diff --git a/uk/ac/sanger/artemis/chado/ChadoCvTermView.java b/uk/ac/sanger/artemis/chado/ChadoCvTermView.java
index 9bd1d2b7c1b85c46fb5517e400cb9fcdd4ef3620..33d1ac7aacd4cc0dcc3c22150c4508fca21dd9bd 100644
--- a/uk/ac/sanger/artemis/chado/ChadoCvTermView.java
+++ b/uk/ac/sanger/artemis/chado/ChadoCvTermView.java
@@ -29,6 +29,7 @@ import org.gmod.schema.cv.CvTerm;
import uk.ac.sanger.artemis.components.genebuilder.JExtendedComboBox;
import uk.ac.sanger.artemis.components.genebuilder.cv.CvTermsComparator;
+import uk.ac.sanger.artemis.util.DatabaseLocationParser;
import java.awt.BorderLayout;
import java.awt.Color;
@@ -345,33 +346,18 @@ public class ChadoCvTermView extends JFrame
pfield = new JPasswordField(16);
bacross.add(pfield);
+
+ DatabaseLocationParser dlp = new DatabaseLocationParser();
// given -Dchado=localhost:port/dbname?username
if(System.getProperty("chado") != null)
{
String db_url = System.getProperty("chado").trim();
- int index;
- if((index = db_url.indexOf(":")) > -1)
- {
- inServer.setText(db_url.substring(0, index));
- int index2;
- if((index2 = db_url.indexOf("/")) > -1)
- {
- inPort.setText(db_url.substring(index + 1, index2));
- int index3;
- if((index3 = db_url.indexOf("?")) > -1)
- {
- inDB.setText(db_url.substring(index2 + 1, index3));
- inUser.setText(db_url.substring(index3 + 1));
-
- /*
- * if(!prompt_user) { location = "jdbc:postgresql://"
- * +inServer.getText().trim()+ ":" +inPort.getText().trim()+ "/"
- * +inDB.getText().trim()+ "?user=" +inUser.getText().trim(); return
- * true; }
- */
- }
- }
- }
+ dlp.setFromURLString(db_url);
+ inServer.setText(dlp.getHost());
+ inPort.setText("" + dlp.getPort());
+ inDB.setText(dlp.getDatabase());
+ inUser.setText(dlp.getUsername());
+
}
int n = JOptionPane.showConfirmDialog(null, bacross,
@@ -379,10 +365,14 @@ public class ChadoCvTermView extends JFrame
JOptionPane.QUESTION_MESSAGE);
if(n == JOptionPane.CANCEL_OPTION)
return false;
-
- location = "jdbc:postgresql://" + inServer.getText().trim() + ":"
- + inPort.getText().trim() + "/" + inDB.getText().trim() + "?user="
- + inUser.getText().trim();
+
+
+ dlp.setHost(inServer.getText());
+ dlp.setPort(inPort.getText());
+ dlp.setDatabase(inDB.getText());
+ dlp.setUsername(inUser.getText());
+
+ location = dlp.getCompleteURL();
System.setProperty("chado", location);
return true;
diff --git a/uk/ac/sanger/artemis/chado/ChadoDemo.java b/uk/ac/sanger/artemis/chado/ChadoDemo.java
index bed09f9ab153228fb4a2af203ac21abe02e987a3..b1b49370b02674b299fac026f011767874846138 100644
--- a/uk/ac/sanger/artemis/chado/ChadoDemo.java
+++ b/uk/ac/sanger/artemis/chado/ChadoDemo.java
@@ -79,7 +79,7 @@ import javax.swing.event.ListSelectionListener;
import javax.swing.event.ListSelectionEvent;
import uk.ac.sanger.artemis.util.ByteBuffer;
-
+import uk.ac.sanger.artemis.util.DatabaseLocationParser;
/**
* Chado data access example code. This searches for features by their
@@ -460,33 +460,18 @@ public class ChadoDemo
pfield = new JPasswordField(16);
bacross.add(pfield);
+
+ DatabaseLocationParser dlp = new DatabaseLocationParser();
// given -Dchado=localhost:port/dbname?username
if(System.getProperty("chado") != null)
{
String db_url = System.getProperty("chado").trim();
- int index;
- if((index = db_url.indexOf(":")) > -1)
- {
- inServer.setText(db_url.substring(0, index));
- int index2;
- if((index2 = db_url.indexOf("/")) > -1)
- {
- inPort.setText(db_url.substring(index + 1, index2));
- int index3;
- if((index3 = db_url.indexOf("?")) > -1)
- {
- inDB.setText(db_url.substring(index2 + 1, index3));
- inUser.setText(db_url.substring(index3 + 1));
-
- /*
- * if(!prompt_user) { location = "jdbc:postgresql://"
- * +inServer.getText().trim()+ ":" +inPort.getText().trim()+ "/"
- * +inDB.getText().trim()+ "?user=" +inUser.getText().trim(); return
- * true; }
- */
- }
- }
- }
+ dlp.setFromURLString(db_url);
+ inServer.setText(dlp.getHost());
+ inPort.setText("" + dlp.getPort());
+ inDB.setText(dlp.getDatabase());
+ inUser.setText(dlp.getUsername());
+
}
int n = JOptionPane.showConfirmDialog(null, bacross,
@@ -495,9 +480,12 @@ public class ChadoDemo
if(n == JOptionPane.CANCEL_OPTION)
return false;
- location = "jdbc:postgresql://" + inServer.getText().trim() + ":"
- + inPort.getText().trim() + "/" + inDB.getText().trim() + "?user="
- + inUser.getText().trim();
+ dlp.setHost(inServer.getText());
+ dlp.setPort(inPort.getText());
+ dlp.setDatabase(inDB.getText());
+ dlp.setUsername(inUser.getText());
+
+ location = dlp.getCompleteURL();
System.setProperty("chado", location);
diff --git a/uk/ac/sanger/artemis/chado/DbSqlConfig.java b/uk/ac/sanger/artemis/chado/DbSqlConfig.java
index 7752fcc4ad56e44d4b995985898b9c5196491cee..f3b7ec639a36550c6c2b475c3af38ab8f992c178 100644
--- a/uk/ac/sanger/artemis/chado/DbSqlConfig.java
+++ b/uk/ac/sanger/artemis/chado/DbSqlConfig.java
@@ -29,6 +29,8 @@ import com.ibatis.sqlmap.client.SqlMapClient;
import com.ibatis.sqlmap.client.SqlMapClientBuilder;
import com.ibatis.common.resources.Resources;
+import uk.ac.sanger.artemis.util.DatabaseLocationParser;
+
import javax.swing.JPasswordField;
import java.util.Properties;
import java.io.Reader;
@@ -62,23 +64,27 @@ public class DbSqlConfig
if(System.getProperty("chado") != null)
{
String url = System.getProperty("chado");
- int index = url.indexOf("?");
- int index2 = url.indexOf("user=");
+ DatabaseLocationParser dlp = new DatabaseLocationParser();
+ dlp.setFromURLString(url);
+// int index = url.indexOf("?");
+// int index2 = url.indexOf("user=");
properties = new Properties();
- int index3 = url.indexOf("://");
- if(index3 < 0)
- index3 = 0;
- else
- index3 = index3+3;
-
- properties.put("chado", url.substring(index3,index));
-
- if(index2 < 0)
- properties.put("username", url.substring(index+1));
- else
- properties.put("username", url.substring(index2+5));
-
+// int index3 = url.indexOf("://");
+// if(index3 < 0)
+// index3 = 0;
+// else
+// index3 = index3+3;
+
+// properties.put("chado", url.substring(index3,index));
+ properties.put("chado",url);
+
+// if(index2 < 0)
+// properties.put("username", url.substring(index+1));
+// else
+// properties.put("username", url.substring(index2+5));
+ properties.put("username",dlp.getUsername());
+
if(fpasswd != null && fpasswd.getPassword().length > 0)
properties.put("password", new String(fpasswd.getPassword()));
}
diff --git a/uk/ac/sanger/artemis/chado/JdbcDAO.java b/uk/ac/sanger/artemis/chado/JdbcDAO.java
index 6f1fa71484ab00c50e4bc4732e87cd81cf518c41..1f7d77ba65d4979ffffd7b5d587c9c6f892963be 100644
--- a/uk/ac/sanger/artemis/chado/JdbcDAO.java
+++ b/uk/ac/sanger/artemis/chado/JdbcDAO.java
@@ -32,6 +32,8 @@ import java.util.Collection;
import java.util.List;
import java.util.Vector;
+import uk.ac.sanger.artemis.util.DatabaseLocationParser;
+
import org.gmod.schema.sequence.Feature;
import org.gmod.schema.sequence.FeatureCvTerm;
import org.gmod.schema.sequence.FeatureCvTermProp;
@@ -81,9 +83,10 @@ public class JdbcDAO extends GmodDAO
conn = DriverManager.getConnection(location);
// assume we have a password
- final int index = location.indexOf("?user=");
- conn = DriverManager.getConnection(location.substring(0, index),
- location.substring(index + 6),
+ DatabaseLocationParser dlp = new DatabaseLocationParser();
+ dlp.setFromURLString(location);
+ conn = DriverManager.getConnection(dlp.getConnectionString(),
+ dlp.getUsername(),
new String(pfield.getPassword()));
}
diff --git a/uk/ac/sanger/artemis/components/ProjectProperty.java b/uk/ac/sanger/artemis/components/ProjectProperty.java
index 1011c641434c1bbcd5d5dc99d5b0d38aa721cd68..23d0eb83de1ea3f2a3b3eeaac3ed33e66089265a 100644
--- a/uk/ac/sanger/artemis/components/ProjectProperty.java
+++ b/uk/ac/sanger/artemis/components/ProjectProperty.java
@@ -76,6 +76,7 @@ import uk.ac.sanger.artemis.components.database.DatabaseEntrySource;
import uk.ac.sanger.artemis.components.database.DatabaseJPanel;
import uk.ac.sanger.artemis.util.Document;
import uk.ac.sanger.artemis.util.FileDocument;
+import uk.ac.sanger.artemis.util.DatabaseLocationParser;
/**
* Project file management system using a properties file.
@@ -726,9 +727,13 @@ public class ProjectProperty extends JFrame
private void openDatabase(final Splash splash, final String featureName)
{
String loc = System.getProperty("chado");
- int idx;
- if((idx = loc.indexOf("?")) > -1 && loc.indexOf("?user=") == -1)
- loc = loc.substring(0, idx+1) + "user=" + loc.substring(idx+1);
+ DatabaseLocationParser dlp = new DatabaseLocationParser();
+ dlp.setFromURLString(loc);
+
+
+// int idx;
+// if((idx = loc.indexOf("?")) > -1 && loc.indexOf("?user=") == -1)
+// loc = loc.substring(0, idx+1) + "user=" + loc.substring(idx+1);
if( entry_source == null ||
!entry_source.getLocation().endsWith(loc) )
diff --git a/uk/ac/sanger/artemis/components/database/DatabaseEntrySource.java b/uk/ac/sanger/artemis/components/database/DatabaseEntrySource.java
index 6eaa7396367b5265fd71fa40b8f227c2dc99cc42..2a41fcedf3c6ae7507d2fba8dcf0a3f61f5f79a4 100644
--- a/uk/ac/sanger/artemis/components/database/DatabaseEntrySource.java
+++ b/uk/ac/sanger/artemis/components/database/DatabaseEntrySource.java
@@ -30,6 +30,7 @@ import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.io.IOException;
import java.io.Serializable;
+import javax.swing.JCheckBox;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
@@ -43,6 +44,7 @@ import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.sequence.Bases;
import uk.ac.sanger.artemis.sequence.NoSequenceException;
import uk.ac.sanger.artemis.util.DatabaseDocument;
+import uk.ac.sanger.artemis.util.DatabaseLocationParser;
import uk.ac.sanger.artemis.util.InputStreamProgressListener;
import uk.ac.sanger.artemis.util.OutOfRangeException;
import uk.ac.sanger.artemis.util.StringVector;
@@ -185,13 +187,14 @@ public class DatabaseEntrySource implements EntrySource, Serializable
}
pfield = promptPanel.getPfield();
+ DatabaseLocationParser dlp = new DatabaseLocationParser();
+ dlp.setHost(promptPanel.getServer());
+ dlp.setPort(promptPanel.getPort());
+ dlp.setDatabase(promptPanel.getDb());
+ dlp.setUsername(promptPanel.getUser());
+ dlp.setSSL(promptPanel.getSSL());
- location = "jdbc:postgresql://" +
- promptPanel.getServer() + ":" +
- promptPanel.getPort() + "/" +
- promptPanel.getDb() + "?user=" +
- promptPanel.getUser();
-
+ location = dlp.getCompleteURL();
return true;
}
@@ -340,6 +343,7 @@ interface ILoginPrompt
String getPort();
String getDb();
String getUser();
+ boolean getSSL();
}
/**
@@ -353,6 +357,7 @@ class DatabaseLoginPrompt extends JPanel implements ILoginPrompt
private JTextField port;
private JTextField db;
private JTextField user;
+ private JCheckBox ssl;
public DatabaseLoginPrompt()
{
super(new GridBagLayout());
@@ -378,6 +383,9 @@ class DatabaseLoginPrompt extends JPanel implements ILoginPrompt
c.gridy = ++nrow;
add(new JLabel("Password : "), c);
+ c.gridy = ++nrow;
+ add(new JLabel("SSL : "), c);
+
// column 2
nrow = 1;
c.anchor = GridBagConstraints.WEST;
@@ -396,12 +404,16 @@ class DatabaseLoginPrompt extends JPanel implements ILoginPrompt
add(db, c);
c.gridy = ++nrow;
- user = new JTextField("afumigatus");
+ user = new JTextField("");
add(user, c);
c.gridy = ++nrow;
pfield = new JPasswordField(16);
add(pfield, c);
+
+ c.gridy = ++nrow;
+ ssl = new JCheckBox();
+ add(ssl, c);
// given -Dchado=localhost:port/dbname?username
if(System.getProperty("chado") != null)
@@ -436,44 +448,13 @@ class DatabaseLoginPrompt extends JPanel implements ILoginPrompt
private void setFromURL(String db_url)
{
- if(db_url.startsWith("jdbc:postgresql://"))
- db_url = db_url.substring(18);
-
- int index;
- if((index = db_url.indexOf(":")) > -1)
- {
- server.setText(db_url.substring(0, index));
- int index2;
- if((index2 = db_url.indexOf("/")) > -1)
- {
- port.setText(db_url.substring(index + 1, index2));
- int index3;
- if((index3 = db_url.indexOf("?")) > -1)
- {
- db.setText(db_url.substring(index2 + 1, index3));
-
- String userStr = db_url.substring(index3 + 1);
- if(userStr.startsWith("user="))
- userStr = userStr.substring(5);
- user.setText(userStr);
-
- /*
- * if(!prompt_user) { location = "jdbc:postgresql://"
- * +inServer.getText().trim()+ ":" +inPort.getText().trim()+ "/"
- * +inDB.getText().trim()+ "?user=" +inUser.getText().trim(); return
- * true; }
- */
- }
- /**
- @TODO GSV determine if the case where a user only passes in db name without a user name should be handled like this:
- } else
- {
- db = (db_url.substring(index2 + 1));
- }
- /*/
-
- }
- }
+ DatabaseLocationParser dlp = new DatabaseLocationParser();
+ dlp.setFromURLString(db_url);
+ server.setText(dlp.getHost());
+ port.setText("" + dlp.getPort());
+ db.setText(dlp.getDatabase());
+ user.setText(dlp.getUsername());
+ ssl.setSelected(dlp.getSSL());
}
/**
@@ -554,6 +535,11 @@ class DatabaseLoginPrompt extends JPanel implements ILoginPrompt
{
return user.getText().trim();
}
+
+ public boolean getSSL()
+ {
+ return ssl.isSelected();
+ }
}
class DatabaseLoginPromptConsole implements ILoginPrompt
@@ -563,6 +549,7 @@ class DatabaseLoginPromptConsole implements ILoginPrompt
private String port;
private String db;
private String user;
+ private String ssl;
public DatabaseLoginPromptConsole()
{
@@ -583,33 +570,13 @@ class DatabaseLoginPromptConsole implements ILoginPrompt
private void setFromURL(String db_url)
{
- if(db_url.startsWith("jdbc:postgresql://"))
- db_url = db_url.substring(18);
-
- int index;
- if((index = db_url.indexOf(":")) > -1)
- {
- server = (db_url.substring(0, index));
- int index2;
- if((index2 = db_url.indexOf("/")) > -1)
- {
- port = (db_url.substring(index + 1, index2));
- int index3;
- if((index3 = db_url.indexOf("?")) > -1)
- {
- db = (db_url.substring(index2 + 1, index3));
-
- String userStr = db_url.substring(index3 + 1);
- if(userStr.startsWith("user="))
- userStr = userStr.substring(5);
- user = (userStr);
-
- } else
- {
- db = (db_url.substring(index2 + 1));
- }
- }
- }
+ DatabaseLocationParser dlp = new DatabaseLocationParser();
+ dlp.setFromURLString(db_url);
+ server = dlp.getHost();
+ port = "" + dlp.getPort();
+ db = dlp.getDatabase();
+ user = dlp.getUsername();
+ ssl = dlp.isSSLEnabled() ? "y" : "";
}
public JPasswordField getPfield()
@@ -638,6 +605,11 @@ class DatabaseLoginPromptConsole implements ILoginPrompt
{
return user;
}
+
+ public boolean getSSL()
+ {
+ return ssl.toLowerCase().equals("y") || ssl.toLowerCase().equals("yes");
+ }
public boolean prompt()
{
@@ -672,6 +644,11 @@ class DatabaseLoginPromptConsole implements ILoginPrompt
password = UI.userInput("Enter Password", true);
userEntered = true;
}
+ if (ssl == null)
+ {
+ ssl = UI.userInput("Use SSL [y/n]", false);
+ userEntered = true;
+ }
/**
GSV found that that this should always return true
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 2c27582bca97f323e63dc3a3a9e1f7ff21db85b4..2e65ae30d7c4119a6800df4011d27f1dd5ca23b4 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -43,6 +43,7 @@ import uk.ac.sanger.artemis.chado.ChadoTransaction;
import uk.ac.sanger.artemis.components.database.DatabaseEntrySource;
import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
import uk.ac.sanger.artemis.components.Splash;
+import uk.ac.sanger.artemis.util.DatabaseLocationParser;
import org.gmod.schema.sequence.Feature;
import org.gmod.schema.sequence.FeatureProp;
@@ -2473,18 +2474,20 @@ public class DatabaseDocument extends Document
}
});
}
- catch(RuntimeException sqlExp)
+ catch(RuntimeException runExp)
{
- JOptionPane.showMessageDialog(null, "SQL Problems...\n"+
+ runExp.printStackTrace();
+ JOptionPane.showMessageDialog(null, "Runtime Problems...\n"+
getLocation()+"\n"+
- sqlExp.getMessage(),
- "SQL Error",
+ runExp.getMessage(),
+ "Runtime Error",
JOptionPane.ERROR_MESSAGE);
- logger4j.debug(sqlExp.getMessage());
+ logger4j.debug(runExp.getMessage());
}
catch(ConnectException exp)
{
+ exp.printStackTrace();
JOptionPane.showMessageDialog(null, "Connection Problems...\n"+
exp.getMessage(),
"Connection Error",
@@ -2494,6 +2497,7 @@ public class DatabaseDocument extends Document
}
catch(java.sql.SQLException sqlExp)
{
+ sqlExp.printStackTrace();
JOptionPane.showMessageDialog(null, "SQL Problems....\n"+
getLocation()+"\n"+
sqlExp.getMessage(),
@@ -2643,13 +2647,17 @@ public class DatabaseDocument extends Document
// "localhost:10001/backup?chado"
String url = (String)getLocation();
- int index = url.indexOf("?");
-
- String userName = url.substring(index+1).trim();
- if(userName.startsWith("user="))
- userName = userName.substring(5);
-
- return userName;
+ DatabaseLocationParser dlp = new DatabaseLocationParser();
+ dlp.setFromURLString(url);
+
+//
+// int index = url.indexOf("?");
+//
+// String userName = url.substring(index+1).trim();
+// if(userName.startsWith("user="))
+// userName = userName.substring(5);
+//
+ return dlp.getUsername();
}
private GmodDAO getDAOOnly()