Fixed error where Properties File was not closed after loading.

Fixed error where File resource was not closed when loading properties
from file.

Also updated incorrect examples.

This update addresses part #1 of issue #13
 (#13)

README.bioc

@@ -14,30 +14,33 @@ Below is an example using BioC Processing with MetaMapLite
 		                   "config/metamaplite.properties");
     Properties configProperties = new Properties();
     // set any in-line properties here.
-	configProperties.load(new FileReader(configPropertiesFilename));
-	configProperties.setProperty("metamaplite.semanticgroup",
-	"acab,anab,bact,cgab,dsyn,emod,inpo,mobd,neop,patf,sosy");
-	Properties properties =
-	  Configuration.mergeConfiguration(configProperties,
+    FileReader fr = new FileReader(configPropertiesFilename);
+    configProperties.load(fr);
+    fr.close();
+
+    configProperties.setProperty("metamaplite.semanticgroup",
+    "acab,anab,bact,cgab,dsyn,emod,inpo,mobd,neop,patf,sosy");
+    Properties properties =
+        Configuration.mergeConfiguration(configProperties,
 					   defaultConfiguration);
-	BioCProcess process = new BioCProcess(properties);
+    BioCProcess process = new BioCProcess(properties);
 
-	// read BioC XML collection
-	Reader inputReader = new FileReader(inputFile);
-	BioCFactory bioCFactory = BioCFactory.newFactory("STANDARD");
-	BioCCollectionReader collectionReader =
-	bioCFactory.createBioCCollectionReader(inputReader);
-	BioCCollection collection = collectionReader.readCollection();
+    // read BioC XML collection
+    Reader inputReader = new FileReader(inputFile);
+    BioCFactory bioCFactory = BioCFactory.newFactory("STANDARD");
+    BioCCollectionReader collectionReader =
+    bioCFactory.createBioCCollectionReader(inputReader);
+    BioCCollection collection = collectionReader.readCollection();
 
-	// Run named entity recognition on collection
-	BioCCollection newCollection = process.processCollection(collection);
+    // Run named entity recognition on collection
+    BioCCollection newCollection = process.processCollection(collection);
 
     // write out the annotated collection
     File outputFile = new File(outputFilename);
-	Writer outputWriter = new PrintWriter(outputFile, "UTF-8");
-	BioCCollectionWriter collectionWriter = bioCFactory.createBioCCollectionWriter(outputWriter);
-	collectionWriter.writeCollection(newCollection);
-	outputWriter.close();
+    Writer outputWriter = new PrintWriter(outputFile, "UTF-8");
+    BioCCollectionWriter collectionWriter = bioCFactory.createBioCCollectionWriter(outputWriter);
+    collectionWriter.writeCollection(newCollection);
+    outputWriter.close();
 
 This process attempts to preserve any annotation present in the
 original BioC XML input.    Some annotations applied to BioC

README.md

@@ -291,8 +291,9 @@ Creating properties for configuring MetaMapLite Instance:
 
 Loading properties file in "config":
 
-    myProperties.load(new FileReader("config/metamaplite.properties"));
-
+    FileReader fr = new FileReader("config/metamaplite.properties");
+    myProperties.load(fr);
+    fr.close();
 
 Creating a metamap lite instance:
 
@@ -583,7 +584,9 @@ directory and specify that in servlet:
           this.properties.setProperty("metamaplite.index.directory","data/ivf/strict");
 		  ...
           // load user properties
-          this.properties.load(new FileReader(configPropertyFilename));
+          FileReader fr = new FileReader(configPropertyFilename);
+          myProperties.load(fr);
+          fr.close();
           this.metaMapLiteInst = new MetaMapLite(this.properties);
 		  ...
       	} catch (Exception e) {

src/main/java/examples/DirectLookup.java

@@ -39,7 +39,9 @@ public DirectLookup()
     this.myProperties.setProperty("metamaplite.excluded.termsfile", "data/specialterms.txt");
     // Loading properties file in "config", overriding previously
     // defined properties.
-    this.myProperties.load(new FileReader("config/metamaplite.properties"));
+    FileReader fr = new FileReader("config/metamaplite.properties");
+    myProperties.load(fr);
+    fr.close();
     this.mmIndexes = new MetaMapIvfIndexes(this.myProperties);
   }
 

src/main/java/examples/DirectLookupTermFile.java

@@ -45,7 +45,9 @@ public DirectLookupTermFile()
     this.myProperties.setProperty("metamaplite.excluded.termsfile", "data/specialterms.txt");
     // Loading properties file in "config", overriding previously
     // defined properties.
-    this.myProperties.load(new FileReader("config/metamaplite.properties"));
+    FileReader fr = new FileReader("config/metamaplite.properties");
+    myProperties.load(fr);
+    fr.close();
     this.mmIndexes = new MetaMapIvfIndexes(this.myProperties);
   }
 

src/main/java/examples/EntityLookup5Client.java

@@ -59,7 +59,9 @@ public EntityLookup5Client() {
       MetaMapLite.expandIndexDir(myProperties, installdir + "/data/ivf/2017AA/USAbase/strict");
       myProperties.setProperty("metamaplite.excluded.termsfile",
 			       installdir + "/data/specialterms.txt");
-      myProperties.load(new FileReader(installdir + "/config/metamaplite.properties"));
+      FileReader fr = new FileReader(installdir + "/config/metamaplite.properties");
+      myProperties.load(fr);
+      fr.close();
       myProperties.list(System.out);
       this.sentenceAnnotator = new OpenNLPPoSTagger(myProperties);
       this.sentenceExtractor = new OpenNLPSentenceExtractor(myProperties);

src/main/java/examples/Example.java

@@ -48,7 +48,9 @@ public static void main(String[] args)
 			     "/export/home/wjrogers/Projects/metamaplite/data/specialterms.txt");
     // Loading properties file in "config", overriding previously
     // defined properties.
-    myProperties.load(new FileReader("config/metamaplite.properties"));
+    FileReader fr = new FileReader("config/metamaplite.properties");
+    myProperties.load(fr);
+    fr.close();
 
     MetaMapLite metaMapLiteInst = new MetaMapLite(myProperties);
 

src/main/java/examples/Example2.java

@@ -52,7 +52,9 @@ public static void main(String[] args)
     MetaMapLite.expandIndexDir(myProperties);
     // Loading properties file in "config", overriding previously
     // defined properties.
-    myProperties.load(new FileReader("config/metamaplite.properties"));
+    FileReader fr = new FileReader("config/metamaplite.properties");
+    myProperties.load(fr);
+    fr.close();
     MetaMapLite metaMapLiteInst = new MetaMapLite(myProperties);
 
     // Processing Section

src/main/java/examples/Example3.java

@@ -65,7 +65,9 @@ public static void main(String[] args)
     MetaMapLite.expandIndexDir(myProperties);
     // Loading properties file in "config", overriding previously
     // defined properties.
-    myProperties.load(new FileReader("config/metamaplite.properties"));
+    FileReader fr = new FileReader("config/metamaplite.properties");
+    myProperties.load(fr);
+    fr.close();
     MetaMapLite metaMapLiteInst = new MetaMapLite(myProperties);
     MMI mmiInstance = new MMI();
     mmiInstance.initProperties(myProperties);

src/main/java/examples/ListAcronyms.java

@@ -61,7 +61,9 @@ public static void main(String[] args)
 			       "/export/home/wjrogers/Projects/metamaplite/data/specialterms.txt");
       MetaMapLite.expandIndexDir(myProperties);
       // override any properties with those in property file.
-      myProperties.load(new FileReader("config/metamaplite.properties"));
+      FileReader fr = new FileReader("config/metamaplite.properties");
+      myProperties.load(fr);
+      fr.close();
       SentenceExtractor sentenceExtractor = new OpenNLPSentenceExtractor(myProperties);
       ExtractAbbrev extractAbbr = new ExtractAbbrev();
       // Processing Section

src/main/java/examples/StreamPassageSentences.java

@@ -218,7 +218,9 @@ public StreamPassageSentences(String metaMapLiteRootDir,
 				    metaMapLiteRootDir + "/data/specialterms.txt");
       // Loading properties file in "config", overriding previously
       // defined properties.
-      // this.myProperties.load(new FileReader("config/metamaplite.properties"));
+      // FileReader fr = new FileReader("config/metamaplite.properties");
+      // myProperties.load(fr);
+      // fr.close();
       // this.mmIndexes = new MetaMapIvfIndexes(this.myProperties);
       this.myProperties.setProperty("metamaplite.postaglist",
 				    "CD,FW,RB,NN,NNS,NNP,NNPS,JJ,JJR,JJS,LS");

src/main/java/gov/nih/nlm/nls/metamap/lite/BioCPipeline.java

@@ -318,7 +318,9 @@ static BioCPipeline initPipeline()
     logger.debug("enter initPipeline");
 
     Properties properties = new Properties();
-    properties.load(new FileReader(configPropertyFilename));
+    FileReader fr = new FileReader(configPropertyFilename);
+    properties.load(fr);
+    fr.close();
     if (logger.isDebugEnabled()) {
       for (Map.Entry<Object,Object> entry: properties.entrySet()) {
 	logger.debug(entry.getKey() + " -> " + entry.getValue());
@@ -457,7 +459,9 @@ static Properties setConfiguration(String propertiesFilename,
       if (verbose) {
 	System.out.println("loading local configuration from " + localConfigurationFile);
       }
-      localConfiguration.load(new FileReader(localConfigurationFile));
+      FileReader fr = new FileReader(localConfigurationFile);
+      localConfiguration.load(fr);
+      fr.close();
       if (verbose) {
 	System.out.println("loaded " + localConfiguration.size() + " records from local configuration");
       }

src/main/java/gov/nih/nlm/nls/metamap/lite/BioCProcess.java

@@ -259,7 +259,9 @@ public static void main(String[] args)
 	String configPropertiesFilename = System.getProperty("metamaplite.propertyfile",
 							     "config/metamaplite.properties");
 	Properties configProperties = new Properties();
-	configProperties.load(new FileReader(configPropertiesFilename));
+	FileReader fr = new FileReader(configPropertiesFilename);
+	configProperties.load(fr);
+	fr.close();
 	Properties properties =
 	  Configuration.mergeConfiguration(configProperties,
 					   defaultConfiguration);

src/main/java/gov/nih/nlm/nls/metamap/lite/Pipeline.java

@@ -131,7 +131,9 @@ static Pipeline initPipeline()
     logger.debug("enter initPipeline");
 
     Properties properties = new Properties();
-    properties.load(new FileReader(configPropertyFilename));
+    FileReader fr = new FileReader(configPropertyFilename);
+    properties.load(fr);
+    fr.close();
     if (logger.isDebugEnabled()) {
       for (Map.Entry<Object,Object> entry: properties.entrySet()) {
 	logger.debug(entry.getKey() + " -> " + entry.getValue());

src/main/java/gov/nih/nlm/nls/metamap/lite/SimplePipeline.java

@@ -150,7 +150,6 @@ public void init()
     throws IOException, FileNotFoundException
   {
     Properties properties = new Properties();
-    // properties.load(?);
     this.entityLookup = new EntityLookup4(properties);
     initSentenceDetector();
     initTokenizer();

src/main/java/gov/nih/nlm/nls/ner/MetaMapLite.java

@@ -627,6 +627,37 @@ public List<AbbrInfo> getAcronymList(List<BioCDocument> documentList) {
     return infos;
   }
 
+  /** Document abbreviation information class */
+  public class DocInfo {
+    /** document id */
+    String id;
+    /** list of abbreviation information instances */
+    List <AbbrInfo> infolist;
+    public DocInfo(String id, List <AbbrInfo> infos) {
+      this.id = id;
+      this.infolist = infos;
+    }
+    public String getId() { return this.id; }
+    public List<AbbrInfo> getInfolist() { return this.infolist; }
+  }
+
+  public List<DocInfo> getDocAcronymList(List<BioCDocument> documentList) {
+    List <DocInfo> docInfoList = new ArrayList<DocInfo>();
+    for (BioCDocument document: documentList) {
+      List <AbbrInfo> infos = new ArrayList<AbbrInfo>();
+      for (BioCPassage passage: document.getPassages()) {
+	// for (Sentence sentence: this.sentenceExtractor.createSentenceList(passage.getText())) {
+	for (AbbrInfo abbrInfo: extractAbbr.extractAbbrPairsString(passage.getText())) {
+	  infos.add(new AbbrInfo(abbrInfo.shortForm.replace("\n", " "), abbrInfo.shortFormIndex,
+				 abbrInfo.longForm.replace("\n", " "), abbrInfo.longFormIndex));
+	}
+	//}
+      }
+      docInfoList.add(new DocInfo(document.getID(), infos));
+    }
+    return docInfoList;
+  }
+
   public static List<String> loadInputFileList(String inputfileListFileName)
     throws FileNotFoundException, IOException
   {
@@ -828,7 +859,9 @@ static Properties setConfiguration(String propertiesFilename,
       if (verbose) {
 	System.out.println("loading local configuration from " + localConfigurationFile);
       }
-      localConfiguration.load(new FileReader(localConfigurationFile));
+      FileReader fr = new FileReader(localConfigurationFile);
+      localConfiguration.load(fr);
+      fr.close();
       logger.info("loaded " + localConfiguration.size() + " records from local configuration");
       if (verbose) {
 	System.out.println("loaded " + localConfiguration.size() + " records from local configuration");
@@ -895,9 +928,12 @@ void listSentences(List<BioCDocument> documentList)
   void listAcronyms(List<BioCDocument> documentList) {
     PrintWriter pw = new PrintWriter(new OutputStreamWriter(System.out,
 							    Charset.forName("utf-8")));
-    for (AbbrInfo acronym: this.getAcronymList(documentList)) {
-      pw.println(acronym.shortForm + "|" + acronym.shortFormIndex + "|" +
-		 acronym.longForm + "|" + acronym.longFormIndex );
+    for (DocInfo docInfo: this.getDocAcronymList(documentList)) {
+      for (AbbrInfo acronym: docInfo.getInfolist()) {
+	pw.println(docInfo.getId() + "|" +
+		   acronym.shortForm + "|" + acronym.shortFormIndex + "|" +
+		   acronym.longForm + "|" + acronym.longFormIndex );
+     }
     }
     pw.flush();
   }
@@ -1011,9 +1047,12 @@ void listAcronyms(String filename,
     File outputFile = abortIfFileExists(outputFilename, overwritefile);
     PrintWriter pw = new PrintWriter(new BufferedWriter
 				     (new FileWriter(outputFile)));
-    for (AbbrInfo acronym: this.getAcronymList(documentList)) {
-      pw.println(acronym.shortForm + "|" + acronym.shortFormIndex + "|" +
-		 acronym.longForm + "|" + acronym.longFormIndex );
+    for (DocInfo docInfo: this.getDocAcronymList(documentList)) {
+      for (AbbrInfo acronym: docInfo.getInfolist()) {
+	pw.println(docInfo.getId() + "|" +
+		   acronym.shortForm + "|" + acronym.shortFormIndex + "|" +
+		   acronym.longForm + "|" + acronym.longFormIndex );
+      }
     }
     pw.close();
   }