[MOBY-guts] biomoby commit
Nina Opushneva
nopushneva at pub.open-bio.org
Thu Apr 14 16:45:37 UTC 2005
nopushneva
Thu Apr 14 12:45:37 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/util
In directory pub.open-bio.org:/tmp/cvs-serv12921
Modified Files:
DBConnector.java Report.java XMLBuilder.java
Log Message:
recent version
moby-live/Java/src/main/org/biomoby/registry/rdfagent/util DBConnector.java,1.1,1.2 Report.java,1.1,1.2 XMLBuilder.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/util/DBConnector.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/util/DBConnector.java 2004/10/28 17:55:43 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/util/DBConnector.java 2005/04/14 16:45:37 1.2
@@ -1,153 +1,155 @@
-package org.biomoby.registry.rdfagent.util;
-
-
-import java.sql.Connection;
-import java.sql.DriverManager;
-import java.sql.SQLException;
-
-
-/**
- * @author Nina Opushneva
- *
- * Establish a connection with a database
- */
-
-public class DBConnector
- {
- private static String url = Constants.DB_URL;
- private static String driverClassName = Constants.DB_DRIVER_CLASS;
- private static String dbUserName = Constants.DB_USER;
- private static String dbPwd = Constants.DB_PASSWD;
-
-
-
-
- public static Connection con;
-
- /** get a connect to database
- *
- * @return Connection
- * If the connection doesn't exists, get the new connection
- * If the connection exists but have been closed, get the new connection
- * Something wrong with the existing connection, get new one
- */
-
- public static Connection getConnection()
- {
-
- if (con == null) //If the connection doesn't exists, get the new connection
- {
- con = getNewConnection();
- }
- else
- {
- try {
- if(con.isClosed()) // If the connection exists but have been closed, get the new connection
- {
- con = getNewConnection();
- }
- }
- catch (SQLException e) // Something wrong with the existing connection, get new one
- {
- Log.info(e.getMessage());
- con = getNewConnection();
- }
- }
- return con;
- }
-
-
- /** close a connect to database
- *
- */
-
- public static void closeConnection()
- {
- if (con != null) //If the connection exists, try to close it
- {
-
- try
- {
- con.close();
- }
- catch (SQLException e)
- {
- Log.severe(e.getMessage());
- // do nothing
- }
- }
- }
-
-/** set a database User name
- * @param userName - the name of user
- *
-*/
-
- public static void setDBUserName(final String userName){
- dbUserName = userName;
- }
-
-
-/** set a database password
- * @param password - the database password
- *
- */
-
- public static void setDBPassword(final String password){
- dbPwd = password;
- }
-
-
-/** set an URL
- * @param URL - URL address for a database
- *
- */
-
- public static void setURL(final String URL){
- url = URL;
- }
-
-
- /** set a Driver class
- * @param driverClass - the name of Driver class
- *
- */
-
- public static void setDriverClass(final String driverClass){
- driverClassName = driverClass;
- }
-
-
-/** get a new connection
- *
- *
- */
-
- private static Connection getNewConnection()
- {
-
- try
- {
- Class.forName(driverClassName);
- }
- catch(ClassNotFoundException e)
- {
- // e.printStackTrace();
- Log.severe(e.getMessage());
- }
-
- try
- {
- con = DriverManager.getConnection(url, dbUserName, dbPwd);
- }
- catch (SQLException e)
- {
- Log.severe(e.getMessage());
- }
-
- return con;
- }
-
-
-
-}
+package org.biomoby.registry.rdfagent.util;
+
+
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.SQLException;
+
+
+/**
+ * @author Nina Opushneva
+ *
+ * Establish a connection with a database
+ */
+
+public class DBConnector
+ {
+ private static String url = Constants.DB_URL;
+ private static String driverClassName = Constants.DB_DRIVER_CLASS;
+ private static String dbUserName = Constants.DB_USER;
+ private static String dbPwd = Constants.DB_PASSWD;
+
+
+
+
+ public static Connection con;
+
+ /** get a connect to database
+ *
+ * @return Connection
+ * If the connection doesn't exists, get the new connection
+ * If the connection exists but have been closed, get the new connection
+ * Something wrong with the existing connection, get new one
+ */
+
+ public static Connection getConnection()
+ {
+
+ if (con == null) //If the connection doesn't exists, get the new connection
+ {
+ con = getNewConnection();
+ }
+ else
+ {
+ try {
+ if(con.isClosed()) // If the connection exists but have been closed, get the new connection
+ {
+ con = getNewConnection();
+ }
+ }
+ catch (SQLException e) // Something wrong with the existing connection, get new one
+ {
+ Log.info(e.getMessage());
+// e.getMessage();
+ con = getNewConnection();
+ }
+ }
+ return con;
+ }
+
+
+ /** close a connect to database
+ *
+ */
+
+ public static void closeConnection()
+ {
+ if (con != null) //If the connection exists, try to close it
+ {
+
+ try
+ {
+ con.close();
+ }
+ catch (SQLException e)
+ {
+ Log.severe(e.getMessage());
+// e.getMessage();
+ }
+ }
+ }
+
+/** set a database User name
+ * @param userName - the name of user
+ *
+*/
+
+ public static void setDBUserName(final String userName){
+ dbUserName = userName;
+ }
+
+
+/** set a database password
+ * @param password - the database password
+ *
+ */
+
+ public static void setDBPassword(final String password){
+ dbPwd = password;
+ }
+
+
+/** set an URL
+ * @param URL - URL address for a database
+ *
+ */
+
+ public static void setURL(final String URL){
+ url = URL;
+ }
+
+
+ /** set a Driver class
+ * @param driverClass - the name of Driver class
+ *
+ */
+
+ public static void setDriverClass(final String driverClass){
+ driverClassName = driverClass;
+ }
+
+
+/** get a new connection
+ *
+ *
+ */
+
+ private static Connection getNewConnection()
+ {
+
+ try
+ {
+ Class.forName(driverClassName);
+ }
+ catch(ClassNotFoundException e)
+ {
+// e.printStackTrace();
+ Log.severe(e.getMessage());
+ }
+
+ try
+ {
+ con = DriverManager.getConnection(url, dbUserName, dbPwd);
+ }
+ catch (SQLException e)
+ {
+ Log.severe(e.getMessage());
+// e.getMessage();
+ }
+
+ return con;
+ }
+
+
+
+}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/util/Report.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/util/Report.java 2004/10/28 17:55:43 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/util/Report.java 2005/04/14 16:45:37 1.2
@@ -16,10 +16,71 @@
import java.io.FileWriter;
import java.io.IOException;
import java.io.File;
+import java.util.ArrayList;
+import org.biomoby.registry.rdfagent.util.*;
+import org.biomoby.registry.rdfagent.verifier.*;
public class Report {
+ static ArrayList mr = null;
+ static ArrayList ds = null;
+
+ public static void add(String line){
+
+ if(mr == null){
+ mr = new ArrayList();
+ }
+ mr.add(line);
+
+ }
+
+ public static void doBuild(String line){
+
+ if(ds == null){
+ ds = new ArrayList();
+ }
+ ds.add(line);
+
+ }
+
+ public static void send(String signURL){
+
+ String message = "";
+
+ if(mr != null){
+
+ StringBuffer mes1 = new StringBuffer();
+
+ for (int i=0; i < mr.size(); i++){
+ mes1.append(mr.get(i).toString()+"\n");
+ }
+ message += mes1;
+ }
+ if(ds != null){
+
+ StringBuffer mes2 = new StringBuffer();
+
+ for (int i=0; i < ds.size(); i++){
+ mes2.append(ds.get(i).toString()+"\n");
+ }
+ message += mes2;
+ }
+
+ if (Constants.MB_MAIL_SERVER != null | Constants.MB_MAIL_SERVER.equals("") ){
+
+ String to = "";
+ to = DataMngr.getContactEmail(signURL);
+
+ if (to.equals("")){
+ to = "opushneva at yahoo.ca";
+
+ }
+ String subject = "The RDFagent Report";
+ Communicator.sendMail(to,subject,message.toString(),Constants.MB_FROM); // send message to the service provider - that service was deregistered
+ }
+ }
+
public static void createFile(String fileName){
try {
File file = new File(fileName);
@@ -34,6 +95,7 @@
file.createNewFile();
}
} catch (IOException e) {
+ Log.warning(e.getMessage());
}
}
@@ -46,11 +108,12 @@
out.newLine();
out.close();
} catch (IOException e) {
+ Log.warning(e.getMessage());
}
}
- public static void doBuild(String line) {
+/* public static void doBuild(String line) {
try {
String path = Constants.RDFagentHome;
@@ -59,10 +122,11 @@
out.newLine();
out.close();
} catch (IOException e) {
+ Log.warning(e.getMessage());
}
}
-
+*/
public static void doSave(String file,String line) {
@@ -73,6 +137,7 @@
out.newLine();
out.close();
} catch (IOException e) {
+ Log.warning(e.getMessage());
}
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/util/XMLBuilder.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/util/XMLBuilder.java 2005/04/07 22:31:34 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/util/XMLBuilder.java 2005/04/14 16:45:37 1.3
@@ -31,6 +31,7 @@
openInpOut("Input");
int authId = DataMngr.getAuthIdByServNameAndSignURL(servName,signURL);
int servInstId = DataMngr.getServInstId(servName,authId);
+//System.out.println("servInstId = "+servInstId);
DataMngr.getSimpleCollectInput(servInstId);
DataMngr.getSecondary(servInstId);
closeInpOut("Input");
@@ -83,8 +84,10 @@
if (nsType!=null){
String[] result = nsType.split(",");
- for (int i=0; i<result.length; i++) {
+ for (int i=0; i<result.length; i++) {
+ if (!result[i].equals("")){
Report.doBuild(" <namespace_type_uris>"+result[i]+"</namespace_type_uris>");
+ }
}
}
@@ -107,6 +110,7 @@
}
}catch(Exception e) {
Log.severe(e.getMessage());
+// e.getMessage();
}
}
@@ -142,7 +146,7 @@
}catch(Exception e) {
Log.severe(e.getMessage());
-
+// e.getMessage();
}
}
@@ -169,6 +173,9 @@
public static void startServiceXml(){
+ Report.doBuild("");
+ Report.doBuild("XMLs of the deleted services:");
+ Report.doBuild("");
Report.doBuild("<?xml version = '1.0'?>");
}
}
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