IO[ExitCode] =
     IO.println(s"Error ${err.getLocalizedMessage()}") *> IO(ExitCode.Error)