37 Root identity (#44)

* Set theme jekyll-theme-slate

* Create index.md

Initialise GH pages

* Update root identity resource to match spec

* Fix test

* Add format and distribution to graph
Remove unused URI property on binary array interface

* Remove unused imports

* Fix output format test

Author: simonoakesepimorphics

binary-array-ld-cli/src/test/kotlin/net/bald/BinaryArrayConvertCliTest.kt

@@ -9,11 +9,6 @@ import java.io.Closeable
  * Should be closed after use.
  */
 interface BinaryArray: Closeable {
-    /**
-     * The URI which identifies the dataset.
-     */
-    val uri: String
-
     /**
      * The prefix mapping to apply to the RDF graph.
      */
@@ -23,4 +18,15 @@ interface BinaryArray: Closeable {
      * The root container.
      */
     val root: Container
+
+    /**
+     * The format of the binary array.
+     */
+    val format: Format
+
+    /**
+     * The distribution of the binary array, if it is available. Otherwise, null.
+     */
+    val distribution: Distribution?
+
 }

binary-array-ld-lib/src/main/kotlin/net/bald/BinaryArray.kt

@@ -0,0 +1,11 @@
+package net.bald
+
+/**
+ * A distribution of a binary array file.
+ */
+interface Distribution {
+    /**
+     * The media type of the binary array file.
+     */
+    val mediaType: String
+}

binary-array-ld-lib/src/main/kotlin/net/bald/Distribution.kt

@@ -0,0 +1,13 @@
+package net.bald
+
+import org.apache.jena.rdf.model.Resource
+
+/**
+ * A binary array format.
+ */
+interface Format {
+    /**
+     * The resource which represents the format.
+     */
+    val identifier: Resource
+}

binary-array-ld-lib/src/main/kotlin/net/bald/Format.kt

@@ -2,18 +2,48 @@ package net.bald.model
 
 import net.bald.BinaryArray
 import net.bald.vocab.BALD
+import org.apache.jena.rdf.model.Literal
 import org.apache.jena.rdf.model.Model
+import org.apache.jena.rdf.model.Resource
+import org.apache.jena.rdf.model.ResourceFactory.createResource
+import org.apache.jena.rdf.model.ResourceFactory.createStringLiteral
 import org.apache.jena.shared.PrefixMapping
+import org.apache.jena.vocabulary.DCAT
+import org.apache.jena.vocabulary.DCTerms
+import org.apache.jena.vocabulary.RDF
 import java.net.URI
 
 class ModelBinaryArrayBuilder(
     private val model: Model,
     private val containerFct: ModelContainerBuilder.Factory
 ) {
     fun addBinaryArray(ba: BinaryArray) {
+        val root = ba.root
+        val res = model.createResource(root.uri)
+
         addPrefixMapping(ba.prefixMapping)
-        val baRes = model.createResource(ba.uri, BALD.Container)
-        containerFct.forParent(baRes).addContainer(ba.root)
+        addFormat(ba, res)
+        addDistribution(ba, res)
+        containerFct.forRoot(model).addContainer(root)
+    }
+
+    private fun addFormat(ba: BinaryArray, root: Resource) {
+        val format = model.createResource()
+            .addProperty(RDF.type, DCTerms.MediaType)
+            .addProperty(DCTerms.identifier, ba.format.identifier)
+        root.addProperty(DCTerms.format, format)
+    }
+
+    private fun addDistribution(ba: BinaryArray, root: Resource) {
+        ba.distribution?.let { dist ->
+            val mediaType = model.createResource()
+                .addProperty(RDF.type, DCTerms.MediaType)
+                .addProperty(DCTerms.identifier, dist.mediaType)
+            val distribution = model.createResource()
+                .addProperty(RDF.type, DCAT.Distribution)
+                .addProperty(DCAT.mediaType, mediaType)
+            root.addProperty(DCAT.distribution, distribution)
+        }
     }
 
     private fun addPrefixMapping(prefixMapping: PrefixMapping) {

binary-array-ld-lib/src/main/kotlin/net/bald/model/ModelBinaryArrayBuilder.kt

@@ -3,19 +3,27 @@ package net.bald.model
 import net.bald.AttributeSource
 import net.bald.Container
 import net.bald.vocab.BALD
+import org.apache.jena.rdf.model.Model
 import org.apache.jena.rdf.model.Resource
 
 open class ModelContainerBuilder(
-    private val parent: Resource,
+    private val model: Model,
+    private val parent: Resource?,
     private val varFct: ModelVarBuilder.Factory,
     private val attrFct: ModelAttributeBuilder.Factory
 ) {
+    constructor(
+        parent: Resource,
+        varFct: ModelVarBuilder.Factory,
+        attrFct: ModelAttributeBuilder.Factory
+    ): this(parent.model, parent, varFct, attrFct)
+
     open fun addContainer(container: Container) {
-        val containerRes = parent.model.createResource(container.uri, BALD.Container)
+        val containerRes = model.createResource(container.uri, BALD.Container)
         addSubContainers(container, containerRes)
         addVars(container, containerRes)
         addAttributes(container, containerRes)
-        parent.addProperty(BALD.contains, containerRes)
+        parent?.addProperty(BALD.contains, containerRes)
     }
 
     private fun addSubContainers(container: Container, containerRes: Resource) {
@@ -40,6 +48,10 @@ open class ModelContainerBuilder(
         open fun forParent(parent: Resource): ModelContainerBuilder {
             return ModelContainerBuilder(parent, varFct, attrFct)
         }
+
+        open fun forRoot(model: Model): ModelContainerBuilder {
+            return ModelContainerBuilder(model, parent = null, varFct, attrFct)
+        }
     }
 }
 

binary-array-ld-lib/src/main/kotlin/net/bald/model/ModelContainerBuilder.kt

@@ -1,51 +1,53 @@
 package net.bald.model
 
 import bald.model.ModelVerifier
-import com.nhaarman.mockitokotlin2.any
 import com.nhaarman.mockitokotlin2.doReturn
 import com.nhaarman.mockitokotlin2.mock
 import com.nhaarman.mockitokotlin2.verify
 import net.bald.BinaryArray
 import net.bald.Container
+import net.bald.Distribution
+import net.bald.Format
 import net.bald.vocab.BALD
 import org.apache.jena.rdf.model.ModelFactory
+import org.apache.jena.rdf.model.ResourceFactory.createResource
 import org.apache.jena.shared.PrefixMapping
-import org.apache.jena.vocabulary.RDF
 import org.apache.jena.vocabulary.SKOS
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.assertThrows
 import java.lang.IllegalArgumentException
 import kotlin.test.assertEquals
 
 class ModelBinaryArrayBuilderTest {
+    private val model = ModelFactory.createDefaultModel()
     private val containerBuilder = mock<ModelContainerBuilder>()
     private val containerFct = mock<ModelContainerBuilder.Factory> {
-        on { forParent(any()) } doReturn containerBuilder
+        on { forRoot(model) } doReturn containerBuilder
     }
-    private val model = ModelFactory.createDefaultModel()
     private val builder = ModelBinaryArrayBuilder.Factory(containerFct).forModel(model)
-    private val root = mock<Container>()
+    private val root = mock<Container> {
+        on { uri } doReturn "http://test.binary-array-ld.net/example/"
+    }
     private val prefix = PrefixMapping.Factory.create()
         .setNsPrefix("bald", BALD.prefix)
         .setNsPrefix("skos", SKOS.uri)
+    private val format = mock<Format> {
+        on { identifier } doReturn createResource("http://vocab.nerc.ac.uk/collection/M01/current/NC/")
+    }
+    private val distribution = mock<Distribution> {
+        on { mediaType } doReturn "application/x-netcdf"
+    }
     private val ba = mock<BinaryArray> {
-        on { uri } doReturn "http://test.binary-array-ld.net/example"
         on { this.root } doReturn root
         on { prefixMapping } doReturn prefix
-    }
-
-    @Test
-    fun addBinaryArray_addsFileContainer() {
-        builder.addBinaryArray(ba)
-        ModelVerifier(model).resource("http://test.binary-array-ld.net/example") {
-            statement(RDF.type, BALD.Container)
-        }
+        on { format } doReturn format
+        on { distribution } doReturn distribution
     }
 
     @Test
     fun addBinaryArray_addsRootContainer() {
         builder.addBinaryArray(ba)
-        verify(containerFct).forParent(model.getResource("http://test.binary-array-ld.net/example"))
+        verify(containerFct).forRoot(model)
         verify(containerBuilder).addContainer(root)
     }
 
@@ -84,4 +86,15 @@ class ModelBinaryArrayBuilderTest {
         }
         assertEquals("Unable to add prefix mapping eg to model: URI must end with / or #.", iae.message)
     }
+
+    @Test
+    fun addBinaryArray_addsFormatAndDistribution() {
+        builder.addBinaryArray(ba)
+        ModelVerifier(model).apply {
+            resource("http://test.binary-array-ld.net/example/") {
+                format()
+                distribution()
+            }
+        }
+    }
 }

binary-array-ld-lib/src/test/kotlin/net/bald/model/ModelBinaryArrayBuilderTest.kt

@@ -3,11 +3,10 @@ package net.bald.model
 import bald.model.ModelVerifier
 import com.nhaarman.mockitokotlin2.doReturn
 import com.nhaarman.mockitokotlin2.mock
-import net.bald.BinaryArray
-import net.bald.Container
-import net.bald.Var
+import net.bald.*
 import net.bald.vocab.BALD
 import org.apache.jena.rdf.model.Model
+import org.apache.jena.rdf.model.ResourceFactory
 import org.apache.jena.shared.PrefixMapping
 import org.apache.jena.vocabulary.DCTerms
 import org.apache.jena.vocabulary.RDF
@@ -46,10 +45,17 @@ class ModelBinaryArrayConverterTest {
             .setNsPrefix("bald", BALD.prefix)
             .setNsPrefix("skos", SKOS.uri)
             .setNsPrefix("dct", DCTerms.NS)
+        val format = mock<Format> {
+            on { identifier } doReturn ResourceFactory.createResource("http://vocab.nerc.ac.uk/collection/M01/current/NC/")
+        }
+        val distribution = mock<Distribution> {
+            on { mediaType } doReturn "application/x-netcdf"
+        }
         val ba = mock<BinaryArray> {
-            on { this.uri } doReturn uri
             on { this.root } doReturn root
             on { prefixMapping } doReturn prefix
+            on { this.format } doReturn format
+            on { this.distribution } doReturn distribution
         }
 
         val model = convert(ba)
@@ -58,19 +64,18 @@ class ModelBinaryArrayConverterTest {
             prefix("bald", BALD.prefix)
             prefix("skos", SKOS.uri)
             prefix("dct", DCTerms.NS)
-            resource("http://test.binary-array-ld.net/example") {
+            resource("http://test.binary-array-ld.net/example/") {
+                format()
                 statement(RDF.type, BALD.Container)
-                statement(BALD.contains, model.createResource("http://test.binary-array-ld.net/example/")) {
-                    statement(RDF.type, BALD.Container)
-                    statement(BALD.contains, model.createResource("http://test.binary-array-ld.net/example/bar")) {
-                        statement(RDF.type, BALD.Resource)
-                    }
-                    statement(BALD.contains, model.createResource("http://test.binary-array-ld.net/example/baz")) {
-                        statement(RDF.type, BALD.Resource)
-                    }
-                    statement(BALD.contains, model.createResource("http://test.binary-array-ld.net/example/foo")) {
-                        statement(RDF.type, BALD.Resource)
-                    }
+                distribution()
+                statement(BALD.contains, model.createResource("http://test.binary-array-ld.net/example/bar")) {
+                    statement(RDF.type, BALD.Resource)
+                }
+                statement(BALD.contains, model.createResource("http://test.binary-array-ld.net/example/baz")) {
+                    statement(RDF.type, BALD.Resource)
+                }
+                statement(BALD.contains, model.createResource("http://test.binary-array-ld.net/example/foo")) {
+                    statement(RDF.type, BALD.Resource)
                 }
             }
         }

binary-array-ld-lib/src/test/kotlin/net/bald/model/ModelBinaryArrayConverterTest.kt

@@ -0,0 +1,25 @@
+package net.bald.model
+
+import bald.model.StatementsVerifier
+import org.apache.jena.rdf.model.ResourceFactory
+import org.apache.jena.vocabulary.DCAT
+import org.apache.jena.vocabulary.DCTerms
+import org.apache.jena.vocabulary.RDF
+
+fun StatementsVerifier.format() {
+    statement(DCTerms.format) {
+        statement(DCTerms.identifier,
+            ResourceFactory.createResource("http://vocab.nerc.ac.uk/collection/M01/current/NC/"))
+        statement(RDF.type, DCTerms.MediaType)
+    }
+}
+
+fun StatementsVerifier.distribution() {
+    statement(DCAT.distribution) {
+        statement(RDF.type, DCAT.Distribution)
+        statement(DCAT.mediaType) {
+            statement(DCTerms.identifier, ResourceFactory.createStringLiteral("application/x-netcdf"))
+            statement(RDF.type, DCTerms.MediaType)
+        }
+    }
+}

binary-array-ld-lib/src/test/kotlin/net/bald/model/StatementsVerifierExt.kt

@@ -1,6 +1,8 @@
 package net.bald.netcdf
 
 import net.bald.BinaryArray
+import net.bald.Distribution
+import net.bald.Format
 import net.bald.alias.AliasDefinition
 import net.bald.context.ModelContext
 import org.apache.jena.shared.PrefixMapping
@@ -15,7 +17,7 @@ import java.io.File
  * Should be closed after use.
  */
 class NetCdfBinaryArray(
-    override val uri: String,
+    val uri: String,
     private val file: NetcdfFile,
     private val context: ModelContext,
     val alias: AliasDefinition
@@ -29,6 +31,9 @@ class NetCdfBinaryArray(
         }
     }
 
+    override val format: Format get() = NetCdfFormat
+    override val distribution: Distribution get() = NetCdfDistribution()
+
     val prefixSrc: String? get() = prefixSourceName()
 
     override fun close() {

binary-array-ld-netcdf/src/main/kotlin/net/bald/netcdf/NetCdfBinaryArray.kt

@@ -0,0 +1,10 @@
+package net.bald.netcdf
+
+import net.bald.Distribution
+
+/**
+ * NetCDF implementation of [Distribution].
+ */
+class NetCdfDistribution: Distribution {
+    override val mediaType: String get() = "application/x-netcdf"
+}

binary-array-ld-netcdf/src/main/kotlin/net/bald/netcdf/NetCdfDistribution.kt

@@ -0,0 +1,13 @@
+package net.bald.netcdf
+
+import net.bald.Format
+import org.apache.jena.rdf.model.Resource
+import org.apache.jena.rdf.model.ResourceFactory
+
+/**
+ * NetCDF implementation of [Format].
+ */
+object NetCdfFormat: Format {
+    override val identifier: Resource
+        get() = ResourceFactory.createResource("http://vocab.nerc.ac.uk/collection/M01/current/NC/")
+}

binary-array-ld-netcdf/src/main/kotlin/net/bald/netcdf/NetCdfFormat.kt

@@ -12,7 +12,10 @@ class NetCdfRootContainer(
     private val ba: NetCdfBinaryArray,
     group: Group,
 ): NetCdfContainer(group) {
-    override val uri: String get() = ba.uri + "/"
+    override val uri: String get() {
+        val uri = ba.uri
+        return if (uri.endsWith("/")) uri else "$uri/"
+    }
     override val alias: AliasDefinition get() = ba.alias
     override val parent: NetCdfContainer? get() = null
     override val root: NetCdfContainer get() = this