Merge branch 'master' of github.com:binary-array-ld/net.binary_array_ld.bald

simonoakesepimorphics · simonoakesepimorphics · commit 10c7c226e478 · 2021-07-30T13:40:04.000+01:00
diff --git a/README.md b/README.md
@@ -22,6 +22,3 @@ the `ncgen` command line tool must be available on your system.
 
 You can use Maven to build this project and each of its modules with `mvn clean package`.
 After building, the JAR for the command line application is located at `binary-array-ld-cli/target/bald-cli.jar`.
-
-
-
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
@@ -21,6 +21,7 @@ class BinaryArrayConvertCli {
         addOption("a", "alias", true, "Comma-delimited list of RDF alias files.")
         addOption("c", "context", true, "Comma-delimited list of JSON-LD context files.")
         addOption("o", "output", true, "Output format. eg. ttl, json-ld, rdfxml.")
+        addOption("d", "download", true, "The URL from which the original file can be downloaded.")
         addOption("h", "help", false, "Show help.")
     }
 
@@ -42,7 +43,7 @@ class BinaryArrayConvertCli {
         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)
+        val ba = NetCdfBinaryArray.create(inputLoc, opts.uri, context, alias, opts.downloadUrl)
         val model = ba.use(ModelBinaryArrayConverter::convert)
         val outputFormat = opts.outputFormat ?: "ttl"
 
diff --git a/binary-array-ld-cli/src/main/kotlin/net/bald/CommandLineOptions.kt b/binary-array-ld-cli/src/main/kotlin/net/bald/CommandLineOptions.kt
@@ -13,5 +13,6 @@ class CommandLineOptions(
     val aliasLocs: List<String> get() = cmd.getOptionValue("alias")?.split(",") ?: emptyList()
     val contextLocs: List<String> get() = cmd.getOptionValue("context")?.split(",") ?: emptyList()
     val outputFormat: String? get() = cmd.getOptionValue("output")
+    val downloadUrl: String? get() = cmd.getOptionValue("download")
     val help: Boolean get() = cmd.hasOption("help")
 }
diff --git a/binary-array-ld-cli/src/test/kotlin/net/bald/BinaryArrayConvertCliTest.kt b/binary-array-ld-cli/src/test/kotlin/net/bald/BinaryArrayConvertCliTest.kt
@@ -97,6 +97,33 @@ class BinaryArrayConvertCliTest {
         }
     }
 
+    @Test
+    fun run_withDownloadUrl_outputsDownloadUrl() {
+        val inputFile = writeToNetCdf("/netcdf/identity.cdl")
+        val outputFile = createTempFile()
+        run(
+            "--uri", "http://test.binary-array-ld.net/example",
+            "--download", "http://test.binary-array-ld.net/download/example.nc",
+            inputFile.absolutePath,
+            outputFile.absolutePath
+        )
+
+        val model = createDefaultModel().read(outputFile.toURI().toString(), "ttl")
+        ModelVerifier(model).apply {
+            resource("http://test.binary-array-ld.net/example/") {
+                format()
+                statement(RDF.type, BALD.Container)
+                distribution("http://test.binary-array-ld.net/download/example.nc")
+                statement(BALD.contains, model.createResource("http://test.binary-array-ld.net/example/var0")) {
+                    statement(RDF.type, BALD.Resource)
+                }
+                statement(BALD.contains, model.createResource("http://test.binary-array-ld.net/example/var1")) {
+                    statement(RDF.type, BALD.Resource)
+                }
+            }
+        }
+    }
+
     @Test
     fun run_withOutputFormat_outputsToFile() {
         val inputFile = writeToNetCdf("/netcdf/identity.cdl")
@@ -569,9 +596,10 @@ class BinaryArrayConvertCliTest {
         }
     }
 
-    private fun StatementsVerifier.distribution() {
+    private fun StatementsVerifier.distribution(downloadUrl: String? = null) {
         statement(DCAT.distribution) {
             statement(RDF.type, DCAT.Distribution)
+            if (downloadUrl != null) statement(DCAT.downloadURL, createResource(downloadUrl))
             statement(DCAT.mediaType) {
                 statement(DCTerms.identifier, createStringLiteral("application/x-netcdf"))
                 statement(RDF.type, DCTerms.MediaType)
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
@@ -27,7 +27,7 @@ public static void convert() throws Exception {
     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);
+        BinaryArray ba = NetCdfBinaryArray.create("/path/to/input.nc", "http://test.binary-array-ld.net/example", context, null, null);
         Model model = ModelBinaryArrayConverter.convert(ba);
 
         try (OutputStream output = new FileOutputStream("/path/to/output.ttl")) {
@@ -38,7 +38,7 @@ public static void convertWithExternalPrefixes() throws Exception {
     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);
+        BinaryArray ba = NetCdfBinaryArray.create("/path/to/input.nc", "http://test.binary-array-ld.net/example", null, alias, null);
         Model model = ModelBinaryArrayConverter.convert(ba);
 
         try (OutputStream output = new FileOutputStream("/path/to/output.ttl")) {
diff --git a/binary-array-ld-lib/src/main/kotlin/net/bald/BinaryArray.kt b/binary-array-ld-lib/src/main/kotlin/net/bald/BinaryArray.kt
@@ -28,5 +28,4 @@ interface BinaryArray: Closeable {
      * The distribution of the binary array, if it is available. Otherwise, null.
      */
     val distribution: Distribution?
-
 }
diff --git a/binary-array-ld-lib/src/main/kotlin/net/bald/Distribution.kt b/binary-array-ld-lib/src/main/kotlin/net/bald/Distribution.kt
@@ -1,5 +1,7 @@
 package net.bald
 
+import org.apache.jena.rdf.model.Resource
+
 /**
  * A distribution of a binary array file.
  */
@@ -8,4 +10,10 @@ interface Distribution {
      * The media type of the binary array file.
      */
     val mediaType: String
+
+    /**
+     * The URL from which this distribution of the file can be downloaded, if it has one.
+     * Otherwise, null.
+     */
+    val downloadUrl: Resource?
 }
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
@@ -42,6 +42,11 @@ class ModelBinaryArrayBuilder(
             val distribution = model.createResource()
                 .addProperty(RDF.type, DCAT.Distribution)
                 .addProperty(DCAT.mediaType, mediaType)
+                .apply {
+                    dist.downloadUrl?.let { downloadUrl ->
+                        addProperty(DCAT.downloadURL, downloadUrl)
+                    }
+                }
             root.addProperty(DCAT.distribution, distribution)
         }
     }
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
@@ -36,6 +36,7 @@ class ModelBinaryArrayBuilderTest {
     }
     private val distribution = mock<Distribution> {
         on { mediaType } doReturn "application/x-netcdf"
+        on { downloadUrl } doReturn createResource("http://test.binary-array-ld.net/download/example.nc")
     }
     private val ba = mock<BinaryArray> {
         on { this.root } doReturn root
@@ -93,7 +94,7 @@ class ModelBinaryArrayBuilderTest {
         ModelVerifier(model).apply {
             resource("http://test.binary-array-ld.net/example/") {
                 format()
-                distribution()
+                distribution("http://test.binary-array-ld.net/download/example.nc")
             }
         }
     }
diff --git a/binary-array-ld-lib/src/test/kotlin/net/bald/model/StatementsVerifierExt.kt b/binary-array-ld-lib/src/test/kotlin/net/bald/model/StatementsVerifierExt.kt
@@ -2,21 +2,22 @@ package net.bald.model
 
 import bald.model.StatementsVerifier
 import org.apache.jena.rdf.model.ResourceFactory
+import org.apache.jena.rdf.model.ResourceFactory.createResource
 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(DCTerms.identifier, createResource("http://vocab.nerc.ac.uk/collection/M01/current/NC/"))
         statement(RDF.type, DCTerms.MediaType)
     }
 }
 
-fun StatementsVerifier.distribution() {
+fun StatementsVerifier.distribution(downloadUrl: String? = null) {
     statement(DCAT.distribution) {
         statement(RDF.type, DCAT.Distribution)
+        if (downloadUrl != null) statement(DCAT.downloadURL, createResource(downloadUrl))
         statement(DCAT.mediaType) {
             statement(DCTerms.identifier, ResourceFactory.createStringLiteral("application/x-netcdf"))
             statement(RDF.type, DCTerms.MediaType)
diff --git a/binary-array-ld-netcdf/src/main/kotlin/net/bald/netcdf/NetCdfBinaryArray.kt b/binary-array-ld-netcdf/src/main/kotlin/net/bald/netcdf/NetCdfBinaryArray.kt
@@ -5,12 +5,14 @@ import net.bald.Distribution
 import net.bald.Format
 import net.bald.alias.AliasDefinition
 import net.bald.context.ModelContext
+import org.apache.jena.rdf.model.ResourceFactory.createResource
 import org.apache.jena.shared.PrefixMapping
 import ucar.nc2.AttributeContainer
 import ucar.nc2.Group
 import ucar.nc2.NetcdfFile
 import ucar.nc2.NetcdfFiles
 import java.io.File
+import java.net.URI
 
 /**
  * NetCDF implementation of [BinaryArray].
@@ -20,7 +22,8 @@ class NetCdfBinaryArray(
     val uri: String,
     private val file: NetcdfFile,
     private val context: ModelContext,
-    val alias: AliasDefinition
+    val alias: AliasDefinition,
+    private val downloadUrl: String?
 ): BinaryArray {
     override val root: NetCdfContainer get() = container(file.rootGroup)
 
@@ -32,7 +35,19 @@ class NetCdfBinaryArray(
     }
 
     override val format: Format get() = NetCdfFormat
-    override val distribution: Distribution get() = NetCdfDistribution()
+
+    override val distribution: Distribution get() {
+        val downloadUrl = downloadUrl ?: file.location.takeIf(::isHttp)
+        val res = downloadUrl?.let(::createResource)
+        return NetCdfDistribution(res)
+    }
+
+    private fun isHttp(loc: String): Boolean {
+        return try {
+            val scheme = URI(loc).scheme
+            scheme == "http" || scheme == "https"
+        } catch (e: Exception) { false }
+    }
 
     val prefixSrc: String? get() = prefixSourceName()
 
@@ -75,18 +90,20 @@ class NetCdfBinaryArray(
          * @param uri The URI which identifies the dataset.
          * @param context The external context with which to resolve prefix mappings.
          * @param alias The alias definition with which to resolve resource and property references.
+         * @param downloadUrl The URL from which the file can be downloaded, if it has one. Otherwise, null.
          * @return A [BinaryArray] representation of the NetCDF file.
          */
         @JvmStatic
         fun create(
             fileLoc: String,
             uri: String? = null,
             context: ModelContext? = null,
-            alias: AliasDefinition? = null
+            alias: AliasDefinition? = null,
+            downloadUrl: String? = null
         ): NetCdfBinaryArray {
             val file = NetcdfFiles.open(fileLoc)
             val requiredUri = uri ?: uri(fileLoc)
-            return create(file, requiredUri, context, alias)
+            return create(file, requiredUri, context, alias, downloadUrl)
         }
 
         /**
@@ -105,11 +122,12 @@ class NetCdfBinaryArray(
             file: NetcdfFile,
             uri: String,
             context: ModelContext? = null,
-            alias: AliasDefinition? = null
+            alias: AliasDefinition? = null,
+            downloadUrl: String? = null
         ): NetCdfBinaryArray {
             val requiredContext = context ?: ModelContext.Empty
             val requiredAlias = alias ?: AliasDefinition.Empty
-            return NetCdfBinaryArray(uri, file, requiredContext, requiredAlias)
+            return NetCdfBinaryArray(uri, file, requiredContext, requiredAlias, downloadUrl)
         }
 
         private fun uri(fileLoc: String): String {
diff --git a/binary-array-ld-netcdf/src/main/kotlin/net/bald/netcdf/NetCdfDistribution.kt b/binary-array-ld-netcdf/src/main/kotlin/net/bald/netcdf/NetCdfDistribution.kt
@@ -1,10 +1,13 @@
 package net.bald.netcdf
 
 import net.bald.Distribution
+import org.apache.jena.rdf.model.Resource
 
 /**
  * NetCDF implementation of [Distribution].
  */
-class NetCdfDistribution: Distribution {
+class NetCdfDistribution(
+    override val downloadUrl: Resource? = null
+): Distribution {
     override val mediaType: String get() = "application/x-netcdf"
 }
diff --git a/binary-array-ld-netcdf/src/test/kotlin/net/bald/netcdf/NetCdfBinaryArrayTest.kt b/binary-array-ld-netcdf/src/test/kotlin/net/bald/netcdf/NetCdfBinaryArrayTest.kt
@@ -18,12 +18,19 @@ import org.apache.jena.vocabulary.SKOS
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.assertThrows
 import kotlin.test.assertEquals
+import kotlin.test.assertNull
 
 class NetCdfBinaryArrayTest {
 
-    private fun fromCdl(cdlLoc: String, uri: String? = null, context: ModelContext? = null, alias: AliasDefinition? = null): BinaryArray {
+    private fun fromCdl(
+        cdlLoc: String,
+        uri: String? = null,
+        context: ModelContext? = null,
+        alias: AliasDefinition? = null,
+        downloadUrl: String? = null
+    ): BinaryArray {
         val file = writeToNetCdf(cdlLoc)
-        return NetCdfBinaryArray.create(file.absolutePath, uri, context, alias)
+        return NetCdfBinaryArray.create(file.absolutePath, uri, context, alias, downloadUrl)
     }
 
     /**
@@ -47,6 +54,24 @@ class NetCdfBinaryArrayTest {
         assertEquals(expectedUri, ba.uri)
     }
 
+    @Test
+    fun distribution_withDownloadUrl_returnsDistribution() {
+        val downloadUrl = "http://test.binary-array-ld.net/download/identity.nc"
+        val ba = fromCdl("/netcdf/identity.cdl", "http://test.binary-array-ld.net/identity.nc", downloadUrl = downloadUrl)
+        val distribution = ba.distribution
+        assertEquals(downloadUrl, distribution?.downloadUrl?.uri)
+        assertEquals("application/x-netcdf", distribution?.mediaType)
+    }
+
+    @Test
+    fun distribution_withoutDownloadUrl_returnsEmptyDistribution() {
+        val ba = fromCdl("/netcdf/identity.cdl", "http://test.binary-array-ld.net/identity.nc")
+        val distribution = ba.distribution
+        assertNull(distribution?.downloadUrl?.uri)
+        assertEquals("application/x-netcdf", distribution?.mediaType)
+    }
+
+
     /**
      * Requirements class A-2
      */
diff --git a/docs/CNAME b/docs/CNAME
@@ -0,0 +1 @@
+kotlin.binary-array-ld.net
diff --git a/docs/alias.md b/docs/alias.md
@@ -40,7 +40,7 @@ and an alias definition to create a `BinaryArray` with both.
 ```java
 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);
+BinaryArray ba = NetCdfBinaryArray.create("/path/to/input.nc", "http://test.binary-array-ld.net/example", null, alias, null);
 Model model = ModelBinaryArrayConverter.convert(ba);
 
 try (OutputStream output = new FileOutputStream("/path/to/output.ttl")) {
diff --git a/docs/cli.md b/docs/cli.md
@@ -46,6 +46,10 @@ You can find the documentation for this feature [here](context.md#cli).
 The CLI supports [aliases](alias.md).
 You can find the documentation for this feature [here](alias.md#cli).
 
+### Download URL
+
+The CLI supports [download URLs](download.md).
+
 ### Quick Reference
 
 You can supply command line options in long form with the `--` prefix or short form with `-`,
@@ -57,4 +61,5 @@ followed by their value.
 | --uri | -u | The URI which identifies the dataset. | Input file URI |
 | --output | -o | Output format, eg. ttl, json-ld, rdfxml. | ttl |
 | --context | -c | Comma-delimited list of JSON-LD context files. ||
-| --alias | -a | Comma-delimited list of RDF alias files. ||
+| --alias | -a | Comma-delimited list of RDF alias files. ||
+| --download | -d | The URL from which the original file can be downloaded, if available. ||
diff --git a/docs/context.md b/docs/context.md
@@ -30,7 +30,7 @@ to create a `BinaryArray` with both.
 ```java
 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);
+BinaryArray ba = NetCdfBinaryArray.create("/path/to/input.nc", "http://test.binary-array-ld.net/example", context, null, null);
 Model model = ModelBinaryArrayConverter.convert(ba);
 
 try (OutputStream output = new FileOutputStream("/path/to/output.ttl")) {
diff --git a/docs/download.md b/docs/download.md
@@ -0,0 +1,32 @@
+# Download URL
+
+The BALD CLI and library allow you to specify a download URL for the given NetCDF file,
+as described in the [draft specification](http://docs.opengeospatial.org/DRAFTS/19-002.html#_download_url).
+
+If you don't specify a download URL, but the given location of the NetCDF file is a remote URL (ie. it has `http` or `https` scheme),
+then the download URL will be inferred to be the same.
+
+## CLI
+
+You can optionally provide the download URL as a command line argument.
+Use the `--download` or `-d` option to specify the download URL for the NetCDF file.
+
+#### Example
+```
+java -jar bald-cli.jar --download http://test.binary-array-ld.net/download/netcdf.nc /path/to/netcdf.nc /path/to/graph.ttl
+```
+
+## Library
+
+You can optionally provide the download URL as a parameter to the `NetCdfBinaryArray.create` method.
+Otherwise, you can simply pass in a null value.
+
+#### Example
+```java
+BinaryArray ba = NetCdfBinaryArray.create("/path/to/input.ttl", "http://test.binary-array-ld.net/example", null, null, "http://test.binary-array-ld.net/download/netcdf.nc");
+Model model = ModelBinaryArrayConverter.convert(ba);
+
+try (OutputStream output = new FileOutputStream("/path/to/output.ttl")) {
+    model.write(output, "ttl");
+}
+```
diff --git a/docs/lib.md b/docs/lib.md
diff --git a/docs/usage.md b/docs/usage.md

Original file line number	Diff line number	Diff line change
`@@ -13,5 +13,6 @@ class CommandLineOptions(`
`13`	`13`	`val aliasLocs: List<String> get() = cmd.getOptionValue("alias")?.split(",") ?: emptyList()`
`14`	`14`	`val contextLocs: List<String> get() = cmd.getOptionValue("context")?.split(",") ?: emptyList()`
`15`	`15`	`val outputFormat: String? get() = cmd.getOptionValue("output")`
	`16`	`+ val downloadUrl: String? get() = cmd.getOptionValue("download")`
`16`	`17`	`val help: Boolean get() = cmd.hasOption("help")`
`17`	`18`	`}`
Original file line number	Diff line number	Diff line change
`@@ -28,5 +28,4 @@ interface BinaryArray: Closeable {`
`28`	`28`	`* The distribution of the binary array, if it is available. Otherwise, null.`
`29`	`29`	`*/`
`30`	`30`	`val distribution: Distribution?`
`31`		`-`
`32`	`31`	`}`
Original file line number	Diff line number	Diff line change
`@@ -42,6 +42,11 @@ class ModelBinaryArrayBuilder(`
`42`	`42`	`val distribution = model.createResource()`
`43`	`43`	`.addProperty(RDF.type, DCAT.Distribution)`
`44`	`44`	`.addProperty(DCAT.mediaType, mediaType)`
	`45`	`+ .apply {`
	`46`	`+ dist.downloadUrl?.let { downloadUrl ->`
	`47`	`+ addProperty(DCAT.downloadURL, downloadUrl)`
	`48`	`+ }`
	`49`	`+ }`
`45`	`50`	`root.addProperty(DCAT.distribution, distribution)`
`46`	`51`	`}`
`47`	`52`	`}`
Original file line number	Diff line number	Diff line change
`@@ -36,6 +36,7 @@ class ModelBinaryArrayBuilderTest {`
`36`	`36`	`}`
`37`	`37`	`private val distribution = mock<Distribution> {`
`38`	`38`	`on { mediaType } doReturn "application/x-netcdf"`
	`39`	`+ on { downloadUrl } doReturn createResource("http://test.binary-array-ld.net/download/example.nc")`
`39`	`40`	`}`
`40`	`41`	`private val ba = mock<BinaryArray> {`
`41`	`42`	`on { this.root } doReturn root`
`@@ -93,7 +94,7 @@ class ModelBinaryArrayBuilderTest {`
`93`	`94`	`ModelVerifier(model).apply {`
`94`	`95`	`resource("http://test.binary-array-ld.net/example/") {`
`95`	`96`	`format()`
`96`		`- distribution()`
	`97`	`+ distribution("http://test.binary-array-ld.net/download/example.nc")`
`97`	`98`	`}`
`98`	`99`	`}`
`99`	`100`	`}`