Command line parser

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> --output-directory <output_folder> <input_path_1> [<input_path_2> ...]
+```
+or you can use the short form as well like - 
+```shell
+java -jar restructurehdfs-0.3.3-all.jar -u <webhdfs_url> -o <output_folder> <input_path_1> [<input_path_2> ...]
 ```
 
-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. Also note that there can be multiple input paths from which to read the files. Eg - `/topicAndroidNew/topic1 /topicAndroidNew/topic2 ...`. At least one input path is required.
+
+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> --output-directory <output_folder>  <input_path_1> [<input_path_2> ...]
 ```
 
 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.compression=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> --output-directory <output_folder> <input_path_1> [<input_path_2> ...]
 ```
 
-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` or `-d`. 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.

build.gradle

@@ -15,6 +15,7 @@ targetCompatibility = '1.8'
 ext.avroVersion = '1.8.2'
 ext.jacksonVersion = '2.8.9'
 ext.hadoopVersion = '2.7.3'
+ext.jCommanderVersion = '1.72'
 
 repositories {
     jcenter()
@@ -27,6 +28,8 @@ dependencies {
     compile group: 'com.fasterxml.jackson.core' , name: 'jackson-databind', version: jacksonVersion
     compile group: 'com.fasterxml.jackson.dataformat' , name: 'jackson-dataformat-csv', version: jacksonVersion
 
+    compile group: 'com.beust', name: 'jcommander', version: jCommanderVersion
+
     runtime group: 'org.apache.hadoop', name: 'hadoop-hdfs', version: hadoopVersion
 
     testCompile group: 'junit', name: 'junit', version: '4.12'

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

@@ -16,6 +16,7 @@
 
 package org.radarcns;
 
+import com.beust.jcommander.JCommander;
 import com.fasterxml.jackson.databind.JsonMappingException;
 import org.apache.avro.Schema.Field;
 import org.apache.avro.file.DataFileReader;
@@ -32,6 +33,7 @@
 import org.radarcns.util.JsonAvroConverter;
 import org.radarcns.util.ProgressBar;
 import org.radarcns.util.RecordConverterFactory;
+import org.radarcns.util.commandline.CommandLineArgs;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -70,27 +72,39 @@ public class RestructureAvroRecords {
 
     private long processedFileCount;
     private long processedRecordsCount;
-    private static final boolean USE_GZIP = "gzip".equalsIgnoreCase(System.getProperty("org.radarcns.compression"));
-
-    // Default set to false because causes loss of records from Biovotion data. https://github.com/RADAR-base/Restructure-HDFS-topic/issues/16
-    private static final boolean DO_DEDUPLICATE = "true".equalsIgnoreCase(System.getProperty("org.radarcns.deduplicate", "false"));
+    private final boolean useGzip;
+    private final boolean doDeduplicate;
 
     public static void main(String [] args) throws Exception {
-        if (args.length != 3) {
-            System.out.println("Usage: hadoop jar restructurehdfs-all-0.2.jar <webhdfs_url> <hdfs_root_directory> <output_folder>");
-            System.exit(1);
+
+        final CommandLineArgs commandLineArgs = new CommandLineArgs();
+        final JCommander parser = JCommander.newBuilder().addObject(commandLineArgs).build();
+
+        parser.setProgramName("hadoop jar restructurehdfs-all-0.3.3.jar");
+        parser.parse(args);
+
+        if(commandLineArgs.help) {
+            parser.usage();
+            System.exit(0);
         }
 
         logger.info(new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(new Date()));
         logger.info("Starting...");
-        logger.info("In:  " + args[0] + args[1]);
-        logger.info("Out: " + args[2]);
 
         long time1 = System.currentTimeMillis();
 
-        RestructureAvroRecords restr = new RestructureAvroRecords(args[0], args[2]);
+        RestructureAvroRecords restr = new RestructureAvroRecords.Builder(commandLineArgs.hdfsUri,
+                commandLineArgs.outputDirectory)
+                .useGzip("gzip".equalsIgnoreCase(commandLineArgs.compression))
+                .doDeduplicate(commandLineArgs.deduplicate).format(commandLineArgs.format)
+                .build();
+
         try {
-            restr.start(args[1]);
+            for(String input : commandLineArgs.inputPaths) {
+                logger.info("In:  " + commandLineArgs.hdfsUri + input);
+                logger.info("Out: " + commandLineArgs.outputDirectory);
+                restr.start(input);
+            }
         } catch (IOException ex) {
             logger.error("Processing failed", ex);
         }
@@ -99,12 +113,16 @@ public static void main(String [] args) throws Exception {
         logger.info("Time taken: {} seconds", (System.currentTimeMillis() - time1)/1000d);
     }
 
-    public RestructureAvroRecords(String inputPath, String outputPath) {
-        this.setInputWebHdfsURL(inputPath);
-        this.setOutputPath(outputPath);
+    private RestructureAvroRecords(RestructureAvroRecords.Builder builder) {
+        this.setInputWebHdfsURL(builder.hdfsUri);
+        this.setOutputPath(builder.outputPath);
+
+        this.useGzip = builder.useGzip;
+        this.doDeduplicate = builder.doDeduplicate;
+        logger.info("Deduplicate set to {}", doDeduplicate);
 
         String extension;
-        if (System.getProperty("org.radarcns.format", "csv").equalsIgnoreCase("json")) {
+        if (builder.format.equalsIgnoreCase("json")) {
             logger.info("Writing output files in JSON format");
             converterFactory = JsonAvroConverter.getFactory();
             extension = "json";
@@ -113,7 +131,7 @@ public RestructureAvroRecords(String inputPath, String outputPath) {
             converterFactory = CsvAvroConverter.getFactory();
             extension = "csv";
         }
-        if (USE_GZIP) {
+        if (this.useGzip) {
             logger.info("Compressing output files in GZIP format");
             extension += ".gz";
         }
@@ -179,7 +197,7 @@ public void start(String directoryName) throws IOException {
 
             // Actually process the files
             for (Map.Entry<String, List<Path>> entry : topicPaths.entrySet()) {
-                try (FileCacheStore cache = new FileCacheStore(converterFactory, 100, USE_GZIP, DO_DEDUPLICATE)) {
+                try (FileCacheStore cache = new FileCacheStore(converterFactory, 100, useGzip, doDeduplicate)) {
                     for (Path filePath : entry.getValue()) {
                         // If JsonMappingException occurs, log the error and continue with other files
                         try {
@@ -347,4 +365,37 @@ public static Date getDate(GenericRecord keyField, GenericRecord valueField) {
         long time = (Long) keyField.get("start");
         return new Date(time);
     }
+
+    public static class Builder {
+        private boolean useGzip;
+        private boolean doDeduplicate;
+        private String hdfsUri;
+        private String outputPath;
+        private String format;
+
+        public Builder(final String uri, final String outputPath) {
+            this.hdfsUri = uri;
+            this.outputPath = outputPath;
+        }
+
+        public Builder useGzip(final boolean gzip) {
+            this.useGzip = gzip;
+            return this;
+        }
+
+        public Builder doDeduplicate(final boolean dedup) {
+            this.doDeduplicate = dedup;
+            return this;
+        }
+
+        public Builder format(final String format) {
+            this.format = format;
+            return this;
+        }
+
+        public RestructureAvroRecords build() {
+            return new RestructureAvroRecords(this);
+        }
+
+    }
 }

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

@@ -0,0 +1,31 @@
+package org.radarcns.util.commandline;
+
+import com.beust.jcommander.Parameter;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class CommandLineArgs {
+
+    @Parameter(description = "<input_path_1> [<input_path_2> ...]", variableArity = true, required = true)
+    public List<String> inputPaths = new ArrayList<>();
+
+    @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";
+
+    // Default set to false because causes loss of records from Biovotion data. https://github.com/RADAR-base/Restructure-HDFS-topic/issues/16
+    @Parameter(names = { "-d", "--deduplicate" }, description = "Boolean to define if to use deduplication or not.")
+    public boolean deduplicate;
+
+    @Parameter(names = { "-u", "--hdfs-uri" }, description = "The HDFS uri to connect to. Eg - 'hdfs://<HOST>:<RPC_PORT>/<PATH>'.", required = true, validateWith = { HdfsUriValidator.class, PathValidator.class })
+    public String hdfsUri;
+
+    @Parameter(names = { "-o", "--output-directory"}, description = "The output folder where the files are to be extracted.", required = true, validateWith = PathValidator.class)
+    public String outputDirectory;
+
+    @Parameter(names = { "-h", "--help"}, help = true, description = "Display the usage of the program with available options.")
+    public boolean help;
+}

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

@@ -0,0 +1,16 @@
+package org.radarcns.util.commandline;
+
+
+import com.beust.jcommander.ParameterException;
+import com.beust.jcommander.IParameterValidator;
+
+public class HdfsUriValidator implements IParameterValidator{
+    @Override
+    public void validate(String name, String value) throws ParameterException {
+        if (! value.matches("((hdfs)|(webhdfs)):(/?/?)[^\\s]+")) {
+            throw new ParameterException("Parameter " + name + " should be a valid HDFS or WebHDFS URI. "
+                    + "Eg - hdfs://<HOST>:<RPC_PORT>/<PATH>. (found " + value
+                    + "). Please run with --help or -h for more information.");
+        }
+    }
+}

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

@@ -0,0 +1,15 @@
+package org.radarcns.util.commandline;
+
+import com.beust.jcommander.ParameterException;
+import com.beust.jcommander.IParameterValidator;
+
+public class PathValidator implements IParameterValidator{
+    @Override
+    public void validate(String name, String value) throws ParameterException {
+        if (value == null || value.isEmpty()) {
+            throw new ParameterException("Parameter " + name + " should be supplied. "
+                    + "It cannot be empty or null. (found " + value +")."
+                    + "Please run with --help or -h for more information.");
+        }
+    }
+}