Add format option and update README

Author: yatharthranjan

README.md

@@ -15,20 +15,30 @@ Build jar from source with
 ```shell
 ./gradlew build
 ```
-and find the output JAR file as `build/libs/restructurehdfs-0.3.1-all.jar`. Then run with:
+and find the output JAR file as `build/libs/restructurehdfs-0.3.3-all.jar`. Then run with:
 
 ```shell
-java -jar restructurehdfs-0.3.1-all.jar <webhdfs_url> <hdfs_topic_path> <output_folder>
+java -jar restructurehdfs-0.3.3-all.jar --hdfs-uri <webhdfs_url> --hdfs-root-directory <hdfs_topic_path> --output-directory <output_folder>
+```
+or you can use the short form as well like - 
+```shell
+java -jar restructurehdfs-0.3.3-all.jar -u <webhdfs_url> -i <hdfs_topic_path> -o <output_folder>
 ```
 
-By default, this will output the data in CSV format. If JSON format is preferred, use the following instead:
+To display the usage and all available options you can use the help option as follows - 
+```shell
+java -jar restructurehdfs-0.3.3-all.jar --help
 ```
-java -Dorg.radarcns.format=json -jar restructurehdfs-0.3.1-all.jar <webhdfs_url> <hdfs_topic_path> <output_folder>
+Note that the options preceded by the `*` in the above output are required to run the app.
+
+By default, this will output the data in CSV format. If JSON format is preferred, use the following instead:
+```shell
+java -jar restructurehdfs-0.3.3-all.jar --format json --hdfs-uri <webhdfs_url> --hdfs-root-directory <hdfs_topic_path> --output-directory <output_folder>
 ```
 
 Another option is to output the data in compressed form. All files will get the `gz` suffix, and can be decompressed with a GZIP decoder. Note that for a very small number of records, this may actually increase the file size.
 ```
-java -Dorg.radarcns.compress=gzip -jar restructurehdfs-0.3.1-all.jar <webhdfs_url> <hdfs_topic_path> <output_folder>
+java -jar restructurehdfs-0.3.3-all.jar --compression gzip  --hdfs-uri <webhdfs_url> --hdfs-root-directory <hdfs_topic_path> --output-directory <output_folder>
 ```
 
-Finally, by default, files records are not deduplicated after writing. To enable this behaviour, specify the option `-Dorg.radarcns.deduplicate=true`. This set to false by default because of an issue with Biovotion data. Please see - [issue #16](https://github.com/RADAR-base/Restructure-HDFS-topic/issues/16) before enabling it.
+Finally, by default, files records are not deduplicated after writing. To enable this behaviour, specify the option `--deduplicate true`. This set to false by default because of an issue with Biovotion data. Please see - [issue #16](https://github.com/RADAR-base/Restructure-HDFS-topic/issues/16) before enabling it.

src/main/java/org/radarcns/RestructureAvroRecords.java

@@ -115,7 +115,7 @@ public RestructureAvroRecords(String inputPath, String outputPath) {
         this.setOutputPath(outputPath);
 
         String extension;
-        if (System.getProperty("org.radarcns.format", "csv").equalsIgnoreCase("json")) {
+        if (commandLineArgs.format.equalsIgnoreCase("json")) {
             logger.info("Writing output files in JSON format");
             converterFactory = JsonAvroConverter.getFactory();
             extension = "json";

src/main/java/org/radarcns/util/commandline/CommandLineArgs.java

@@ -3,6 +3,10 @@
 import com.beust.jcommander.Parameter;
 
 public class CommandLineArgs {
+
+    @Parameter(names = { "-f", "--format" }, description = "Format to use when converting the files. JSON and CSV is available.")
+    public String format = "csv";
+
     @Parameter(names = { "-c", "--compression" }, description = "Compression to use when converting the files. Gzip is available.")
     public String compression = "none";