RDF output format (#25)

* Add option to specify output format

* Remove unnecessary variable

Author: simonoakesepimorphics

README.md

@@ -77,6 +77,10 @@ Where `inputFile` is the location of the NetCDF file to convert,
 and `outputFile` is the location of the file in which to output the RDF graph.
 If you don't specify an `outputFile`, the graph will be printed on the command line.
 
+By default, the RDF graph output will be in [Turtle](https://www.w3.org/TR/turtle/) format.
+You can use the `--output` or `-o` option to specify the RDF format to emit.
+This option can accept any of the RDF formats supported by Apache Jena, eg. JSON-LD and RDFXML.
+
 You can also supply various options.
 Use the `-h` or `--help` option to emit full documentation for the available options.
 ```

binary-array-ld-cli/src/main/kotlin/net/bald/BinaryArrayConvertCli.kt

@@ -9,8 +9,7 @@ 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.File
-import java.io.OutputStream
+import java.io.*
 import kotlin.system.exitProcess
 
 /**
@@ -21,6 +20,7 @@ class BinaryArrayConvertCli {
         addOption("u", "uri", true, "The URI which identifies the dataset.")
         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("h", "help", false, "Show help.")
     }
 
@@ -44,9 +44,10 @@ class BinaryArrayConvertCli {
             .withContext(opts.contextLocs)
             .withAlias(opts.aliasLocs)
         val model = ba.use(ModelBinaryArrayConverter::convert)
+        val outputFormat = opts.outputFormat ?: "ttl"
 
         modelOutput(opts.outputLoc).use { output ->
-            model.write(output, "ttl")
+            model.write(output, outputFormat)
         }
     }
 
@@ -77,7 +78,11 @@ class BinaryArrayConvertCli {
     }
 
     private fun modelOutput(outputLoc: String?): OutputStream {
-        return outputLoc?.let(::File)?.outputStream() ?: System.out
+        return outputLoc?.let(::File)?.outputStream() ?: object: FilterOutputStream(System.out) {
+            override fun close() {
+                // do nothing, leave System.out open
+            }
+        }
     }
 }
 

binary-array-ld-cli/src/main/kotlin/net/bald/CommandLineOptions.kt

@@ -12,5 +12,6 @@ class CommandLineOptions(
     val uri: String? get() = cmd.getOptionValue("uri")
     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 help: Boolean get() = cmd.hasOption("help")
 }

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

@@ -6,6 +6,7 @@ import bald.netcdf.CdlConverter.writeToNetCdf
 import net.bald.vocab.BALD
 import org.apache.jena.rdf.model.ModelFactory.createDefaultModel
 import org.apache.jena.rdf.model.ResourceFactory.*
+import org.apache.jena.riot.RiotException
 import org.apache.jena.vocabulary.*
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.assertThrows
@@ -93,6 +94,36 @@ class BinaryArrayConvertCliTest {
         }
     }
 
+    @Test
+    fun run_withOutputFormat_outputsToFile() {
+        val inputFile = writeToNetCdf("/netcdf/identity.cdl")
+        val outputFile = createTempFile()
+        run(
+            "--uri", "http://test.binary-array-ld.net/example",
+            "--output", "json-ld",
+            inputFile.absolutePath,
+            outputFile.absolutePath
+        )
+        val result = outputFile.readText()
+        val expected = javaClass.getResource("/jsonld/identity.json").readText()
+        assertEquals(expected, result)
+    }
+
+    @Test
+    fun run_withInvalidFormat_throwsException() {
+        val inputFile = writeToNetCdf("/netcdf/identity.cdl")
+        val outputFile = createTempFile()
+        val re = assertThrows<RiotException> {
+            run(
+                "--uri", "http://test.binary-array-ld.net/example",
+                "--output", "foo",
+                inputFile.absolutePath,
+                outputFile.absolutePath
+            )
+        }
+        assertEquals("No graph writer for 'foo'", re.message)
+    }
+
     private fun run_withPrefixMapping_outputsPrefixMapping(cdlLoc: String) {
         val inputFile = writeToNetCdf(cdlLoc)
         val outputFile = createTempFile()

binary-array-ld-test/src/main/resources/jsonld/identity.json

@@ -0,0 +1,23 @@
+{
+  "@graph" : [ {
+    "@id" : "http://test.binary-array-ld.net/example",
+    "@type" : "https://www.opengis.net/def/binary-array-ld/Container",
+    "contains" : "http://test.binary-array-ld.net/example/"
+  }, {
+    "@id" : "http://test.binary-array-ld.net/example/",
+    "@type" : "https://www.opengis.net/def/binary-array-ld/Container",
+    "contains" : [ "http://test.binary-array-ld.net/example/var1", "http://test.binary-array-ld.net/example/var0" ]
+  }, {
+    "@id" : "http://test.binary-array-ld.net/example/var0",
+    "@type" : "https://www.opengis.net/def/binary-array-ld/Resource"
+  }, {
+    "@id" : "http://test.binary-array-ld.net/example/var1",
+    "@type" : "https://www.opengis.net/def/binary-array-ld/Resource"
+  } ],
+  "@context" : {
+    "contains" : {
+      "@id" : "https://www.opengis.net/def/binary-array-ld/contains",
+      "@type" : "@id"
+    }
+  }
+}