Merge pull request #85 from labra/issue83

Issue83

CONTRIBUTING.md

@@ -0,0 +1,44 @@
+# Guide for contributors
+
+This project follows a standard [fork and pull][fork-and-pull] model for accepting contributions via
+GitHub pull requests:
+
+0. [Pick (or report) an issue](#pick-or-report-an-issue)
+1. [Write code](#write-code)
+2. [Write tests](#write-tests)
+3. [Submit a pull request](#submit-a-pull-request)
+
+## Pick or report an issue
+
+We always welcome bug reports and feature requests—please don't feel like you need to have time to
+contribute a fix or implementation for your issue to be appreciated.
+
+## Write code
+
+We prefer functional programming for the code. 
+
+* Code and comments should be formatted to a width no greater than 100 columns.
+* Files should not contain trailing spaces.
+* Imports should be sorted alphabetically.
+
+When in doubt, please run `sbt scalastyle` and let us know if you have any questions.
+
+## Write tests
+
+Shaclex uses [ScalaTest][scalatest] for testing.
+
+## Submit a pull request
+
+* Pull requests should be submitted from a separate branch (e.g. using
+  `git checkout -b "username/fix-123"`).
+* In general we discourage force pushing to an active pull-request branch that other people are
+  commenting on or contributing to, and suggest using `git merge master` during development. 
+  Once development is complete, use `git rebase master` and force push to [clean up the history][squash].
+* The first line of a commit message should be no more than 72 characters long (to accommodate
+  formatting in various environments).
+* Commit messages should general use the present tense, normal sentence capitalization, and no final
+  punctuation.
+* If a pull request decreases code coverage more than by 2%, please file an issue to make sure that
+  tests get added.
+
+This guide for contributors is inspired by [circe's guide](https://github.com/circe/circe/blob/master/CONTRIBUTING.md).

build.sbt

@@ -37,6 +37,7 @@ lazy val http4sVersion         = "0.18.0-M8"
 lazy val scalatagsVersion      = "0.6.7"
 lazy val scallopVersion        = "3.1.1"
 lazy val jenaVersion           = "3.6.0"
+lazy val rdf4jVersion          = "2.2.4"
 lazy val jgraphtVersion        = "1.1.0"
 lazy val diffsonVersion        = "2.2.5"
 lazy val xercesVersion         = "2.11.0"
@@ -59,6 +60,9 @@ lazy val jgraphtCore       = "org.jgrapht"                % "jgrapht-core"
 lazy val antlr4            = "org.antlr"                  % "antlr4"               % antlrVersion
 lazy val xercesImpl        = "xerces"                     % "xercesImpl"           % xercesVersion
 lazy val jenaArq           = "org.apache.jena"            % "jena-arq"             % jenaVersion
+lazy val rdf4j             = "org.eclipse.rdf4j"          % "rdf4j"                % rdf4jVersion
+lazy val rdf4jModel        = "org.eclipse.rdf4j"          % "rdf4j-model"          % rdf4jVersion
+lazy val rdf4j_rioTurtle   = "org.eclipse.rdf4j"          % "rdf4j-rio-turtle"     % rdf4jVersion
 lazy val scalaLogging      = "com.typesafe.scala-logging" %% "scala-logging"       % loggingVersion
 lazy val scallop           = "org.rogach"                 %% "scallop"             % scallopVersion
 lazy val scalactic         = "org.scalactic"              %% "scalactic"           % scalacticVersion
@@ -94,8 +98,8 @@ lazy val shaclex = project
 //    buildInfoPackage := "es.weso.shaclex.buildinfo" 
 //  )
   .settings(commonSettings, packagingSettings, publishSettings, ghPagesSettings, wixSettings)
-  .aggregate(schema, shacl, shex, manifest, srdfJena, srdf, utils, converter, rbe, typing, validating, server, shapeMaps, depGraphs)
-  .dependsOn(schema, shacl, shex, manifest, srdfJena, srdf, utils, converter, rbe, typing, validating, server, shapeMaps, depGraphs)
+  .aggregate(schema, shacl, shex, manifest, srdfJena, srdf4j, srdf, utils, converter, rbe, typing, validating, server, shapeMaps, depGraphs)
+  .dependsOn(schema, shacl, shex, manifest, srdfJena, srdf4j, srdf, utils, converter, rbe, typing, validating, server, shapeMaps, depGraphs)
   .settings(
     unidocProjectFilter in (ScalaUnidoc, unidoc) := inAnyProject -- inProjects(noDocProjects: _*),
     libraryDependencies ++= Seq(
@@ -132,7 +136,12 @@ lazy val shacl = project
   .in(file("modules/shacl"))
   .disablePlugins(RevolverPlugin)
   .settings(commonSettings, publishSettings)
-  .dependsOn(srdfJena, manifest, utils, typing, validating)
+  .dependsOn(srdf,
+    manifest,
+    utils,
+    typing,
+    validating,
+    srdfJena % Test)
   .settings(
     logBuffered in Test       := false,
     parallelExecution in Test := false,
@@ -164,7 +173,18 @@ lazy val shex = project
     testOptions in Test := Seq(Tests.Filter(testFilter)),
     testOptions in CompatTest := Seq(Tests.Filter(compatFilter)),
   )
-  .dependsOn(srdfJena, srdf, typing, utils % "test -> test; compile -> compile", validating, shapeMaps, rbe, manifest, depGraphs)
+  .dependsOn(
+    srdf,
+    typing,
+    utils % "test -> test; compile -> compile",
+    validating,
+    shapeMaps,
+    rbe,
+    manifest,
+    depGraphs,
+    srdfJena % Test,
+    srdf4j % Test
+  )
   .settings(
     libraryDependencies ++= Seq(
       typesafeConfig % Test,
@@ -181,10 +201,13 @@ lazy val shapeMaps = project
   .enablePlugins(Antlr4Plugin)
   .disablePlugins(RevolverPlugin)
   .settings(commonSettings, publishSettings, antlrSettings("es.weso.shapeMaps.parser"))
-  .dependsOn(srdfJena)
+  .dependsOn(
+    srdf,
+    utils,
+    srdfJena % Test)
   .settings(
     libraryDependencies ++= Seq(
-      sext,
+      sext % Test,
       scalaLogging,
       catsCore,
       catsKernel,
@@ -221,7 +244,7 @@ lazy val manifest = project
   .in(file("modules/manifest"))
   .disablePlugins(RevolverPlugin)
   .settings(commonSettings, publishSettings)
-  .dependsOn(srdfJena, utils)
+  .dependsOn(srdf, utils, srdfJena)
   .settings(
     libraryDependencies ++= Seq(
       typesafeConfig % Test,
@@ -278,6 +301,23 @@ lazy val srdfJena = project
     )
   )
 
+lazy val srdf4j = project
+  .in(file("modules/srdf4j"))
+  .disablePlugins(RevolverPlugin)
+  .dependsOn(srdf, utils)
+  .settings(commonSettings, publishSettings)
+  .settings(
+    libraryDependencies ++= Seq(
+      logbackClassic,
+      scalaLogging,
+      typesafeConfig % Test,
+      rdf4j, rdf4jModel, rdf4j_rioTurtle,
+      catsCore,
+      catsKernel,
+      catsMacros
+    )
+  )
+
 lazy val typing = project
   .in(file("modules/typing"))
   .disablePlugins(RevolverPlugin)
@@ -312,7 +352,7 @@ lazy val utils = project
 lazy val validating = project
   .in(file("modules/validating"))
   .disablePlugins(RevolverPlugin)
-  .dependsOn(srdfJena, utils % "test -> test; compile -> compile")
+  .dependsOn(srdf, srdfJena % Test, utils % "test -> test; compile -> compile")
   .settings(commonSettings, publishSettings)
   .settings(
     libraryDependencies ++= Seq(

modules/converter/README.md

@@ -0,0 +1,3 @@
+# Converter module
+
+Converts between ShEx and SHACL

modules/converter/src/main/scala/es/weso/shacl/converter/shacl2ShEx.scala

@@ -67,6 +67,6 @@ object Shacl2ShEx extends Converter {
     shex.IRILabel(iri)
 
   def mkBNodeLabel(n: Int): shex.ShapeLabel =
-    shex.BNodeLabel(BNodeId(n.toString))
+    shex.BNodeLabel(BNode(n.toString))
 
 }

modules/converter/src/main/scala/es/weso/shex/converter/shex2shacl.scala

@@ -18,7 +18,7 @@ object ShEx2Shacl extends Converter {
 
   def newBNode: RDFNode = {
     bNodeCounter += 1
-    BNodeId("shape" + (bNodeCounter))
+    BNode("shape" + (bNodeCounter))
   }
 
   var shapesMap: Map[shacl.ShapeRef, shacl.Shape] = Map()

modules/depGraphs/README.md

@@ -0,0 +1,3 @@
+# Dependency Graphs module
+
+Checks if there are cycles in dependency graphs

modules/manifest/src/main/scala/es/weso/manifest/RDF2Manifest.scala

@@ -117,7 +117,7 @@ case class RDF2Manifest(base: Option[IRI],
         case iri: IRI =>
           if (noType(iri, rdf)) Right(IRIResult(iri))
           else compoundResult(iri, rdf)
-        case bNode: BNodeId => compoundResult(bNode, rdf)
+        case bNode: BNode => compoundResult(bNode, rdf)
         case _ => parseFail("Unexpected type of result " + n)
       }
     }

modules/rbe/README.md

@@ -0,0 +1,3 @@
+# RBE (Regular Bag Expressions) implementation
+
+This module implements Regular Bag Expressions

modules/schema/README.md

@@ -0,0 +1,4 @@
+# Schema
+
+This module defines a generic Schema interface which can be used to validate elements. 
+We provide two implementations of this interface, for ShEx and for SHACL. 

modules/schema/src/main/scala/es/weso/schema/ShaclexSchema.scala

@@ -59,7 +59,7 @@ case class ShaclexSchema(schema: ShaclSchema) extends Schema {
   private def cnvShape(s: Shape): ShapeMapLabel = {
     s.id match {
       case iri: IRI => IRILabel(iri)
-      case bnode: BNodeId => BNodeLabel(bnode)
+      case bnode: BNode => BNodeLabel(bnode)
       case _ => throw new Exception(s"cnvShape: unexpected ${s.id}")
     }
   }

modules/server/README.md

@@ -0,0 +1,11 @@
+# Server module
+
+This module implements a simple server based on the [http4s](http://http4s.org/) library.
+
+The server contains a simple REST API defined [here](https://github.com/labra/shaclex/blob/master/modules/server/src/main/scala/es/weso/server/APIService.scala) and a web service that calls the REST API. 
+The web service has been implemented using [Twirl templates](https://www.playframework.com/documentation/2.6.x/ScalaTemplates) 
+which are defined [in this folder](https://github.com/labra/shaclex/tree/master/modules/server/src/main/twirl/es/weso). 
+Some parts of the web service are implemennted in plain Javascript [here](https://github.com/labra/shaclex/tree/master/modules/server/src/main/resources/staticviews/js). 
+In the future, it would be better to replace that Javascript code by ScalaJs.
+
+The server is deployed at [shaclex](http://shaclex.validatingrdf.com).

modules/shacl/README.md

@@ -0,0 +1,3 @@
+# SHACL implementation
+
+This module implements [SHACL](https://www.w3.org/TR/shacl/) on top of the [SRDF] interface so it can be used by [Apache Jena](https://jena.apache.org/) or [RDF4j](http://rdf4j.org/).

modules/shacl/src/main/scala/es/weso/shacl/Shacl.scala

@@ -128,7 +128,7 @@ sealed abstract class Shape {
   def showId: String =
     id match {
       case iri: IRI => iri.str
-      case bnode: BNodeId => bnode.toString
+      case bnode: BNode => bnode.toString
     }
 
   def targetNodes: Seq[RDFNode] =

modules/shacl/src/main/scala/es/weso/shacl/converter/RDF2Shacl.scala

@@ -238,7 +238,7 @@ object RDF2Shacl extends RDFParser with LazyLogging {
   def parsePath: RDFParser[SHACLPath] = (n, rdf) => {
     n match {
       case iri: IRI => Right(PredicatePath(iri))
-      case bnode: BNodeId => someOf(
+      case bnode: BNode => someOf(
         inversePath,
         oneOrMorePath,
         zeroOrMorePath,

modules/shacl/src/main/scala/es/weso/shacl/validator/Validator.scala

@@ -783,7 +783,7 @@ case class Validator(schema: Schema) extends LazyLogging {
   private def equalsNode(n1: RDFNode, n2: RDFNode): Boolean = (n1, n2) match {
     case (l1: Literal, l2: Literal) => l1 == l2
     case (i1: IRI, i2: IRI) => i1 == i2
-    case (b1: BNodeId, b2: BNodeId) => b1 == b2
+    case (b1: BNode, b2: BNode) => b1 == b2
     case (_, _) => false
   }
 
@@ -796,7 +796,7 @@ case class Validator(schema: Schema) extends LazyLogging {
     case (DatatypeLiteral(n1, d1), DatatypeLiteral(n2, d2)) => d1 == d2 && n1 < n2
     case (LangLiteral(n1, l1), LangLiteral(n2, l2)) => n1 < n2
     case (i1: IRI, i2: IRI) => i1.str < i2.str
-    case (b1: BNodeId, b2: BNodeId) => b1.id < b2.id
+    case (b1: BNode, b2: BNode) => b1.id < b2.id
     case (_, _) => false
   }
   private def lessThanOrEqualNode(n1: RDFNode, n2: RDFNode): Boolean = (n1, n2) match {
@@ -807,7 +807,7 @@ case class Validator(schema: Schema) extends LazyLogging {
     case (DatatypeLiteral(n1, d1), DatatypeLiteral(n2, d2)) => d1 == d2 && n1 <= n2
     case (LangLiteral(n1, l1), LangLiteral(n2, l2)) => n1 <= n2
     case (i1: IRI, i2: IRI) => i1.str <= i2.str
-    case (b1: BNodeId, b2: BNodeId) => b1.id <= b2.id
+    case (b1: BNode, b2: BNode) => b1.id <= b2.id
     case (_, _) => false
   }
 

modules/shacl/src/test/scala/es/weso/shacl/AbstractSyntaxTest.scala

@@ -8,7 +8,7 @@ class AbstractSyntaxTest extends FunSpec with Matchers {
 
   describe("Abstract Syntax") {
     it("should be able to create a shape") {
-      val x = BNodeId("x")
+      val x = BNode("x")
       val c: PropertyShape =
         PropertyShape(
           id = x,

modules/shapeMaps/README.md

@@ -0,0 +1,3 @@
+# Shape maps implementation
+
+Implementation of [shape maps](http://shex.io/shape-map/) which can be used to trigger validation. Although shape maps were defined by the ShEx community group they can also be used in SHACL.

modules/shapeMaps/src/main/scala/es/weso/shapeMaps/Association.scala

@@ -5,7 +5,7 @@ import io.circe.syntax._
 import NodeSelector._
 import ShapeMapLabel._
 import es.weso.json.DecoderUtils._
-import es.weso.rdf.nodes.{ BNodeId, IRI, RDFNode }
+import es.weso.rdf.nodes.{ BNode, IRI, RDFNode }
 
 case class Association(node: NodeSelector, shape: ShapeMapLabel, info: Info = Info()) {
 
@@ -44,7 +44,7 @@ object Association {
       s => Left(DecodingFailure(s, Nil)),
       node => node match {
         case iri: IRI => Right(IRILabel(iri))
-        case bnode: BNodeId => Right(BNodeLabel(bnode))
+        case bnode: BNode => Right(BNodeLabel(bnode))
         case _ => Left(DecodingFailure(s"Cannot parse shapeMapLabel $node", Nil))
       }))
   }

modules/shapeMaps/src/main/scala/es/weso/shapeMaps/ShapeMapLabel.scala

@@ -1,5 +1,5 @@
 package es.weso.shapeMaps
-import es.weso.rdf.nodes.{ BNodeId, IRI }
+import es.weso.rdf.nodes.{ BNode, IRI }
 import io.circe.{ Encoder, Json }
 
 abstract class ShapeMapLabel {
@@ -14,7 +14,7 @@ abstract class ShapeMapLabel {
 }
 
 case class IRILabel(iri: IRI) extends ShapeMapLabel
-case class BNodeLabel(bnode: BNodeId) extends ShapeMapLabel
+case class BNodeLabel(bnode: BNode) extends ShapeMapLabel
 case object Start extends ShapeMapLabel
 
 object ShapeMapLabel {

modules/shex/README.md

@@ -0,0 +1,5 @@
+# ShEx library
+
+ShEx 2.0 implementation. 
+
+The implementation is defined in terms of the [SRDF](https://github.com/labra/shaclex/tree/master/modules/srdf) interface so it can work with both [Apache Jena](https://jena.apache.org/) and [RDF4j](http://rdf4j.org/).

modules/shex/src/main/scala/es/weso/shex/compact/SchemaMaker.scala

@@ -1170,8 +1170,8 @@ class SchemaMaker extends ShExDocBaseVisitor[Any] with LazyLogging {
     }
   }
 
-  override def visitBlankNode(ctx: BlankNodeContext): Builder[BNodeId] = {
-    ok(BNodeId(removeUnderscore(ctx.BLANK_NODE_LABEL().getText())))
+  override def visitBlankNode(ctx: BlankNodeContext): Builder[BNode] = {
+    ok(BNode(removeUnderscore(ctx.BLANK_NODE_LABEL().getText())))
   }
 
   def removeUnderscore(str: String): String =

modules/shex/src/main/scala/es/weso/shex/implicits/decoderShex.scala

@@ -37,8 +37,8 @@ object decoderShEx {
   /*  implicit lazy val keyDecoderShapeLabel: KeyDecoder[ShapeLabel] =
     KeyDecoder.instance { str => parseShapeLabel(str).toOption } */
 
-  implicit lazy val decodeBNodeId: Decoder[BNodeId] =
-    Decoder[String].map(BNodeId(_))
+  implicit lazy val decodeBNodeId: Decoder[BNode] =
+    Decoder[String].map(BNode(_))
 
   implicit lazy val decodeIRI: Decoder[IRI] =
     Decoder[String].emap(parseIRI(_))
@@ -412,7 +412,7 @@ object decoderShEx {
   def parseShapeLabel(str: String): Either[String, ShapeLabel] = {
     str match {
       // Be careful with the order...
-      case bNodeRegex(bNodeId) => Either.right(BNodeLabel(BNodeId(bNodeId)))
+      case bNodeRegex(bNodeId) => Either.right(BNodeLabel(BNode(bNodeId)))
       case iriRegex(i) => parseIRI(i).map(iri => IRILabel(iri))
       case _ => Either.left(s"$str doesn't match IRI or BNode")
     }

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

@@ -410,7 +410,7 @@ abstract sealed trait ShapeLabel {
   }
 }
 case class IRILabel(iri: IRI) extends ShapeLabel
-case class BNodeLabel(bnode: BNodeId) extends ShapeLabel
+case class BNodeLabel(bnode: BNode) extends ShapeLabel
 
 object Schema {
 

modules/shex/src/main/scala/es/weso/shex/shexR/RDF2ShEx.scala

@@ -68,7 +68,7 @@ trait RDF2ShEx extends RDFParser with LazyLogging {
 
   private def mkId(n: RDFNode): Option[ShapeLabel] = n match {
     case iri: IRI => Some(IRILabel(iri))
-    case bnode: BNodeId => Some(BNodeLabel(bnode))
+    case bnode: BNode => Some(BNodeLabel(bnode))
     case _ => None // TODO: Raise an exception?
   }
 

modules/shex/src/main/scala/es/weso/shex/validator/ShapeTyping.scala

@@ -50,7 +50,7 @@ case class ShapeTyping(t: Typing[RDFNode, ShapeType, ViolationError, String]) ex
     case None => Left(s"Can't create Result shape map for a shape expression without label. ShapeExpr: ${s.shape}")
     case Some(lbl) => lbl.toRDFNode match {
       case i: IRI => Either.right(IRIMapLabel(i))
-      case b: BNodeId => Either.right(BNodeLabel(b))
+      case b: BNode => Either.right(BNodeLabel(b))
       case _ => Left(s"Can't create Result shape map for a shape expression with label: $lbl")
     }
   }