application properties override

src/main/java/services/change_detection/ChangeDetectionImpl.java

@@ -35,6 +35,7 @@
 import org.openrdf.query.resultio.text.tsv.SPARQLResultsTSVWriter;
 import org.openrdf.repository.RepositoryException;
 import org.diachron.detection.repositories.SesameVirtRep;
+import utils.PropertiesManager;
 
 /**
  * REST Web Service
@@ -44,7 +45,7 @@
 @Path("change_detection")
 public class ChangeDetectionImpl {
 
-    private static String propFile = "C:/config.properties";
+    PropertiesManager propertiesManager = PropertiesManager.getPropertiesManager();
 
     public ChangeDetectionImpl() {
     }
@@ -110,26 +111,14 @@ public Response changeDetectJSON(String inputMessage) {
                     throw new ParseException(-1);
                 }
                 ///
-                Properties properties = new Properties();
-                try {
-                    properties.load(new FileInputStream(propFile));
-//                    properties.load(this.getClass().getResourceAsStream(propFile));
-                } catch (IOException ex) {
-                    String message = ex.getMessage();
-                    boolean result = false;
-                    int code = 400;
-                    String json = "{ \"Message\" : " + message + ", \"Result\" : " + result + " }";
-                    return Response.status(code).entity(json).build();
-                }
-                ///
-                String datasetUri = properties.getProperty("Dataset_Uri");
-                String changesOntologySchema = properties.getProperty("Changes_Ontology_Schema");
+                String datasetUri = propertiesManager.getPropertyValue("Dataset_Uri");
+                String changesOntologySchema = propertiesManager.getPropertyValue("Changes_Ontology_Schema");
                 ChangesDetector detector = null;
                 try {
-                    ChangesManager cManager = new ChangesManager(properties, datasetUri, oldVersion, newVersion, false);
+                    ChangesManager cManager = new ChangesManager(propertiesManager.getProperties(), datasetUri, oldVersion, newVersion, false);
                     String changesOntology = cManager.getChangesOntology();
                     cManager.terminate();
-                    detector = new ChangesDetector(properties, changesOntology, changesOntologySchema);
+                    detector = new ChangesDetector(propertiesManager.getProperties(), changesOntology, changesOntologySchema);
                 } catch (Exception ex) {
                     String json = "{ \"Success\" : false, "
                             + "\"Message\" : \"Exception Occured: " + ex.getMessage() + " \" }";
@@ -186,16 +175,14 @@ public Response changeDetectJSON(String inputMessage) {
     @Produces(MediaType.APPLICATION_JSON)
     public Response queryChangesOntologyGet(@QueryParam("query") String query,
             @QueryParam("format") String format) {
-        Properties prop = new Properties();
         OutputStream output = null;
         try {
-            prop.load(new FileInputStream(propFile));
 //            prop.load(this.getClass().getResourceAsStream(propFile));
-            String ip = prop.getProperty("Repository_IP");
-            String username = prop.getProperty("Repository_Username");
-            String password = prop.getProperty("Repository_Password");
-            String changesOntol = prop.getProperty("Changes_Ontology");
-            int port = Integer.parseInt(prop.getProperty("Repository_Port"));
+            String ip = propertiesManager.getPropertyValue("Repository_IP");
+            String username = propertiesManager.getPropertyValue("Repository_Username");
+            String password = propertiesManager.getPropertyValue("Repository_Password");
+            String changesOntol = propertiesManager.getPropertyValue("Changes_Ontology");
+            int port = Integer.parseInt(propertiesManager.getPropertyValue("Repository_Port"));
             SesameVirtRep sesame = new SesameVirtRep(ip, port, username, password);
             query = query.replace(" where ", " from <" + changesOntol + "> ");
             TupleQuery tupleQuery = sesame.getCon().prepareTupleQuery(QueryLanguage.SPARQL, query);
@@ -233,8 +220,6 @@ public String toString() {
             tupleQuery.evaluate(writer);
         } catch (MalformedQueryException | QueryEvaluationException | TupleQueryResultHandlerException | RepositoryException ex) {
             return Response.status(400).entity(ex.getMessage()).build();
-        } catch (IOException ex) {
-            return Response.status(400).entity(ex.getMessage()).build();
         }
         return Response.status(200).entity(output.toString()).build();
     }
@@ -297,14 +282,12 @@ public Response queryChangesOntologyPost(String inputMessage) {
                     throw new ParseException(-1);
                 }
                 ///
-                Properties prop = new Properties();
-                prop.load(new FileInputStream(propFile));
 //                prop.load(this.getClass().getResourceAsStream(propFile));
-                String ip = prop.getProperty("Repository_IP");
-                String username = prop.getProperty("Repository_Username");
-                String password = prop.getProperty("Repository_Password");
-                String changesOntol = prop.getProperty("Changes_Ontology");
-                int port = Integer.parseInt(prop.getProperty("Repository_Port"));
+                String ip = propertiesManager.getPropertyValue("Repository_IP");
+                String username = propertiesManager.getPropertyValue("Repository_Username");
+                String password = propertiesManager.getPropertyValue("Repository_Password");
+                String changesOntol = propertiesManager.getPropertyValue("Changes_Ontology");
+                int port = Integer.parseInt(propertiesManager.getPropertyValue("Repository_Port"));
                 SesameVirtRep sesame = new SesameVirtRep(ip, port, username, password);
                 query = query.replace(" where ", " from <" + changesOntol + "> ");
                 TupleQuery tupleQuery = sesame.getCon().prepareTupleQuery(QueryLanguage.SPARQL, query);
@@ -344,8 +327,6 @@ public String toString() {
             }
         } catch (MalformedQueryException | QueryEvaluationException | TupleQueryResultHandlerException | RepositoryException ex) {
             return Response.status(400).entity(ex.getMessage()).build();
-        } catch (IOException ex) {
-            return Response.status(400).entity(ex.getMessage()).build();
         } catch (ParseException ex) {
             String message = "JSON input message could not be parsed.";
             String json = "{ \"Success\" : false, "

src/main/java/services/change_detection/ComplexChangeImpl.java

@@ -24,6 +24,7 @@
 import org.diachron.detection.complex_change.CCDefinitionError.CODE;
 import org.diachron.detection.complex_change.CCManager;
 import org.diachron.detection.repositories.JDBCVirtuosoRep;
+import utils.PropertiesManager;
 import utils.Utils;
 
 /**
@@ -34,7 +35,7 @@
 @Path("complex_change")
 public class ComplexChangeImpl {
 
-    private static String propFile = "C:/config.properties";
+    PropertiesManager propertiesManager = PropertiesManager.getPropertiesManager();
 
     /**
      * Creates a new instance of ComplexChangeImpl
@@ -91,26 +92,16 @@ public Response getCCJSON(@PathParam("com_change") String name) {
         boolean result = false;
         String message = null;
         int code = 0;
-        Properties prop = new Properties();
-        try {
-            prop.load(new FileInputStream(propFile));
-//            prop.load(this.getClass().getResourceAsStream(propFile));
-        } catch (IOException ex) {
-            message = ex.getMessage();
-            result = false;
-            code = 400;
-            String json = "{ \"Message\" : " + message + ", \"Result\" : " + result + " }";
-            return Response.status(code).entity(json).build();
-        }
+
         JDBCVirtuosoRep jdbcRep;
         try {
-            jdbcRep = new JDBCVirtuosoRep(prop);
+            jdbcRep = new JDBCVirtuosoRep(propertiesManager.getProperties());
         } catch (ClassNotFoundException | SQLException | IOException ex) {
             result = false;
             String json = "{ \"Message\" : \"Exception Occured: " + ex.getMessage() + ", \"Result\" : " + result + " }";
             return Response.status(400).entity(json).build();
         }
-        String ontologySchema = prop.getProperty("Changes_Ontology_Schema");
+        String ontologySchema = propertiesManager.getPropertyValue("Changes_Ontology_Schema");
         String query = "select ?json from <" + ontologySchema + "> where { ?s co:name \"" + name + "\"; co:json ?json. }";
         ResultSet res = jdbcRep.executeSparqlQuery(query, false);
         try {
@@ -157,23 +148,15 @@ public Response getCCJSON(@PathParam("com_change") String name) {
     @Path("{com_change}")
     @Produces(MediaType.APPLICATION_JSON)
     public Response deleteCCJSON(@PathParam("com_change") String name) {
-        Properties properties = new Properties();
         String message = null;
         int code;
         boolean result = false;
-        try {
-            properties.load(new FileInputStream(propFile));
-//            properties.load(this.getClass().getResourceAsStream(propFile));
-        } catch (IOException ex) {
-            result = false;
-            String json = "{ \"Message\" : \"Exception Occured: " + ex.getMessage() + ", \"Result\" : " + result + " }";
-            return Response.status(400).entity(json).build();
-        }
-        String changesOntologySchema = properties.getProperty("Changes_Ontology_Schema");
-        String datasetUri = properties.getProperty("Dataset_Uri");
+
+        String changesOntologySchema = propertiesManager.getPropertyValue("Changes_Ontology_Schema");
+        String datasetUri = propertiesManager.getPropertyValue("Dataset_Uri");
         CCManager manager = null;
         try {
-            manager = new CCManager(properties, changesOntologySchema);
+            manager = new CCManager(propertiesManager.getProperties(), changesOntologySchema);
         } catch (Exception ex) {
             result = false;
             String json = "{ \"Message\" : \"Exception Occured: " + ex.getMessage() + ", \"Result\" : " + result + " }";
@@ -289,19 +272,11 @@ public Response deleteCCJSON(@PathParam("com_change") String name) {
     @Consumes(MediaType.APPLICATION_JSON)
     @Produces(MediaType.APPLICATION_JSON)
     public Response defineCCJSON(String inputMessage) {
-        Properties properties = new Properties();
-        try {
-            properties.load(new FileInputStream(propFile));
-//            properties.load(this.getClass().getResourceAsStream(propFile));
-        } catch (IOException ex) {
-            boolean result = false;
-            String json = "{ \"Message\" : \"Exception Occured: " + ex.getMessage() + ", \"Result\" : " + result + " }";
-            return Response.status(400).entity(json).build();
-        }
+
         CCManager ccDef = null;
-        String changesOntologySchema = properties.getProperty("Changes_Ontology_Schema");
+        String changesOntologySchema = propertiesManager.getPropertyValue("Changes_Ontology_Schema");
         try {
-            ccDef = JSONMessagesParser.createCCDefinition(properties, inputMessage, changesOntologySchema);
+            ccDef = JSONMessagesParser.createCCDefinition(propertiesManager.getProperties(), inputMessage, changesOntologySchema);
         } catch (Exception ex) {
             boolean result = false;
             String json = "{ \"Message\" : \"Exception Occured: " + ex.getMessage() + ", \"Result\" : " + result + " }";

src/main/java/utils/PropertiesManager.java

@@ -0,0 +1,56 @@
+package utils;
+
+import java.io.*;
+import java.util.Properties;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+/**
+ * @author Simon Jupp
+ * @date 08/05/2015
+ * Samples, Phenotypes and Ontologies Team, EMBL-EBI
+ */
+public class PropertiesManager {
+
+    private static PropertiesManager propManager = null;
+    private static String initFilePath = "config.properties";
+    private static Properties prop;
+
+    public static PropertiesManager getPropertiesManager()
+    {
+        if(propManager==null)
+        {
+            try {
+                ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
+                InputStream input = classLoader.getResourceAsStream(initFilePath);
+                prop = new Properties();
+                if (input != null) {
+                    prop.load(input);
+                }
+
+                if (System.getProperty("diachron.config.location") != null) {
+                    InputStream overideInput = new FileInputStream(new File(System.getProperty("diachron.config.location")));
+                    Properties override = new Properties();
+                    override.load(overideInput);
+                    prop.putAll(override);
+                }
+
+                propManager = new PropertiesManager();
+            } catch (IOException ex) {
+                Logger.getLogger(PropertiesManager.class.getName()).log(Level.SEVERE, null, ex);
+            }
+        }
+
+        return propManager;
+    }
+
+    public String getPropertyValue(String key)
+    {
+        return prop.getProperty(key);
+    }
+
+    public Properties getProperties () {
+        return prop;
+    }
+}
+