Merge branch 'master' of github.com:binary-array-ld/net.binary_array_…

…ld.bald
binary-array-ld · Aug 27, 2021 · 7a2c799 · 7a2c799
2 parents f9626bc + f96aaf3
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diff --git a/binary-array-ld-api/pom.xml b/binary-array-ld-api/pom.xml
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <parent>
+        <artifactId>binary-array-ld</artifactId>
+        <groupId>net.binary-array-ld</groupId>
+        <version>1.0.0-SNAPSHOT</version>
+    </parent>
+    <modelVersion>4.0.0</modelVersion>
+
+    <artifactId>binary-array-ld-api</artifactId>
+    <packaging>jar</packaging>
+
+    <name>Binary Array Linked Data - API</name>
+    <description>API for Binary Array LD functionality.</description>
+
+    <dependencies>
+        <!-- LIB -->
+        <dependency>
+            <groupId>org.apache.jena</groupId>
+            <artifactId>jena-core</artifactId>
+            <version>${jena.version}</version>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.jetbrains.dokka</groupId>
+                <artifactId>dokka-maven-plugin</artifactId>
+            </plugin>
+        </plugins>
+    </build>
+
+</project>
diff --git a/...lib/src/main/kotlin/net/bald/Attribute.kt → ...api/src/main/kotlin/net/bald/Attribute.kt b/...lib/src/main/kotlin/net/bald/Attribute.kt → ...api/src/main/kotlin/net/bald/Attribute.kt
diff --git a/...c/main/kotlin/net/bald/AttributeSource.kt → ...c/main/kotlin/net/bald/AttributeSource.kt b/...c/main/kotlin/net/bald/AttributeSource.kt → ...c/main/kotlin/net/bald/AttributeSource.kt
diff --git a/...b/src/main/kotlin/net/bald/BinaryArray.kt → ...i/src/main/kotlin/net/bald/BinaryArray.kt b/...b/src/main/kotlin/net/bald/BinaryArray.kt → ...i/src/main/kotlin/net/bald/BinaryArray.kt
diff --git a/...lib/src/main/kotlin/net/bald/Container.kt → ...api/src/main/kotlin/net/bald/Container.kt b/...lib/src/main/kotlin/net/bald/Container.kt → ...api/src/main/kotlin/net/bald/Container.kt
diff --git a/binary-array-ld-api/src/main/kotlin/net/bald/Converter.kt b/binary-array-ld-api/src/main/kotlin/net/bald/Converter.kt
@@ -0,0 +1,27 @@
+package net.bald
+
+import org.apache.jena.rdf.model.Model
+import java.net.URI
+
+/**
+ * A binary array to linked data converter.
+ */
+interface Converter {
+    /**
+     * Convert a binary array file to a linked data graph.
+     * @param input The location of the NetCDF binary array file to convert.
+     * @param uri The URI that identifies the binary array.
+     * @param contexts The location of files containing JSON-LD contexts.
+     * @param aliases The location of files containing alias definitions.
+     * @param downloadUrl The URL from which the NetCDF file can be downloaded, if one exists. Otherwise, null.
+     * @return The linked data graph.
+     */
+    fun convert(
+        input: URI,
+        uri: String? = null,
+        contexts: List<URI>? = null,
+        aliases: List<URI>? = null,
+        downloadUrl: String? = null
+    ): Model
+}
+
diff --git a/...c/main/kotlin/net/bald/CoordinateRange.kt → ...c/main/kotlin/net/bald/CoordinateRange.kt b/...c/main/kotlin/net/bald/CoordinateRange.kt → ...c/main/kotlin/net/bald/CoordinateRange.kt
diff --git a/...lib/src/main/kotlin/net/bald/Dimension.kt → ...api/src/main/kotlin/net/bald/Dimension.kt b/...lib/src/main/kotlin/net/bald/Dimension.kt → ...api/src/main/kotlin/net/bald/Dimension.kt
diff --git a/.../src/main/kotlin/net/bald/Distribution.kt → .../src/main/kotlin/net/bald/Distribution.kt b/.../src/main/kotlin/net/bald/Distribution.kt → .../src/main/kotlin/net/bald/Distribution.kt
diff --git a/...ld-lib/src/main/kotlin/net/bald/Format.kt → ...ld-api/src/main/kotlin/net/bald/Format.kt b/...ld-lib/src/main/kotlin/net/bald/Format.kt → ...ld-api/src/main/kotlin/net/bald/Format.kt
diff --git a/...ay-ld-lib/src/main/kotlin/net/bald/Var.kt → ...ay-ld-api/src/main/kotlin/net/bald/Var.kt b/...ay-ld-lib/src/main/kotlin/net/bald/Var.kt → ...ay-ld-api/src/main/kotlin/net/bald/Var.kt
diff --git a/.../kotlin/net/bald/alias/AliasDefinition.kt → .../kotlin/net/bald/alias/AliasDefinition.kt b/.../kotlin/net/bald/alias/AliasDefinition.kt → .../kotlin/net/bald/alias/AliasDefinition.kt
diff --git a/...n/kotlin/net/bald/context/ModelContext.kt → ...n/kotlin/net/bald/context/ModelContext.kt b/...n/kotlin/net/bald/context/ModelContext.kt → ...n/kotlin/net/bald/context/ModelContext.kt
diff --git a/...ib/src/main/kotlin/net/bald/vocab/BALD.kt → ...pi/src/main/kotlin/net/bald/vocab/BALD.kt b/...ib/src/main/kotlin/net/bald/vocab/BALD.kt → ...pi/src/main/kotlin/net/bald/vocab/BALD.kt
diff --git a/binary-array-ld-cli/pom.xml b/binary-array-ld-cli/pom.xml
@@ -27,6 +27,16 @@
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-arq</artifactId>
             <version>${jena.version}</version>
+            <exclusions>
+                <exclusion>
+                    <artifactId>jackson-core</artifactId>
+                    <groupId>com.fasterxml.jackson.core</groupId>
+                </exclusion>
+                <exclusion>
+                    <artifactId>jackson-databind</artifactId>
+                    <groupId>com.fasterxml.jackson.core</groupId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>net.binary-array-ld</groupId>

diff --git a/binary-array-ld-cli/src/main/kotlin/net/bald/BinaryArrayConvertCli.kt b/binary-array-ld-cli/src/main/kotlin/net/bald/BinaryArrayConvertCli.kt
@@ -1,15 +1,13 @@
 package net.bald
 
-import net.bald.alias.AliasDefinition
-import net.bald.context.ModelContext
-import net.bald.alias.ModelAliasDefinition
-import net.bald.model.ModelBinaryArrayConverter
-import net.bald.netcdf.NetCdfBinaryArray
+import net.bald.netcdf.NetCdfLdConverter
 import org.apache.commons.cli.DefaultParser
 import org.apache.commons.cli.HelpFormatter
 import org.apache.commons.cli.Options
-import org.apache.jena.rdf.model.ModelFactory
-import java.io.*
+import java.io.File
+import java.io.FilterOutputStream
+import java.io.OutputStream
+import java.net.URI
 import kotlin.system.exitProcess
 
 /**
@@ -40,32 +38,20 @@ class BinaryArrayConvertCli {
     }
 
     private fun doRun(opts: CommandLineOptions) {
-        val context = context(opts.contextLocs)
-        val alias = alias(opts.aliasLocs)
-        val inputLoc = opts.inputLoc ?: throw IllegalArgumentException("First argument is required: NetCDF file to convert.")
-        val ba = NetCdfBinaryArray.create(inputLoc, opts.uri, context, alias, opts.downloadUrl)
-        val model = ba.use(ModelBinaryArrayConverter::convert)
+        val input = opts.inputLoc?.let(::URI) ?: throw IllegalArgumentException("First argument is required: NetCDF file to convert.")
+        val uri = opts.uri
+        val context = opts.contextLocs.map(::URI)
+        val alias = opts.aliasLocs.map(::URI)
+        val downloadUrl = opts.downloadUrl
+
+        val model = NetCdfLdConverter.getInstance().convert(input, uri, context, alias, downloadUrl)
         val outputFormat = opts.outputFormat ?: "ttl"
 
         modelOutput(opts.outputLoc).use { output ->
             model.write(output, outputFormat)
         }
     }
 
-    private fun context(contextLocs: List<String>): ModelContext {
-        val prefixes = contextLocs.map { contextLoc ->
-            ModelFactory.createDefaultModel().read(contextLoc, "json-ld")
-        }
-
-        return ModelContext.create(prefixes)
-    }
-
-    private fun alias(aliasLocs: List<String>): AliasDefinition {
-        return ModelFactory.createDefaultModel().apply {
-            aliasLocs.forEach(::read)
-        }.let(ModelAliasDefinition::create)
-    }
-
     private fun options(opts: Options, vararg args: String): CommandLineOptions {
         return DefaultParser().parse(opts, args).let(::CommandLineOptions)
     }

diff --git a/binary-array-ld-cli/src/test/kotlin/net/bald/BinaryArrayConvertSpecTest.kt b/binary-array-ld-cli/src/test/kotlin/net/bald/BinaryArrayConvertSpecTest.kt
@@ -0,0 +1,8 @@
+package net.bald
+
+import bald.spec.BaseSpecTest
+import net.bald.netcdf.NetCdfLdConverter
+
+class BinaryArrayConvertSpecTest: BaseSpecTest() {
+    override val converter: Converter = NetCdfLdConverter.getInstance()
+}
diff --git a/binary-array-ld-demo/src/main/java/net/bald/NetCdfConvertJava.java b/binary-array-ld-demo/src/main/java/net/bald/NetCdfConvertJava.java
@@ -1,45 +1,51 @@
 package net.bald;
 
-import net.bald.alias.AliasDefinition;
-import net.bald.context.ModelContext;
-import net.bald.alias.ModelAliasDefinition;
-import net.bald.model.ModelBinaryArrayConverter;
-import net.bald.netcdf.NetCdfBinaryArray;
+import net.bald.netcdf.NetCdfLdConverter;
 import org.apache.jena.rdf.model.Model;
-import org.apache.jena.rdf.model.ModelFactory;
-import org.apache.jena.shared.PrefixMapping;
+
+import java.io.File;
 import java.io.FileOutputStream;
 import java.io.OutputStream;
+import java.net.URI;
+import java.util.Arrays;
 
 /**
  * Demonstration of how to call the API in Java code.
  */
 public class NetCdfConvertJava {
     public static void convert() throws Exception {
-        BinaryArray ba = NetCdfBinaryArray.create("/path/to/input.nc", "http://test.binary-array-ld.net/example");
-        Model model = ModelBinaryArrayConverter.convert(ba);
+        URI input = new File("/path/to/input.nc").toURI();
+        Model model = NetCdfLdConverter.Companion.getInstance().convert(input, "http://test.binary-array-ld.net/example", null, null, null);
 
         try (OutputStream output = new FileOutputStream("/path/to/output.ttl")) {
             model.write(output, "ttl");
         }
     }
 
     public static void convertWithExternalPrefixes() throws Exception {
-        PrefixMapping prefix = ModelFactory.createDefaultModel().read("/path/to/context.json", "json-ld");
-        ModelContext context = ModelContext.create(prefix);
-        BinaryArray ba = NetCdfBinaryArray.create("/path/to/input.nc", "http://test.binary-array-ld.net/example", context, null, null);
-        Model model = ModelBinaryArrayConverter.convert(ba);
+        URI input = new File("/path/to/input.nc").toURI();
+        URI context = new File("/path/to/context.json").toURI();
+        Model model = NetCdfLdConverter.Companion.getInstance().convert(input, "http://test.binary-array-ld.net/example", Arrays.asList(context), null, null);
 
         try (OutputStream output = new FileOutputStream("/path/to/output.ttl")) {
             model.write(output, "ttl");
         }
     }
 
     public static void convertWithAliases() throws Exception {
-        Model aliasModel = ModelFactory.createDefaultModel().read("/path/to/alias.ttl", "ttl");
-        AliasDefinition alias = ModelAliasDefinition.create(aliasModel);
-        BinaryArray ba = NetCdfBinaryArray.create("/path/to/input.nc", "http://test.binary-array-ld.net/example", null, alias, null);
-        Model model = ModelBinaryArrayConverter.convert(ba);
+        URI input = new File("/path/to/input.nc").toURI();
+        URI alias = new File("/path/to/alias.ttl").toURI();
+        Model model = NetCdfLdConverter.Companion.getInstance().convert(input, "http://test.binary-array-ld.net/example", null, Arrays.asList(alias), null);
+
+        try (OutputStream output = new FileOutputStream("/path/to/output.ttl")) {
+            model.write(output, "ttl");
+        }
+    }
+
+    public static void convertWithDownloadUrl() throws Exception {
+        String downloadUrl = "http://test.binary-array-ld.net/download/netcdf.nc";
+        URI input = new File("/path/to/input.nc").toURI();
+        Model model = NetCdfLdConverter.Companion.getInstance().convert(input, "http://test.binary-array-ld.net/example", null, null, downloadUrl);
 
         try (OutputStream output = new FileOutputStream("/path/to/output.ttl")) {
             model.write(output, "ttl");

diff --git a/binary-array-ld-lib/pom.xml b/binary-array-ld-lib/pom.xml
@@ -18,6 +18,11 @@
 
     <dependencies>
         <!-- LIB -->
+        <dependency>
+            <groupId>net.binary-array-ld</groupId>
+            <artifactId>binary-array-ld-api</artifactId>
+            <version>${project.parent.version}</version>
+        </dependency>
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-core</artifactId>
@@ -47,6 +52,13 @@
             <plugin>
                 <groupId>org.jetbrains.dokka</groupId>
                 <artifactId>dokka-maven-plugin</artifactId>
+                <configuration>
+                    <externalDocumentationLinks>
+                        <link>
+                            <url>http://kotlin.binary-array-ld.net/javadoc/binary-array-ld-api</url>
+                        </link>
+                    </externalDocumentationLinks>
+                </configuration>
             </plugin>
         </plugins>
     </build>

diff --git a/...in/net/bald/alias/ModelAliasDefinition.kt → ...in/net/bald/model/ModelAliasDefinition.kt b/...in/net/bald/alias/ModelAliasDefinition.kt → ...in/net/bald/model/ModelAliasDefinition.kt
@@ -1,5 +1,6 @@
-package net.bald.alias
+package net.bald.model
 
+import net.bald.alias.AliasDefinition
 import net.bald.vocab.BALD
 import org.apache.jena.rdf.model.*
 import org.apache.jena.riot.RDFLanguages

diff --git a/binary-array-ld-lib/src/main/kotlin/net/bald/model/ModelBinaryArrayBuilder.kt b/binary-array-ld-lib/src/main/kotlin/net/bald/model/ModelBinaryArrayBuilder.kt
@@ -1,12 +1,8 @@
 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

diff --git a/binary-array-ld-lib/src/main/kotlin/net/bald/model/ModelBinaryArrayConverter.kt b/binary-array-ld-lib/src/main/kotlin/net/bald/model/ModelBinaryArrayConverter.kt
@@ -3,7 +3,6 @@ package net.bald.model
 import net.bald.BinaryArray
 import org.apache.jena.rdf.model.Model
 import org.apache.jena.rdf.model.ModelFactory
-import org.apache.jena.shared.PrefixMapping
 
 /**
  * API for converting a [BinaryArray] to a linked data [Model].

diff --git a/binary-array-ld-lib/src/main/kotlin/net/bald/model/ModelReferenceBuilder.kt b/binary-array-ld-lib/src/main/kotlin/net/bald/model/ModelReferenceBuilder.kt
@@ -3,9 +3,10 @@ package net.bald.model
 import net.bald.Dimension
 import net.bald.Var
 import net.bald.vocab.BALD
+import org.apache.jena.datatypes.xsd.XSDDatatype
 import org.apache.jena.rdf.model.Literal
 import org.apache.jena.rdf.model.Resource
-import org.apache.jena.rdf.model.ResourceFactory
+import org.apache.jena.rdf.model.ResourceFactory.createTypedLiteral
 import org.apache.jena.vocabulary.RDF
 
 class ModelReferenceBuilder(
@@ -40,13 +41,15 @@ class ModelReferenceBuilder(
 
         fun shape(dimIds: List<String>): Iterator<Literal> {
             return dimIds.asSequence().map { dimId ->
-                dimsById[dimId]?.size?.let(ResourceFactory::createTypedLiteral) ?: unitNode
+                dimsById[dimId]?.size?.let { size ->
+                    createTypedLiteral(size.toString(), XSDDatatype.XSDinteger)
+                } ?: unitNode
             }.iterator()
         }
     }
 
     companion object {
-        private val unitNode = ResourceFactory.createTypedLiteral(1)
+        private val unitNode = createTypedLiteral("1", XSDDatatype.XSDinteger)
     }
 
     open class Factory {

diff --git a/binary-array-ld-lib/src/main/kotlin/net/bald/model/ModelVarBuilder.kt b/binary-array-ld-lib/src/main/kotlin/net/bald/model/ModelVarBuilder.kt
@@ -4,7 +4,9 @@ import net.bald.AttributeSource
 import net.bald.Dimension
 import net.bald.Var
 import net.bald.vocab.BALD
-import org.apache.jena.rdf.model.*
+import org.apache.jena.datatypes.xsd.XSDDatatype
+import org.apache.jena.rdf.model.RDFNode
+import org.apache.jena.rdf.model.Resource
 import org.apache.jena.rdf.model.ResourceFactory.createTypedLiteral
 
 open class ModelVarBuilder(
@@ -24,9 +26,7 @@ open class ModelVarBuilder(
 
     private fun addAttributes(source: AttributeSource, resource: Resource) {
         val builder = attrFct.forResource(resource)
-        source.attributes().filterNot { attr ->
-            BALD.references.hasURI(attr.uri)
-        }.forEach(builder::addAttribute)
+        source.attributes().forEach(builder::addAttribute)
     }
 
     private fun addCoordinateRange(v: Var, resource: Resource) {
@@ -79,7 +79,7 @@ open class ModelVarBuilder(
         }
 
         private fun size(dim: Dimension): RDFNode {
-            return createTypedLiteral(dim.size)
+            return createTypedLiteral(dim.size.toString(), XSDDatatype.XSDinteger)
         }
 
         override fun addReferences(resource: Resource) {

diff --git a/binary-array-ld-lib/src/test/kotlin/net/bald/model/ModelAliasDefinitionTest.kt b/binary-array-ld-lib/src/test/kotlin/net/bald/model/ModelAliasDefinitionTest.kt
@@ -1,6 +1,5 @@
 package net.bald.model
 
-import net.bald.alias.ModelAliasDefinition
 import net.bald.vocab.BALD
 import org.apache.jena.rdf.model.ModelFactory
 import org.apache.jena.rdf.model.ResourceFactory.createProperty
@@ -9,7 +8,6 @@ import org.apache.jena.vocabulary.RDFS
 import org.apache.jena.vocabulary.SKOS
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.assertThrows
-import java.lang.IllegalStateException
 import kotlin.test.assertEquals
 import kotlin.test.assertFalse
 import kotlin.test.assertNull

diff --git a/binary-array-ld-lib/src/test/kotlin/net/bald/model/ModelAttributeBuilderTest.kt b/binary-array-ld-lib/src/test/kotlin/net/bald/model/ModelAttributeBuilderTest.kt
@@ -6,10 +6,10 @@ import com.nhaarman.mockitokotlin2.mock
 import com.nhaarman.mockitokotlin2.stub
 import net.bald.Attribute
 import org.apache.jena.rdf.model.ModelFactory
-import org.apache.jena.rdf.model.ResourceFactory.*
-import org.apache.jena.vocabulary.RDF
+import org.apache.jena.rdf.model.ResourceFactory.createPlainLiteral
+import org.apache.jena.rdf.model.ResourceFactory.createResource
 import org.apache.jena.vocabulary.RDFS
-import org.junit.jupiter.api.*
+import org.junit.jupiter.api.Test
 
 class ModelAttributeBuilderTest {
     private val uri = "http://test.binary-array-ld.net/example/var0"

diff --git a/binary-array-ld-lib/src/test/kotlin/net/bald/model/ModelBinaryArrayBuilderTest.kt b/binary-array-ld-lib/src/test/kotlin/net/bald/model/ModelBinaryArrayBuilderTest.kt
@@ -15,7 +15,6 @@ import org.apache.jena.shared.PrefixMapping
 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 {

diff --git a/binary-array-ld-lib/src/test/kotlin/net/bald/model/ModelBinaryArrayConverterTest.kt b/binary-array-ld-lib/src/test/kotlin/net/bald/model/ModelBinaryArrayConverterTest.kt
@@ -11,7 +11,7 @@ import org.apache.jena.shared.PrefixMapping
 import org.apache.jena.vocabulary.DCTerms
 import org.apache.jena.vocabulary.RDF
 import org.apache.jena.vocabulary.SKOS
-import org.junit.jupiter.api.*
+import org.junit.jupiter.api.Test
 
 /**
  * Test the full Binary Array -> Linked Data conversion process using a mock binary array.