Refactoring, add converter instantiation

src/main/java/org/ld4l/bib2lod/clean/marcxml/MarcxmlCleaner.java

@@ -1,11 +1,10 @@
 package org.ld4l.bib2lod.clean.marcxml;
 
 import org.ld4l.bib2lod.clean.BaseCleaner;
+import org.ld4l.bib2lod.configuration.Configuration;
 
 public class MarcxmlCleaner extends BaseCleaner {
 
-    public MarcxmlCleaner()  {
-        // TODO Auto-generated constructor stub
-    }
+
 
 }

src/main/java/org/ld4l/bib2lod/configuration/Configuration.java

@@ -10,9 +10,12 @@
 import org.apache.commons.cli.ParseException;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.ld4l.bib2lod.conversion.Converter;
 import org.ld4l.bib2lod.uri.UriMinter;
 
+import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.RuntimeJsonMappingException;
 
 public class Configuration {
@@ -23,6 +26,11 @@ public class Configuration {
     private String localNamespace;
     private UriMinter uriMinter;
     private List<File> input;
+
+    // TODO Convert to list later
+    // private List<Converter> converters;
+    private Converter converter;
+
     // cleaner, parser, converters
     // private Reader reader;
     // private Writer writer;
@@ -44,29 +52,21 @@ public Configuration(String[] args) throws ClassNotFoundException,
         // Get the configuration used to configure the application and create 
         // the services.      
 
-        OptionsReader configurer = new OptionsReader(args);
-        JsonNode config = ((OptionsReader) configurer).getConfig();
+        OptionsReader optionsReader = new OptionsReader(args);
+        JsonNode config = optionsReader.configure();
 
         LOGGER.debug(config.toString());
-
-        JsonNode services = config.get("services");
-
-        LOGGER.debug(services.toString());
-
+
         String localNamespace = getJsonStringValue(config, "localNamespace");
         setLocalNamespace(localNamespace);
 
-        makeUriMinter(getJsonStringValue(services, "uriMinter"));
-
-        // TODO Add same for other services...
+        buildServices(config);
 
-        // TODO Throw error if not defined
-        JsonNode inputNode = config.get("input");
-        String inputPath = getJsonStringValue(inputNode, "location");
-        String inputFormat = getJsonStringValue(inputNode, "format");
-        String fileExtension = getJsonStringValue(inputNode, "extension");
-        buildInputFileList(inputPath, inputFormat, fileExtension);
+        buildInputFileList(config);
 
+        // buildConverters(config);
+        buildConverter(config);
+
         // TODO Add same for other config elements...
 
     }
@@ -78,17 +78,35 @@ public String getLocalNamespace() {
     public UriMinter getUriMinter() {
         return uriMinter;
     }
-
 
     // TODO Or just return the input string from config file?
     public List<File> getInput() {
         return input;
     }
 
+//    public List<Converter> getConverters() {
+//        return converters;
+//    }
+    public Converter getConverter() {
+        return converter;
+    }
+
     protected void setLocalNamespace(String localNamespace) {
         this.localNamespace = localNamespace;
     }
 
+    protected void buildServices(JsonNode config) 
+            throws ClassNotFoundException, ReflectiveOperationException {   
+
+        JsonNode services = config.get("services");       
+        LOGGER.debug(services.toString());   
+
+       makeUriMinter(getJsonStringValue(services, "uriMinter"));
+
+        // TODO Add same for other services...
+
+    }
+
     protected void makeUriMinter(String minterClassName) 
             throws ClassNotFoundException, ReflectiveOperationException {
 
@@ -106,8 +124,14 @@ protected void makeUriMinter(String minterClassName)
      */
     // TODO Also pass in file type and make sure we get only the files of this
     // type
-    protected void buildInputFileList(String inputPath, String fileFormat, 
-            String fileExtension) throws FileNotFoundException {
+    protected void buildInputFileList(JsonNode config) 
+            throws FileNotFoundException {
+
+        // TODO Throw error if not defined
+        JsonNode inputNode = config.get("input");
+        String inputPath = getJsonStringValue(inputNode, "location");
+        String inputFormat = getJsonStringValue(inputNode, "format");
+        String fileExtension = getJsonStringValue(inputNode, "extension");
 
         this.input = new ArrayList<File>(); 
 
@@ -126,6 +150,27 @@ protected void buildInputFileList(String inputPath, String fileFormat,
         }        
     }
 
+    protected void buildConverter(JsonNode config) 
+            throws ClassNotFoundException, InstantiationException, 
+                IllegalAccessException {
+
+        // ObjectMapper mapper = new ObjectMapper();
+
+        // JsonNode converterList = config.get("converters"); 
+        // TODO Should be an array of strings or a string. For now just handle
+        // an array.
+        // if string...convert to list
+        // else
+
+        // TODO Get this to work. Hard-coding as a single converter for now
+        // TypeReference ref = new TypeReference<List<Converter>>() {};
+        // converters = mapper.readValue(converterList, ref);
+       String converter = getJsonStringValue(config, "converter");
+       Class<?> c = Class.forName(converter);
+       this.converter = (Converter) c.newInstance();
+
+    }
+
     private String getJsonStringValue(JsonNode node, String key) {
 
         JsonNode value = node.get(key);

src/main/java/org/ld4l/bib2lod/configuration/OptionsReader.java

@@ -31,35 +31,11 @@ public class OptionsReader {
     public OptionsReader(String[] args)  {
         this.args = args;
     }
+
 
     /**
-     * Parse commandline options.
-     * @param options
-     * @param args
-     * @return
-     * @throws ParseException
-     */
-    protected CommandLine getCommandLine(Options options, String[] args) 
-            throws ParseException {
-
-        // Parse program arguments
-        CommandLineParser parser = new DefaultParser();
-
-        return parser.parse(options, args);           
-    }
-
-//  /**
-//  * Print help text.
-//  * @param options
-//  */
- // TODO Currently not used. What is best way to do this? If print here,
- // need to catch exceptions and return null up the chain. If print from
- // manager or elsewhere, need to supply a method to provide the help string.
- // See HelpFormatter.renderOptions() or HelpFormatter.renderWrappedText().
-// private void printHelp(Options options) {
-//     
-    /**
-     * 
+     * Get configuration option values from config file or commandline;
+     * commandline overrides config file.
      * @return
      * @throws IOException
      * @throws ParseException
@@ -69,9 +45,9 @@ protected CommandLine getCommandLine(Options options, String[] args)
     // than using whatever json library they choose. However, if we are also 
     // using Jackson inside the core converter, it doesn't matter. Consider this 
     // later. 
-    public JsonNode getConfig() throws IOException, ParseException {
+    public JsonNode configure() throws IOException, ParseException {
 
-        JsonNode jsonConfig = null;
+        JsonNode config = null;
 
         Options options = buildOptions();
 
@@ -89,13 +65,13 @@ public JsonNode getConfig() throws IOException, ParseException {
 
         try {
             ObjectMapper mapper = new ObjectMapper();
-            jsonConfig = mapper.readTree(configFile);
+            config = mapper.readTree(configFile);
 
             // Note: currently the only commandline option is the config file 
             // location. Later others may be supported, in which case this 
             // will method override the config file values with the commandline 
             // option values and return the result.
-            return jsonConfig;
+            return config;
 
         } catch (JsonParseException e) {
             throw new IOException(
@@ -133,4 +109,19 @@ private Options buildOptions() {
         return options;
     }
 
+    /**
+     * Parse commandline options.
+     * @param options
+     * @param args
+     * @return
+     * @throws ParseException
+     */
+    protected CommandLine getCommandLine(Options options, String[] args) 
+            throws ParseException {
+
+        // Parse program arguments
+        CommandLineParser parser = new DefaultParser();    
+        return parser.parse(options, args);           
+    }
+
 }

src/main/java/org/ld4l/bib2lod/conversion/BaseConverter.java

@@ -0,0 +1,15 @@
+package org.ld4l.bib2lod.conversion;
+
+import java.io.File;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.ld4l.bib2lod.configuration.Configuration;
+
+// TODO Does this do anything? If not, remove
+public abstract class BaseConverter implements Converter {
+
+    private static final Logger LOGGER = 
+            LogManager.getLogger(BaseConverter.class);
+
+}

src/main/java/org/ld4l/bib2lod/conversion/MarcxmlToLd4lRdf.java → src/main/java/org/ld4l/bib2lod/conversion/BaseRecord.java

@@ -1,8 +1,8 @@
 package org.ld4l.bib2lod.conversion;
 
-public class MarcxmlToLd4lRdf {
+public class BaseRecord implements Record {
 
-    public MarcxmlToLd4lRdf() {
+    public BaseRecord() {
         // TODO Auto-generated constructor stub
     }
 

src/main/java/org/ld4l/bib2lod/conversion/Converter.java

@@ -0,0 +1,12 @@
+package org.ld4l.bib2lod.conversion;
+
+import java.io.File;
+
+public interface Converter {
+
+    public String convertFile(String text);
+
+    public String convertFile(File file);
+
+    // public String convertRecord(Record record);
+}

src/main/java/org/ld4l/bib2lod/conversion/Record.java

@@ -0,0 +1,5 @@
+package org.ld4l.bib2lod.conversion;
+
+public interface Record {
+
+}

src/main/java/org/ld4l/bib2lod/conversion/RecordConverter.java → src/main/java/org/ld4l/bib2lod/conversion/to_rdf/MarcxmlToLd4lRdf.java

@@ -1,30 +1,29 @@
-package org.ld4l.bib2lod.conversion;
+package org.ld4l.bib2lod.conversion.to_rdf;
 
 import java.io.File;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.ld4l.bib2lod.configuration.Configuration;
+import org.ld4l.bib2lod.conversion.BaseConverter;
+
+public class MarcxmlToLd4lRdf extends BaseConverter {
 
-// TODO figure out whether we need an interface and/or base class
-public class RecordConverter {
-
     private static final Logger LOGGER = 
-            LogManager.getLogger(RecordConverter.class);
-
-
-    public RecordConverter(Configuration config) {
-        // from config, get cleaner, parser, converters and instantiate all
-
-    }
+            LogManager.getLogger(MarcxmlToLd4lRdf.class);
 
+    @Override
     public String convertFile(File file) {
-        // TODO Auto-generated method stub
+
         // Loop through records. For each: clean, parse, and loop through 
         // converters to convert
         // TODO Do we need a Record implementation?
         return null;
     }
-
 
+    @Override
+    public String convertFile(String text) {
+        // TODO Auto-generated method stub
+        return null;
+    }
 }

src/main/java/org/ld4l/bib2lod/manager/SimpleManager.java

@@ -1,16 +1,16 @@
 package org.ld4l.bib2lod.manager;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.List;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.ld4l.bib2lod.configuration.Configuration;
-import org.ld4l.bib2lod.conversion.RecordConverter;
 
 // TODO Put common methods (like getInputFiles() into a base class or a 
 // utility class?
-public class SimpleManager {
+public final class SimpleManager {
 
     private static final Logger LOGGER = 
             LogManager.getLogger(SimpleManager.class);
@@ -38,15 +38,22 @@ public static void main(String[] args) {
 
     /**
      * Convert a list of input files
+     * @throws IOException 
      */
-    private static void convertFiles(Configuration configuration) {
-
-        //RecordConverter recordConverter = new RecordConverter(configuration);
+    private static void convertFiles(Configuration configuration) 
+            throws IOException {
+
         List<File> inputFiles = configuration.getInput();
+
         for (File file : inputFiles) {
 
-            //String converted = recordConverter.convertFile(file);
-            // TODO get back output and write it (use configuration writer)
+            // TODO Make work as a loop for a chain of converters?
+            // Then need to first convert to string, so each converter takes a
+            // string as input and returns a string, which is input to next
+            // converter.
+
+            configuration.getConverter().convertFile(file);
+
         }       
     }