dictionaries in zip files

CHANGELOG

@@ -2,4 +2,9 @@
 
 ## Version 1.0, 2020-03-03
 
-First version of the component.
\ No newline at end of file
+First version of the component.
+
+## Version 1.1, 2020-03-10
+
+Posibility of adding a .zip file in the dictionary definition.
+Parameter -l ---> Dictionary List definitions. A lists.def Gate-formatted file separated by tab can be provided or a zip file that contains the dictionary/gazetteer files including the lists.def
\ No newline at end of file

README.md

@@ -17,7 +17,7 @@ https://gate.ac.uk/sale/thakker-jape-tutorial/GATE%20JAPE%20manual.pdf
 
 This library is very useful if you need to execute gazeteers lookup and JAPE rules in batch mode, inside a Nextflow pipeline for example. 
 
-## Actual Version: 1.0, 2020-03-04
+## Actual Version: 1.1, 2020-03-04
 ## [Changelog](https://gitlab.bsc.es/inb/text-mining/generic-tools/import-json-to-mongo/blob/master/CHANGELOG) 
 ## Docker
 
@@ -43,7 +43,7 @@ Parameters:
 -ia Input Annotation Set. If you want to provided different input annotation, set this parameter. By default the -a output annotation set is used as input.  
 </p>
 <p>
--l list definition of the dictionary in GATE format.
+-l Dictionary List definitions. A lists.def Gate-formatted file separated by tab can be provided or a zip file that contains the dictionary/gazetteer files including the lists.def
 </p>
 <p>
 -j main.jape path with the JAPE rules to be executed.

src/main/java/es/bsc/inb/nlp/gate/generic/component/main/App.java

 package es.bsc.inb.nlp.gate.generic.component.main;
 
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.net.URL;
 import java.nio.file.Paths;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
@@ -43,7 +46,8 @@ public class App {
         output.setRequired(true);
         options.addOption(output);
         
-        Option listDefinitions = new Option("l", "lists_definitions", true, "Dictionary List definitions, Gate format.");
+        Option listDefinitions = new Option("l", "lists_definitions", true, "Dictionary List definitions. "
+        		+ "A lists.def Gate-formatted file separated by tab can be provided or a zip file that contains the dictionary/gazetteer files including the lists.def ");
         listDefinitions.setRequired(false);
         options.addOption(listDefinitions);
         
@@ -106,13 +110,34 @@ public class App {
         	System.out.println("No dictionary was provided.");
         }else {
         	listsDefinitionsPath = workdirPath+listsDefinitionsPath;
+        	System.out.println("Dictionary Path " + listsDefinitionsPath);
         	execution = true;
         	if (!java.nio.file.Files.isRegularFile(Paths.get(listsDefinitionsPath))) {
-        		System.out.println("Please set a correct path to the list of dictionaries to annotate");
+        		System.out.println("Please set the list of dictionaries to annotate. You can provide the list.def file or a zip file. Please if you provided a zip file remember that it must contain a list.def file inside");
     			System.exit(1);
             }
+        	
+        	if(listsDefinitionsPath.endsWith(".zip")) {
+            	try {
+    	       		File file = new File(listsDefinitionsPath);
+    	       		String dictionaryFolderPath =  file.getName().substring(0, file.getName().indexOf(".zip"));
+    	       		unZipIt(listsDefinitionsPath,  workdirPath  + dictionaryFolderPath );
+    	       		listsDefinitionsPath = workdirPath  + dictionaryFolderPath + File.separator + "lists.def";
+    	       		if (!java.nio.file.Files.isRegularFile(Paths.get(listsDefinitionsPath))) {
+    	               	System.out.println("Please if you provided a zip file remember that it must contain a list.def file inside.");
+    	       			System.exit(1);
+    	           	}
+            	}catch(Exception e) {
+                   	System.out.println("Error unziping directory, please if you provided a zip file remember that it must contain a list.def file inside. ");
+                   	System.exit(1);
+                }
+            }else if(listsDefinitionsPath.endsWith(".def")) {
+            	System.out.println(" Please set the list of dictionaries to annotate.  No list.def file or .zip file provided.");
+            	System.exit(1);
+            }
+        	
         }
-        
+
         if(japeMainPath==null) {
         	System.out.println("No Jape Main Rules were provided.");
         }else {
@@ -231,4 +256,50 @@ public class App {
     }
     
     
+    /**
+     * Basic unzipping folder method
+     * @param input
+     * @param output
+     * @throws IOException
+     */
+    private static void unZipIt(String zipFile, String outputFolder){
+    	byte[] buffer = new byte[1024];
+        try{
+	       	//create output directory is not exists
+	       	File folder = new File(outputFolder);
+	       	if(!folder.exists()){
+	       		folder.mkdir();
+	       	}
+	       	//get the zip file content
+	       	ZipInputStream zis =
+	       		new ZipInputStream(new FileInputStream(zipFile));
+	       	//get the zipped file list entry
+	       	ZipEntry ze = zis.getNextEntry();
+	       	if(ze==null) {
+	       		System.out.println("Error unziping file, please review if you zip file provided is not corrupt file remember that it must contain a list.def file inside.");
+               	System.exit(1);
+	       	}
+	       	while(ze!=null){
+	       	   String fileName = ze.getName();
+	           File newFile = new File(outputFolder + File.separator + fileName);
+	           System.out.println("file unzip : "+ newFile.getAbsoluteFile());
+	           //create all non exists folders
+	           //else you will hit FileNotFoundException for compressed folder
+	           new File(newFile.getParent()).mkdirs();
+	           FileOutputStream fos = new FileOutputStream(newFile);
+	           int len;
+	           while ((len = zis.read(buffer)) > 0) {
+	        	   fos.write(buffer, 0, len);
+	           }
+	           fos.close();
+	           ze = zis.getNextEntry();
+	       	}
+	       	zis.closeEntry();
+	       	zis.close();
+	       	System.out.println("Done");
+       }catch(IOException ex){
+          ex.printStackTrace();
+       }
+    }
+    
 }