Committer: Cyril Labbe

Makefile

@@ -11,7 +11,7 @@ JAVACLASSPATH = -cp lib/pdfbox-app-1.8.8.jar
 
 default: all
 
-all: classes doc jar
+all: classes doc jar run
 
 classes:
 	mkdir -p classes
@@ -24,5 +24,8 @@ jar:
 	cd classes ; jar -cfvm ../ScigenChecker_Local`date +%Y-%m-%d`.jar ../MANIFEST.MF *; cd ..
 	cp  ScigenChecker_Local`date +%Y-%m-%d`.jar ScigenChecker_Local.jar 
 
+run:
+	java -jar ScigenChecker_local.jar -l checklog.txt -c Test
+
 clean:
 	rm -r classes; rm -r doc;

manifest.mf

 Manifest-Version: 1.0
+Class-Path: lib/pdfbox-app-1.8.8.jar
 X-COMMENT: Main-Class will be added automatically by build
+Main-Class: fr.imag.Scidetect.scigenchecker_local.ScigenChecker_Local
 

src/fr/imag/Scidetect/Checker/Classifier.java

@@ -25,13 +25,23 @@ import java.io.PrintWriter;
 import java.util.HashMap;
 
 /**
- *
+ * Classifier is tagging input files has being of a certain class. Example of classes are SCIgen, Mathgen,...
+ * The decision is made according to the distance between the tested file and its nearest neighbor 
+ * in each class. Thresholds for assignation are read in file specified in the configuration file 
+ * (default config.txt).
  * @author Nguyen Minh Tien - minh-tien.nguyen@imag.frs
  */
 public class Classifier {
-
+    /**
+     * The key is the class name and value is a couple of Double.
+     * This couple is composed of a threshold for quasi-certain classification and another for suspicion.
+     */
     HashMap<String, Double[]> Threshold = new HashMap<String, Double[]>();
-
+    /**
+     * Reads threshold in the configuration file (default config.txt).
+     * @throws FileNotFoundException
+     * @throws IOException
+     */
     public void readconfig() throws FileNotFoundException, IOException {
         File conf = new File("config.txt");
         BufferedReader br = new BufferedReader(new FileReader(conf));
@@ -49,7 +59,13 @@ public class Classifier {
         }
 
     }
-
+    /**
+     * Classify is classifying each document given the matrix of distances (distant).
+     * For each entry it gives the class (or more) to which the text can be assigned 
+     * @param distant is a matrix of distances 
+     * @return the assigned class
+     * @throws IOException
+     */
     public String classify(HashMap<String, HashMap<String, Double>> distant) throws IOException {
 
         String result = "";
@@ -77,7 +93,11 @@ public class Classifier {
         return conclusion;
 
     }
-
+    /**
+     * Check if the distance is lower, between of upper the two threshold. 
+     * @param result a string composed having for each classe the value of its NN 
+     * @return
+     */
     private String checkdistant(String result) {
         String conclution = "";
         String[] eachtype = result.split("\n");
@@ -105,7 +125,10 @@ public class Classifier {
         }
         return conclution;
     }
-
+    /**
+     * @param result
+     * @return
+     */
     private String findmindistant(String result) {
         Double mindistant = 1.0;
         String[] eachtype = result.split("\n");
@@ -120,7 +143,11 @@ public class Classifier {
         }
         return conclu;
     }
-
+    /**
+     * 
+     * @param indexpath
+     * @return
+     */
     private String gettype(String indexpath) {
         File indexfile = new File(indexpath);
         String parent = indexfile.getParent();
@@ -129,6 +156,10 @@ public class Classifier {
         return parent;
     }
 
+    /**
+     * @param distantto
+     * @return
+     */
     private String find_NN(HashMap<String, Double> distantto) {
         HashMap<String, Double> distotype = new HashMap<String, Double>();
         HashMap<String, String> NNname = new HashMap<String, String>();

src/fr/imag/Scidetect/Checker/Indexer.java

@@ -29,6 +29,11 @@ public class Indexer {
 
     private Object content;
 
+    /**
+     * @param content
+     * @param textfile
+     * @throws FileNotFoundException
+     */
     public void index(String content, File textfile) throws FileNotFoundException {
         String filename = textfile.getName().substring(0,textfile.getName().lastIndexOf("."));
         filename+=".txt";

src/fr/imag/Scidetect/Logger/Log.java

@@ -53,6 +53,9 @@ public class Log {
         }
     }
 
+    /**
+     * @param conclusion
+     */
     public void savelog(String conclusion) {
          File distantout ;
         if (!loglocation.equals("logs/")) {
@@ -70,8 +73,9 @@ public class Log {
 
             out.close();
         } catch (FileNotFoundException e) {
-            // TODO Auto-generated catch block
-            e.printStackTrace();
+        	System.out.println("***** Scidetect : Output file error \n");    
+            System.out.println("***** Most probably the specified file is a Dir \n");
+            //e.printStackTrace();
         }
     }
 }

src/fr/imag/Scidetect/TextExtractor/pdfextractor.java

@@ -44,14 +44,21 @@ public class pdfextractor {
         try {
             pd = PDDocument.load(pdf.getPath());
             wr = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(totxt)));
-            stripper.writeText(pd, wr);
+            try {stripper.writeText(pd, wr);}
+            catch (Exception e) {
+                System.out.println("* Something went wrong during:");
+                System.out.println(" - txt extraction from pdf:"+pdf);
+                System.out.println("* Continuing anyway...");
+            }
             if (pd != null) {
                 pd.close();
             }
             // I use close() to flush the stream.
             wr.close();
         } catch (Exception e) {
-            // TODO: handle exception
+            System.out.println("* Something went wrong during:");
+            System.out.println(" - txt extraction from pdf:"+pdf);
+            System.out.println("* Continuing anyway...");
         }
 	//this seems to be faster but it seems like the app server does not support pdftotext
         //commandexecutor cm = new commandexecutor();

src/fr/imag/Scidetect/scigenchecker_local/ScigenChecker_Local.java

@@ -50,6 +50,13 @@ public class ScigenChecker_Local {
     private HashMap<String, HashMap<String, Double>> distant = new HashMap<String, HashMap<String, Double>>();
     private Boolean savedetaillog = false;
 
+    /**
+     * Read in the config file: 
+     *- places where to find samples of each class
+     *- default places where to write results.
+     * @throws FileNotFoundException
+     * @throws IOException
+     */
     private void readconfig() throws FileNotFoundException, IOException {
         File conf = new File("config.txt");
         BufferedReader br = new BufferedReader(new FileReader(conf));
@@ -75,6 +82,9 @@ public class ScigenChecker_Local {
 
     }
 
+    /**
+     * @throws IOException
+     */
     private void compute() throws IOException {
         if (testpath != null) {
             DateFormat dateFormat = new SimpleDateFormat("HH:mm dd.MM.yyyy");
@@ -88,8 +98,12 @@ public class ScigenChecker_Local {
                 tests = reader.readtests(testpath);
 
             } catch (Exception e) {
-
-                e.printStackTrace();
+                System.out.println("* Something went wrong during:");
+                System.out.println(" - reading the config file");
+                System.out.println(" - reading the samples (dir data)");
+                System.out.println(" - txt extraction from pdf");
+                System.out.println("* Continuing anyway...");
+                //e.printStackTrace();
             }
 
             DistantCalculator dc = new DistantCalculator();
@@ -103,31 +117,59 @@ public class ScigenChecker_Local {
                 log.savedetaillog(distant);
             }
         } else {
-            System.out.println("can not read path to test folder");
+            System.out.println("***** Can not read path to the folder:"+testpath);
+            System.out.println("***** The folder should contains file to check");
         }
     }
 
+	/**
+     * Parsing of the command line arguments: 
+     * where to find pdf files, where results should be written 
+     * @param args
+     */
     public void readargs(String[] args) {
-
-        for (int i = 0; i < args.length; i += 1) {
-            // System.out.println(args[i]);
-            if (args[i].equals("-l")) {
-                Log.loglocation = args[i + 1];
-            }
-            if (args[i].equals("-c")) {
-                testpath = args[i + 1];
-            }
-            if (args[i].equals("-d")) {
-                savedetaillog = true;
-            }
-        }
+    	if (args.length > 0) {
+    		for (int i = 0; i < args.length; i += 1) {
+    			// System.out.println(args[i]);
+    			if (args[i].equals("-l")) {
+    				Log.loglocation = args[i + 1];
+    			}
+    			if (args[i].equals("-c")) {
+    				testpath = args[i + 1];
+    			}
+    			if (args[i].equals("-d")) {
+    				savedetaillog = true;
+    			}
+    			if (args[i].equals("-h")) {
+    				printUsage();
+    			}
+    		}
+    	} else
+    		{printUsage();}
     }
 
     /**
+     * To print usage (-h) 
+     */
+    private static void printUsage() {
+    	System.out.println("***** Scigen & Co Checker \n");    
+    	System.out.println("To test all files in a directory <pathToFilesDirToTest>:");
+    	System.out.println("java -jar ScigenChecker_local.jar -l <pathToLogFile> -c <pathToFilesDirToTest> \n");
+    	System.out.println("To print usage:");
+    	System.out.println("java -jar ScigenChecker_local.jar -h \n");
+        System.out.println("***** \n");
+    }
+    
+    /**
+     * This is the standalone checker. All pdf files in the dir specified after -c are 
+     * checked against classes found in the dir "data". Results are written in the log 
+     * file specified by the -l option. If -d is given a detailled log is produced. 
+     * Example: testing all pdf files in a directory MyConf/PDF/ and having results 
+     * in the MyConf/checklog.txt:
+     * java -jar ScigenChecker_local.jar -l MyConf/checklog.txt -c MyConf/PDF/
      * @param args the command line arguments
      */
     public static void main(String[] args) throws IOException {
-
         ScigenChecker_Local a = new ScigenChecker_Local();
         a.readconfig();
         a.readargs(args);