Attributes (#22)

* Add vocab reference object

* Add classes for composing RDF model

* Add RDF model test utils and tests

* Add binary array to model conversion API impl

* Add NetCDF binary array factory method impl, tests

* Add CLI impl, test, docs

* Fix Java version in maven compiler plugin

* Add prefix mapping concept on binary array

* Add prefix mapping to model composition, tests

* Add NetCDF impl of prefix mapping concept

* Add tests, upgrade test format to NetCDF4 to support prefix group.

* Add logback config on CLI to suppress debug logs

* NetCDF4 considerations in tests

* Add option to supply external prefixes for NetCDF to model conversion

* Add external prefix / context parameter to CLI, add test

* Update Java example with external prefixes.

* Rename var

* Improve error message wording

* Add file container, refactor

* Add file container to tests

* Fix tests

* Add NetCDF URI parser class

* Replace BALD PrefixMapping concept with standard Jena PrefixMapping

* Add attribute, attribute source concepts

* Add NetCDF implementation of attribute concepts

* Add root group and variable attributes to RDF model composition

* Add attribute tests

* Add separate class for handling NetCDF attributes, hide reserved attributes.

* Fix existing tests

* Add attributes CLI test

* Changed test data to CDL format

* Fix test

* Remove NCML references

* Fix Java version on demo

* ADD name and subgroups to container concept

* Enhance binary array converter to describe subgroups

* Fix test consistency

* Add prefix var support

* Remove prefix group / var from graph

* Replace BALD prefix mapping concept with Jena prefix mapping

* Fix merge issue

* Use common test method

* Add prefix mapping validation

* Refactor the RDF context impl as a decorator

* Add prefix conflict validation

* Fix reduce on empty list

* Restore closeable interface

* Add extension function for URI composition

* Fix tests

* Tidy up

Author: simonoakesepimorphics

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

@@ -5,10 +5,8 @@ import bald.model.ModelVerifier
 import bald.netcdf.CdlConverter.writeToNetCdf
 import net.bald.vocab.BALD
 import org.apache.jena.rdf.model.ModelFactory.createDefaultModel
-import org.apache.jena.vocabulary.DCTerms
-import org.apache.jena.vocabulary.RDF
-import org.apache.jena.vocabulary.SKOS
-import org.apache.jena.vocabulary.XSD
+import org.apache.jena.rdf.model.ResourceFactory.*
+import org.apache.jena.vocabulary.*
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.assertThrows
 import java.io.File
@@ -101,6 +99,7 @@ class BinaryArrayConvertCliTest {
                     statement(BALD.contains, model.createResource("http://test.binary-array-ld.net/example/var1")) {
                         statement(RDF.type, BALD.Resource)
                     }
+                    statement(BALD.isPrefixedBy, createPlainLiteral("prefix_list"))
                 }
             }
         }
@@ -184,6 +183,43 @@ class BinaryArrayConvertCliTest {
                 statement(BALD.contains, model.createResource("http://test.binary-array-ld.net/example/var1")) {
                     statement(RDF.type, BALD.Resource)
                 }
+                statement(BALD.isPrefixedBy, createPlainLiteral("prefix_list"))
+            }
+        }
+    }
+
+    @Test
+    fun run_withAttributes_outputsAttributes() {
+        val inputFile = writeToNetCdf("/netcdf/attributes.cdl")
+        val outputFile = createTempFile()
+        val contextFile = ContextReader.toFile("/jsonld/context.json")
+
+        run(
+            "--uri", "http://test.binary-array-ld.net/example",
+            "--context", contextFile.absolutePath,
+            inputFile.absolutePath,
+            outputFile.absolutePath
+        )
+
+        val model = createDefaultModel().read(outputFile.toURI().toString(), "ttl")
+        ModelVerifier(model).apply {
+            prefix("bald", BALD.prefix)
+            prefix("skos", SKOS.uri)
+            prefix("dct", DCTerms.NS)
+            resource("http://test.binary-array-ld.net/example/") {
+                statement(DCTerms.publisher, createResource("${BALD.prefix}Organisation"))
+                statement(createProperty("http://test.binary-array-ld.net/example/date"), createPlainLiteral("2020-10-29"))
+                statement(RDF.type, BALD.Container)
+                statement(SKOS.prefLabel, createPlainLiteral("Attributes metadata example"))
+                statement(BALD.contains, model.createResource("http://test.binary-array-ld.net/example/var0")) {
+                    statement(RDF.type, BALD.Array)
+                    statement(RDF.type, BALD.Resource)
+                    statement(SKOS.prefLabel, createPlainLiteral("Variable 0"))
+                }
+                statement(BALD.contains, model.createResource("http://test.binary-array-ld.net/example/var1")) {
+                    statement(RDF.type, BALD.Resource)
+                }
+                statement(BALD.isPrefixedBy, createPlainLiteral("prefix_list"))
             }
         }
     }

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

@@ -0,0 +1,23 @@
+package net.bald
+
+import org.apache.jena.rdf.model.RDFNode
+
+/**
+ * A description of a property of an [AttributeSource] entity.
+ */
+interface Attribute {
+    /**
+     * The URI which identifies the attribute, if it has one. Otherwise, null.
+     */
+    val uri: String?
+
+    /**
+     * The local name of the attribute.
+     */
+    val name: String
+
+    /**
+     * The values of the attribute, expressed as RDF resource or literal nodes.
+     */
+    val values: List<RDFNode>
+}

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

@@ -0,0 +1,13 @@
+package net.bald
+
+/**
+ * An entity which is described by its [Attribute]s.
+ */
+interface AttributeSource {
+    /**
+     * Obtain the list of attributes that describe this entity.
+     * @param prefixMapping The prefix mapping to use to expand compact URIs.
+     * @return The list of attributes.
+     */
+    fun attributes(prefixMapping: org.apache.jena.shared.PrefixMapping): List<Attribute>
+}

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

@@ -4,7 +4,7 @@ package net.bald
  * Represents a container of resources.
  * See https://www.opengis.net/def/binary-array-ld/Container
  */
-interface Container {
+interface Container: AttributeSource {
     /**
      * The local name of the container, if it has one.
      * The root container may have no name or an empty name.

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

@@ -3,7 +3,7 @@ package net.bald
 /**
  * Represents a binary array variable.
  */
-interface Var {
+interface Var: AttributeSource {
     /**
      * The local name of the variable.
      */

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

@@ -0,0 +1,22 @@
+package net.bald.model
+
+import net.bald.Attribute
+import org.apache.jena.rdf.model.Resource
+
+open class ModelAttributeBuilder(
+    private val resource: Resource
+) {
+    open fun addAttribute(attr: Attribute) {
+        val propUri = attr.uri ?: resource.withTrailingSlash() + attr.name
+        val prop = resource.model.createProperty(propUri)
+        attr.values.forEach { value ->
+            resource.addProperty(prop, value)
+        }
+    }
+
+    open class Factory {
+        open fun forResource(resource: Resource): ModelAttributeBuilder {
+            return ModelAttributeBuilder(resource)
+        }
+    }
+}

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

@@ -10,8 +10,9 @@ import org.apache.jena.shared.PrefixMapping
  */
 object ModelBinaryArrayConverter {
     private val modelFct = run {
-        val varFct = ModelVarBuilder.Factory()
-        val containerFct = ModelContainerBuilder.Factory(varFct)
+        val attrFct = ModelAttributeBuilder.Factory()
+        val varFct = ModelVarBuilder.Factory(attrFct)
+        val containerFct = ModelContainerBuilder.Factory(varFct, attrFct)
         ModelBinaryArrayBuilder.Factory(containerFct)
     }
 

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

@@ -1,43 +1,45 @@
 package net.bald.model
 
+import net.bald.AttributeSource
 import net.bald.vocab.BALD
 import net.bald.Container
 import org.apache.jena.rdf.model.Resource
 
 open class ModelContainerBuilder(
     private val parent: Resource,
-    private val varFct: ModelVarBuilder.Factory
+    private val varFct: ModelVarBuilder.Factory,
+    private val attrFct: ModelAttributeBuilder.Factory
 ) {
     open fun addContainer(container: Container) {
-        val containerUri = containerUri(container)
+        val containerUri = parent.withTrailingSlash() + (container.name ?: "")
         val containerRes = parent.model.createResource(containerUri, BALD.Container)
-        buildSubgroups(container, containerRes)
-        buildVars(container, containerRes)
+        addSubContainers(container, containerRes)
+        addVars(container, containerRes)
+        addAttributes(container, containerRes)
         parent.addProperty(BALD.contains, containerRes)
     }
 
-    private fun containerUri(container: Container): String {
-        val parentUri = parent.uri
-        val prefix = if (parentUri.endsWith('/')) parentUri else "$parentUri/"
-        return prefix + (container.name ?: "")
+    private fun addSubContainers(container: Container, containerRes: Resource) {
+        val builder = ModelContainerBuilder(containerRes, varFct, attrFct)
+        container.subContainers().forEach(builder::addContainer)
     }
 
-    private fun buildSubgroups(container: Container, containerRes: Resource) {
-        val builder = ModelContainerBuilder(containerRes, varFct)
-        container.subContainers().forEach(builder::addContainer)
+    private fun addVars(container: Container, containerRes: Resource) {
+        val builder = varFct.forContainer(containerRes)
+        container.vars().forEach(builder::addVar)
     }
 
-    private fun buildVars(container: Container, containerRes: Resource) {
-        varFct.forContainer(containerRes).apply {
-            container.vars().forEach(::addVar)
-        }
+    private fun addAttributes(source: AttributeSource, resource: Resource) {
+        val builder = attrFct.forResource(resource)
+        source.attributes(resource.model).forEach(builder::addAttribute)
     }
 
     open class Factory(
-        private val varFct: ModelVarBuilder.Factory
+        private val varFct: ModelVarBuilder.Factory,
+        private val attrFct: ModelAttributeBuilder.Factory
     ) {
         open fun forParent(parent: Resource): ModelContainerBuilder {
-            return ModelContainerBuilder(parent, varFct)
+            return ModelContainerBuilder(parent, varFct, attrFct)
         }
     }
 }

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

@@ -1,28 +1,31 @@
 package net.bald.model
 
+import net.bald.AttributeSource
 import net.bald.Var
 import net.bald.vocab.BALD
 import org.apache.jena.rdf.model.Resource
-import org.apache.jena.vocabulary.RDF
 
 open class ModelVarBuilder(
-    private val container: Resource
+    private val container: Resource,
+    private val attrFct: ModelAttributeBuilder.Factory
 ) {
     open fun addVar(v: Var) {
-        val varUri = varUri(v)
+        val varUri = container.withTrailingSlash() + v.name
         val vRes = container.model.createResource(varUri, BALD.Resource)
         container.addProperty(BALD.contains, vRes)
+        addAttributes(v, vRes)
     }
 
-    private fun varUri(v: Var): String {
-        val containerUri = container.uri
-        val prefix = if (containerUri.endsWith('/')) containerUri else "$containerUri/"
-        return prefix + v.name
+    private fun addAttributes(source: AttributeSource, resource: Resource) {
+        val builder = attrFct.forResource(resource)
+        source.attributes(resource.model).forEach(builder::addAttribute)
     }
 
-    open class Factory {
+    open class Factory(
+        private val attrFct: ModelAttributeBuilder.Factory
+    ) {
         open fun forContainer(container: Resource): ModelVarBuilder {
-            return ModelVarBuilder(container)
+            return ModelVarBuilder(container, attrFct)
         }
     }
 }

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

@@ -0,0 +1,7 @@
+package net.bald.model
+
+import org.apache.jena.rdf.model.Resource
+
+fun Resource.withTrailingSlash(): String {
+    return if (uri.endsWith('/')) uri else "$uri/"
+}