public ExptLocatorTree(Genome g) {
super();
try {
java.sql.Connection c = DatabaseFactory.getConnection(ExptLocator.dbRole);
int species = g.getSpeciesDBID();
int genome = g.getDBID();
Statement s = c.createStatement();
ResultSet rs = null;
rs =
s.executeQuery(
"select e.name, e.version from experiment e, exptToGenome eg where e.active=1 and "
+ "e.id=eg.experiment and eg.genome="
+ genome);
while (rs.next()) {
String name = rs.getString(1);
String version = rs.getString(2);
ChipChipLocator loc = new ChipChipLocator(g, name, version);
this.addElement(loc.getTreeAddr(), loc);
}
rs.close();
rs =
s.executeQuery(
"select ra.name, ra.version from rosettaanalysis ra, rosettaToGenome rg where "
+ "ra.id = rg.analysis and ra.active=1 and rg.genome="
+ genome);
while (rs.next()) {
String name = rs.getString(1);
String version = rs.getString(2);
MSPLocator msp = new MSPLocator(g, name, version);
this.addElement(msp.getTreeAddr(), msp);
}
rs.close();
rs =
s.executeQuery(
"select ra.name, ra.version from bayesanalysis ra, bayesToGenome rg where "
+ "ra.id = rg.analysis and ra.active=1 and rg.genome="
+ genome);
while (rs.next()) {
String name2 = rs.getString(1);
String version2 = rs.getString(2);
ExptLocator loc2 = new BayesLocator(g, name2, version2);
addElement(loc2.getTreeAddr(), loc2);
}
rs.close();
s.close();
DatabaseFactory.freeConnection(c);
} catch (SQLException se) {
se.printStackTrace(System.err);
throw new RuntimeException(se);
} catch (UnknownRoleException e) {
e.printStackTrace();
}
}
private void insertTestData() {
try {
DatabaseManagerCommon.createTestTables(sStatement);
refreshTree();
txtCommand.setText(DatabaseManagerCommon.createTestData(sStatement));
refreshTree();
for (int i = 0; i < DatabaseManagerCommon.testDataSql.length; i++) {
addToRecent(DatabaseManagerCommon.testDataSql[i]);
}
execute();
} catch (SQLException e) {
e.printStackTrace();
}
}
private void connect(Connection c) {
if (c == null) {
return;
}
if (cConn != null) {
try {
cConn.close();
} catch (SQLException e) {
}
}
cConn = c;
try {
dMeta = cConn.getMetaData();
sStatement = cConn.createStatement();
refreshTree();
} catch (SQLException e) {
e.printStackTrace();
}
}
private void testPerformance() {
String all = txtCommand.getText();
StringBuffer b = new StringBuffer();
long total = 0;
for (int i = 0; i < all.length(); i++) {
char c = all.charAt(i);
if (c != '\n') {
b.append(c);
}
}
all = b.toString();
String g[] = new String[4];
g[0] = "ms";
g[1] = "count";
g[2] = "sql";
g[3] = "error";
gResult.setHead(g);
int max = 1;
lTime = System.currentTimeMillis() - lTime;
while (!all.equals("")) {
int i = all.indexOf(';');
String sql;
if (i != -1) {
sql = all.substring(0, i);
all = all.substring(i + 1);
} else {
sql = all;
all = "";
}
if (sql.startsWith("--#")) {
max = Integer.parseInt(sql.substring(3));
continue;
} else if (sql.startsWith("--")) {
continue;
}
g[2] = sql;
long l = 0;
try {
l = DatabaseManagerCommon.testStatement(sStatement, sql, max);
total += l;
g[0] = "" + l;
g[1] = "" + max;
g[3] = "";
} catch (SQLException e) {
g[0] = g[1] = "n/a";
g[3] = e.toString();
}
gResult.addRow(g);
System.out.println(l + " ms : " + sql);
}
g[0] = "" + total;
g[1] = "total";
g[2] = "";
gResult.addRow(g);
lTime = System.currentTimeMillis() - lTime;
updateResult();
}
private void execute() {
gResult.clear();
String sCmd = null;
if (4096 <= ifHuge.length()) {
sCmd = ifHuge;
} else {
sCmd = txtCommand.getText();
}
if (sCmd.startsWith("-->>>TEST<<<--")) {
testPerformance();
return;
}
String g[] = new String[1];
try {
lTime = System.currentTimeMillis();
sStatement.execute(sCmd);
int r = sStatement.getUpdateCount();
if (r == -1) {
formatResultSet(sStatement.getResultSet());
} else {
g[0] = "update count";
gResult.setHead(g);
g[0] = "" + r;
gResult.addRow(g);
}
lTime = System.currentTimeMillis() - lTime;
addToRecent(txtCommand.getText());
gResult.fireTableChanged(null);
} catch (SQLException e) {
lTime = System.currentTimeMillis() - lTime;
g[0] = "SQL Error";
gResult.setHead(g);
String s = e.getMessage();
s += " / Error Code: " + e.getErrorCode();
s += " / State: " + e.getSQLState();
g[0] = s;
gResult.addRow(g);
gResult.fireTableChanged(null);
}
updateResult();
System.gc();
}
/* Clear all existing nodes from the tree model and rebuild from scratch.
*/
protected void refreshTree() {
DefaultMutableTreeNode propertiesNode;
DefaultMutableTreeNode leaf;
// First clear the existing tree by simply enumerating
// over the root node's children and removing them one by one.
while (treeModel.getChildCount(rootNode) > 0) {
DefaultMutableTreeNode child = (DefaultMutableTreeNode) treeModel.getChild(rootNode, 0);
treeModel.removeNodeFromParent(child);
child.removeAllChildren();
child.removeFromParent();
}
treeModel.nodeStructureChanged(rootNode);
treeModel.reload();
tScrollPane.repaint();
// Now rebuild the tree below its root
try {
// Start by naming the root node from its URL:
rootNode.setUserObject(dMeta.getURL());
// get metadata about user tables by building a vector of table names
String usertables[] = {"TABLE", "GLOBAL TEMPORARY", "VIEW"};
ResultSet result = dMeta.getTables(null, null, null, usertables);
Vector tables = new Vector();
// sqlbob@users Added remarks.
Vector remarks = new Vector();
while (result.next()) {
tables.addElement(result.getString(3));
remarks.addElement(result.getString(5));
}
result.close();
// For each table, build a tree node with interesting info
for (int i = 0; i < tables.size(); i++) {
String name = (String) tables.elementAt(i);
DefaultMutableTreeNode tableNode = makeNode(name, rootNode);
ResultSet col = dMeta.getColumns(null, null, name, null);
// sqlbob@users Added remarks.
String remark = (String) remarks.elementAt(i);
if ((remark != null) && !remark.trim().equals("")) {
makeNode(remark, tableNode);
}
// With a child for each column containing pertinent attributes
while (col.next()) {
String c = col.getString(4);
DefaultMutableTreeNode columnNode = makeNode(c, tableNode);
String type = col.getString(6);
makeNode("Type: " + type, columnNode);
boolean nullable = col.getInt(11) != DatabaseMetaData.columnNoNulls;
makeNode("Nullable: " + nullable, columnNode);
}
col.close();
DefaultMutableTreeNode indexesNode = makeNode("Indices", tableNode);
ResultSet ind = dMeta.getIndexInfo(null, null, name, false, false);
String oldiname = null;
// A child node to contain each index - and its attributes
while (ind.next()) {
DefaultMutableTreeNode indexNode = null;
boolean nonunique = ind.getBoolean(4);
String iname = ind.getString(6);
if ((oldiname == null || !oldiname.equals(iname))) {
indexNode = makeNode(iname, indexesNode);
makeNode("Unique: " + !nonunique, indexNode);
oldiname = iname;
}
// And the ordered column list for index components
makeNode(ind.getString(9), indexNode);
}
ind.close();
}
// Finally - a little additional metadata on this connection
propertiesNode = makeNode("Properties", rootNode);
makeNode("User: "******"ReadOnly: " + cConn.isReadOnly(), propertiesNode);
makeNode("AutoCommit: " + cConn.getAutoCommit(), propertiesNode);
makeNode("Driver: " + dMeta.getDriverName(), propertiesNode);
makeNode("Product: " + dMeta.getDatabaseProductName(), propertiesNode);
makeNode("Version: " + dMeta.getDatabaseProductVersion(), propertiesNode);
} catch (SQLException se) {
propertiesNode = makeNode("Error getting metadata:", rootNode);
makeNode(se.getMessage(), propertiesNode);
makeNode(se.getSQLState(), propertiesNode);
}
treeModel.nodeStructureChanged(rootNode);
treeModel.reload();
tScrollPane.repaint();
}