fix(rdf): code quality improvements

backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/ColumnTypeRdfMapper.java

@@ -2,6 +2,8 @@
 
 import static java.util.Map.entry;
 import static org.eclipse.rdf4j.model.util.Values.literal;
+import static org.molgenis.emx2.Constants.API_FILE;
+import static org.molgenis.emx2.rdf.RdfUtils.getSchemaNamespace;
 
 import com.google.common.net.UrlEscapers;
 import java.time.LocalDateTime;
@@ -15,7 +17,6 @@
 import org.eclipse.rdf4j.model.base.CoreDatatype;
 import org.eclipse.rdf4j.model.util.Values;
 import org.molgenis.emx2.*;
-import org.molgenis.emx2.utils.TypeUtils;
 import org.molgenis.emx2.utils.URIUtils;
 
 /**
@@ -200,7 +201,8 @@ Set<Value> retrieveValues(String baseURL, Row row, Column column) {
             Values.iri(
                 baseURL
                     + schemaPath
-                    + "/api/file/"
+                    + API_FILE
+                    + "/"
                     + tablePath
                     + "/"
                     + columnPath
@@ -274,14 +276,6 @@ public CoreDatatype.XSD getCoreDatatype() {
       this.coreDatatype = coreDatatype;
     }
 
-    // TODO: Fix code duplicity with RDFService.
-    private static Namespace getSchemaNamespace(final String baseURL, final SchemaMetadata schema) {
-      final String schemaName = UrlEscapers.urlPathSegmentEscaper().escape(schema.getName());
-      final String url = baseURL + schemaName + "/api/rdf/";
-      final String prefix = TypeUtils.convertToPascalCase(schema.getName());
-      return Values.namespace(prefix, url);
-    }
-
     /**
      * Generic retrieval function. Can be used for {@link Values#literal(Object)} or any custom
      * function which outputs a {@link Value}.

backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/RDFService.java

@@ -5,6 +5,7 @@
 import static org.molgenis.emx2.FilterBean.f;
 import static org.molgenis.emx2.Operator.EQUALS;
 import static org.molgenis.emx2.SelectColumn.s;
+import static org.molgenis.emx2.rdf.RdfUtils.getSchemaNamespace;
 
 import com.google.common.net.UrlEscapers;
 import java.io.IOException;
@@ -25,7 +26,6 @@
 import org.eclipse.rdf4j.rio.WriterConfig;
 import org.eclipse.rdf4j.rio.helpers.BasicWriterSettings;
 import org.molgenis.emx2.*;
-import org.molgenis.emx2.utils.TypeUtils;
 
 // TODO check null value handling
 // TODO check value types
@@ -55,7 +55,8 @@ public class RDFService {
   public static final IRI IRI_CONTROLLED_VOCABULARY =
       Values.iri("http://purl.obolibrary.org/obo/NCIT_C48697");
 
-  private static final String SETTING_CUSTOM_RDF = "custom_rdf";
+  // Advanced setting containing valid Turtle-formatted RDF.
+  public static final String SETTING_CUSTOM_RDF = "custom_rdf";
 
   /**
    * SIO:001055 = observing (definition: observing is a process of passive interaction in which one
@@ -225,7 +226,7 @@ private void buildgenericRdf(ModelBuilder builder, Schema[] schemas) throws IOEx
     boolean allIncludeCustomRdf = true;
     // Define the schemas at the start of the document.
     for (final Schema schema : schemas) {
-      final Namespace ns = getSchemaNamespace(schema);
+      final Namespace ns = getSchemaNamespace(baseURL, schema);
       builder.setNamespace(ns);
       // Adds custom RDF to model.
       if (schema.hasSetting(SETTING_CUSTOM_RDF)) {
@@ -281,37 +282,20 @@ protected void describeRoot(final ModelBuilder builder) {
         .add(DCTERMS.CREATOR, IRI_MOLGENIS);
   }
 
-  /**
-   * Get the namespace for this schema
-   *
-   * @param schema the schema
-   * @return A namespace that defines a local unique prefix for this schema.
-   */
-  private Namespace getSchemaNamespace(final SchemaMetadata schema) {
-    final String schemaName = UrlEscapers.urlPathSegmentEscaper().escape(schema.getName());
-    final String url = baseURL + schemaName + "/api/rdf/";
-    final String prefix = TypeUtils.convertToPascalCase(schema.getName());
-    return Values.namespace(prefix, url);
-  }
-
-  private Namespace getSchemaNamespace(final Schema schema) {
-    return getSchemaNamespace(schema.getMetadata());
-  }
-
   /**
    * Get an IRI for the table. Taking the schema in which the table resides into consideration.
    *
    * @param table the table
    * @return An IRI that is based on the schema namespace.
    */
   private IRI getTableIRI(final Table table) {
-    final Namespace ns = getSchemaNamespace(table.getSchema());
+    final Namespace ns = getSchemaNamespace(baseURL, table.getSchema());
     return Values.iri(ns, table.getIdentifier());
   }
 
   private void describeSchema(final ModelBuilder builder, final Schema schema) {
     // The name from a name space is the IRI.
-    final String subject = getSchemaNamespace(schema).getName();
+    final String subject = getSchemaNamespace(baseURL, schema).getName();
     builder
         .subject(subject)
         .add(RDFS.LABEL, schema.getName())
@@ -393,7 +377,7 @@ private IRI getColumnIRI(final Column column) {
     Schema schema = table.getTable().getSchema();
     final String tableName = UrlEscapers.urlPathSegmentEscaper().escape(table.getIdentifier());
     final String columnName = UrlEscapers.urlPathSegmentEscaper().escape(column.getIdentifier());
-    final Namespace ns = getSchemaNamespace(schema);
+    final Namespace ns = getSchemaNamespace(baseURL, schema);
     return Values.iri(ns, tableName + "/column/" + columnName);
   }
 
@@ -647,7 +631,7 @@ private IRI getIriForRow(final Row row, final TableMetadata metadata) {
         keyParts.put(column.getIdentifier(), row.get(column).toString());
       }
     }
-    final Namespace ns = getSchemaNamespace(metadata.getRootTable().getSchema());
+    final Namespace ns = getSchemaNamespace(baseURL, metadata.getRootTable().getSchema());
     PrimaryKey key = new PrimaryKey(keyParts);
     return Values.iri(ns, rootTableName + "?" + key.getEncodedValue());
   }

backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/RdfUtils.java

@@ -0,0 +1,30 @@
+package org.molgenis.emx2.rdf;
+
+import static org.molgenis.emx2.Constants.API_RDF;
+
+import com.google.common.net.UrlEscapers;
+import org.eclipse.rdf4j.model.Namespace;
+import org.eclipse.rdf4j.model.util.Values;
+import org.molgenis.emx2.Schema;
+import org.molgenis.emx2.SchemaMetadata;
+import org.molgenis.emx2.utils.TypeUtils;
+
+abstract class RdfUtils {
+  /**
+   * Get the namespace for a schema
+   *
+   * @param baseURL the baseURL that needs to be used
+   * @param schema the schema
+   * @return A namespace that defines a local unique prefix for this schema.
+   */
+  static Namespace getSchemaNamespace(final String baseURL, final SchemaMetadata schema) {
+    final String schemaName = UrlEscapers.urlPathSegmentEscaper().escape(schema.getName());
+    final String url = baseURL + schemaName + API_RDF + "/";
+    final String prefix = TypeUtils.convertToPascalCase(schema.getName());
+    return Values.namespace(prefix, url);
+  }
+
+  static Namespace getSchemaNamespace(final String baseURL, final Schema schema) {
+    return getSchemaNamespace(baseURL, schema.getMetadata());
+  }
+}

backend/molgenis-emx2-rdf/src/test/java/org/molgenis/emx2/rdf/RdfUtilsTest.java

@@ -0,0 +1,44 @@
+package org.molgenis.emx2.rdf;
+
+import org.eclipse.rdf4j.model.Namespace;
+import org.eclipse.rdf4j.model.util.Values;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.molgenis.emx2.Database;
+import org.molgenis.emx2.Schema;
+import org.molgenis.emx2.sql.TestDatabaseFactory;
+
+class RdfUtilsTest {
+  static final String TEST_SCHEMA = "TestRdfUtils";
+  static final String BASE_URL = "http://molgenis.org/";
+  static final String NAMESPACE_IRI = BASE_URL + TEST_SCHEMA + "/api/rdf/";
+
+  static Database database;
+  static Schema rdfUtilsTest;
+
+  @BeforeAll
+  public static void setup() {
+    database = TestDatabaseFactory.getTestDatabase();
+    rdfUtilsTest = database.dropCreateSchema(TEST_SCHEMA);
+  }
+
+  @AfterAll
+  public static void tearDown() {
+    database = TestDatabaseFactory.getTestDatabase();
+    database.dropSchema(rdfUtilsTest.getName());
+  }
+
+  @Test
+  void testSchemaNamespaceRetrieval() {
+    Namespace expected = Values.namespace(TEST_SCHEMA, NAMESPACE_IRI);
+
+    Assertions.assertAll(
+        () ->
+            Assertions.assertEquals(expected, RdfUtils.getSchemaNamespace(BASE_URL, rdfUtilsTest)),
+        () ->
+            Assertions.assertEquals(
+                expected, RdfUtils.getSchemaNamespace(BASE_URL, rdfUtilsTest.getMetadata())));
+  }
+}

backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/GraphGenomeApi.java

@@ -1,5 +1,7 @@
 package org.molgenis.emx2.web;
 
+import static org.molgenis.emx2.Constants.API_RDF;
+
 import io.javalin.Javalin;
 import io.javalin.http.Context;
 import java.io.IOException;
@@ -37,7 +39,7 @@ private static int graphGenomeForDatabase(Context ctx) throws IOException {
             + (ctx.port() > 0 ? ":" + ctx.port() : "")
             + (!ctx.path().isEmpty() ? "/" + ctx.path() + "/" : "/");
     var format = RDFApi.selectFormat(ctx);
-    new GraphGenome(baseURL, RDFApi.RDF_API_LOCATION, format)
+    new GraphGenome(baseURL, API_RDF, format)
         .graphGenomeAsRDF(
             outputStream, gene, assembly, ucscgenome, GRAPH_GENOME_API_LOCATION, tables);
     outputStream.flush();

backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/RDFApi.java

@@ -1,5 +1,8 @@
 package org.molgenis.emx2.web;
 
+import static org.molgenis.emx2.Constants.API_JSONLD;
+import static org.molgenis.emx2.Constants.API_RDF;
+import static org.molgenis.emx2.Constants.API_TTL;
 import static org.molgenis.emx2.web.MolgenisWebservice.*;
 
 import io.javalin.Javalin;
@@ -21,9 +24,6 @@
 public class RDFApi {
   public static final String FORMAT = "format";
   private static MolgenisSessionManager sessionManager;
-  public static final String RDF_API_LOCATION = "/api/rdf";
-  public static final String TTL_API_LOCATION = "/api/ttl";
-  public static final String JSONLD_API_LOCATION = "/api/jsonld";
 
   private static final List<RDFFormat> acceptedRdfFormats =
       List.of(
@@ -41,9 +41,9 @@ public static void create(Javalin app, MolgenisSessionManager sm) {
     // created on-the-fly, there is no way of knowing (or is there?)
     sessionManager = sm;
 
-    defineApiRoutes(app, RDF_API_LOCATION, null);
-    defineApiRoutes(app, TTL_API_LOCATION, RDFFormat.TURTLE);
-    defineApiRoutes(app, JSONLD_API_LOCATION, RDFFormat.JSONLD);
+    defineApiRoutes(app, API_RDF, null);
+    defineApiRoutes(app, API_TTL, RDFFormat.TURTLE);
+    defineApiRoutes(app, API_JSONLD, RDFFormat.JSONLD);
   }
 
   private static void defineApiRoutes(Javalin app, String apiLocation, RDFFormat format) {
@@ -111,7 +111,7 @@ private static void rdfForSchema(Context ctx, RDFFormat format) throws IOExcepti
     }
     final String baseURL = URLUtils.extractBaseURL(ctx);
 
-    RDFService rdf = new RDFService(baseURL, RDF_API_LOCATION, format);
+    RDFService rdf = new RDFService(baseURL, API_RDF, format);
     ctx.contentType(rdf.getMimeType());
 
     OutputStream outputStream = ctx.outputStream();
@@ -130,7 +130,7 @@ private static void rdfForTable(Context ctx, RDFFormat format) throws IOExceptio
     }
     final String baseURL = URLUtils.extractBaseURL(ctx);
 
-    RDFService rdf = new RDFService(baseURL, RDF_API_LOCATION, format);
+    RDFService rdf = new RDFService(baseURL, API_RDF, format);
     ctx.contentType(rdf.getMimeType());
 
     OutputStream outputStream = ctx.outputStream();
@@ -145,7 +145,7 @@ private static void rdfForRow(Context ctx, RDFFormat format) throws IOException
     String rowId = sanitize(ctx.pathParam("row"));
 
     final String baseURL = URLUtils.extractBaseURL(ctx);
-    RDFService rdf = new RDFService(baseURL, RDF_API_LOCATION, format);
+    RDFService rdf = new RDFService(baseURL, API_RDF, format);
     ctx.contentType(rdf.getMimeType());
 
     OutputStream outputStream = ctx.outputStream();
@@ -162,7 +162,7 @@ private static void rdfForColumn(Context ctx, RDFFormat format) throws IOExcepti
 
     final String baseURL = URLUtils.extractBaseURL(ctx);
 
-    RDFService rdf = new RDFService(baseURL, RDF_API_LOCATION, format);
+    RDFService rdf = new RDFService(baseURL, API_RDF, format);
     ctx.contentType(rdf.getMimeType());
 
     OutputStream outputStream = ctx.outputStream();

backend/molgenis-emx2/src/main/java/org/molgenis/emx2/Constants.java

@@ -114,6 +114,11 @@ public class Constants {
   public static final String CONTACT_RECIPIENTS_QUERY_SETTING_KEY = "contactRecipientsQuery";
   public static final String CONTACT_BCC_ADDRESS = "contactBccAddress";
 
+  public static final String API_RDF = "/api/rdf";
+  public static final String API_TTL = "/api/ttl";
+  public static final String API_JSONLD = "/api/jsonld";
+  public static final String API_FILE = "/api/file";
+
   private Constants() {
     // hide constructor
   }