private void initGui() {
this.setLayout(new GridBagLayout());
this.setBorder(
new TitledBorder(new EtchedBorder(), dsElement.getAttributeValue(Resources.get("NAME"))));
// find all partition tables in this dataset
List<Element> ptList = dsElement.getChildren(Resources.get("PARTITIONTABLE"));
for (Element ptElement : ptList) {
List<ArrayList<String>> ptTable = JDomUtils.ptElement2Table(ptElement);
ptTableMap.put(ptElement.getAttributeValue(Resources.get("NAME")), ptTable);
// default 0
ptCurrentIndex.put(ptElement.getAttributeValue(Resources.get("NAME")), 0);
}
// find the one has the same user and gui
HashMap<String, String> conditions = new HashMap<String, String>();
List<Element> myContainers =
JDomUtils.findChildElements(dsElement, Resources.get("CONTAINER"), conditions);
Set<String> ftSet = this.getFlattenPTableName();
GridBagConstraints c = new GridBagConstraints();
c.gridy = 0;
c.gridx = 0;
c.anchor = GridBagConstraints.FIRST_LINE_START;
for (Element container : myContainers) {
if (JDomUtils.isElementHiden(container)) continue;
// if container is empty, don't add it
if (!this.isContainerEmpty(container)) {
this.add(createContainerPanel(container, dsElement, ftSet, false), c);
c.gridx = c.gridx + 1;
}
}
}
private boolean isContainerEmpty(Element container) {
if (JDomUtils.searchElement(container, Resources.get("FILTER"), null) == null
&& JDomUtils.searchElement(container, Resources.get("ATTRIBUTE"), null) == null
&& JDomUtils.searchElement(container, Resources.get("ATTRIBUTEPOINTER"), null) == null) {
return true;
} else return false;
}
private List<Element> getFlattenPTable() {
Map<String, String> conditions = new HashMap<String, String>();
conditions.put(Resources.get("FLATTEN"), "1");
List<Element> flatPtList =
JDomUtils.findDescendentElements(dsElement, Resources.get("PARTITIONTABLE"), conditions);
return flatPtList;
}
private boolean isDsColMasked(Element dsTableElement, String dsColName) {
if (dsTableElement == null) // if it is dragged from other dataset
return false;
Element attributeElement =
JDomUtils.searchElement(dsTableElement, Resources.get("ATTRIBUTE"), dsColName);
if (attributeElement == null) // check later
return false;
String maskStr = attributeElement.getAttributeValue(Resources.get("maskColumnTitle"));
if ("1".equals(maskStr)) return true;
else return false;
}
private Set<String> getFlattenPTableName() {
Set<String> ptSet = new HashSet<String>();
List<Element> ptEList = this.getFlattenPTable();
for (Element ptElement : ptEList) {
ptSet.add(ptElement.getAttributeValue(Resources.get("DSTABLE")));
}
return ptSet;
}
private void updateLabels() {
Iterator<Entry<JComponent, Element>> it = this.updateList.entrySet().iterator();
while (it.hasNext()) {
Entry<JComponent, Element> entry = it.next();
String oldName = entry.getValue().getAttributeValue(Resources.get("NAME"));
String newName = this.renameWithPartitionInfo(oldName, ptTableMap);
if (entry.getKey().getClass().getName().equals(JLabel.class.getName()))
((JLabel) entry.getKey()).setText(newName);
else ((JCheckBox) entry.getKey()).setText(newName);
}
}
/**
* create a PK for table, if the table has candidate columns, use them, otherwise use keyGuessing
*
* @param table
* @param hasPK
* @param pkCols
*/
private void createPKforTable(Table table, List<Column> pkCols) {
if (table == null) return;
if (pkCols.isEmpty() && this.isKeyGuessing()) {
// create PK by keyguessing
// Did DMD find a PK? If not, which is really unusual but
// potentially may happen, attempt to find one by looking for a
// single column with the same name as the table or with '_id'
// appended if it is source. For the mart, pk is the columns with '_key'.
// Only do this if we are using key-guessing.
// Plain version first.
Column candidateCol = table.getColumnByName(table.getName());
// Try with '_id' appended if plain version turned up
// nothing.
if (candidateCol == null)
candidateCol = table.getColumnByName(table.getName() + Resources.get("primaryKeySuffix"));
// Found something? Add it to the primary key columns map,
// with a dummy key of 1. (Use Short for the key because
// that
// is what DMD would have used had it found anything
// itself).
if (candidateCol != null) pkCols.add(candidateCol);
}
// create PK
if (!pkCols.isEmpty()) {
PrimaryKey pkObject;
try {
List<Column> columns = new ArrayList<Column>();
for (Column cc : pkCols) {
columns.add(cc);
}
pkObject = new PrimaryKey(columns);
} catch (final Throwable th) {
throw new BioMartError(th);
}
try {
table.setPrimaryKey(pkObject);
} catch (final Throwable th) {
throw new BioMartError(th);
}
}
}
private String renamePartitionReference(
String reference, Map<String, List<ArrayList<String>>> ptTableMap) {
String[] arr = reference.split(Resources.get("COLPREFIX"));
String res = "";
if (arr.length != 2) return res;
String ptName = arr[0];
String colStr = arr[1];
int col = 0;
try {
col = Integer.parseInt(colStr);
} catch (Exception e) {
return res;
}
List<ArrayList<String>> ptTable = ptTableMap.get(ptName);
int index = ptCurrentIndex.get(ptName);
try {
res = "(" + ptTable.get(index).get(col - 1) + ")";
} catch (Exception e) {
return res;
}
return res;
}
private void setColor(Element element) {
// color for dataset
if (element.getName().equalsIgnoreCase(Resources.get("DATASET"))) {
// FIXME should have a separate class to handle the XML error
if (element.getAttributeValue(Resources.get("MATERIALIZED")) != null) {
if (element.getAttributeValue(Resources.get("MATERIALIZED")).equalsIgnoreCase("true"))
setForeground(McColorUtils.materializedColor);
} else setForeground(McColorUtils.nonMaterializedColor);
// } else if(element.getName().equalsIgnoreCase(Resources.get("MART"))) {
} else if (element.getName().equals(Resources.get("MARTREGISTRY"))) {
setForeground(McColorUtils.nonMaterializedColor);
} else if (element.getName().equals(Resources.get("LOCATION"))
|| element.getName().equals(Resources.get("MART"))) {
this.setEnabled(false);
} else setForeground(McColorUtils.elementColor);
if (JDomUtils.isElementHiden(element)) setForeground(McColorUtils.hidedColor);
}
private JPanel createContainerPanel(
Element e, Element dsElement, Set<String> flattenTableSet, boolean clone) {
// element is a container element
boolean hasFlattenAttribute = false;
List<ArrayList<String>> flattendata = null;
String dsTableName = "";
JPanel containerPanel = new JPanel(new GridBagLayout());
GridBagConstraints c = new GridBagConstraints();
c.anchor = GridBagConstraints.FIRST_LINE_START;
c.insets = new Insets(0, 5, 0, 5);
int labelx = 0;
int tfx = 1;
int y = 0;
containerPanel.setBorder(
new TitledBorder(new EtchedBorder(), e.getAttributeValue(Resources.get("NAME"))));
List<Element> childList = e.getChildren();
for (Element child : childList) {
if (JDomUtils.isElementHiden(child)) continue;
if (child.getName().equals(Resources.get("CONTAINER"))) {
if (!this.isContainerEmpty(child)) {
c.gridx = labelx;
c.gridy = y;
containerPanel.add(createContainerPanel(child, dsElement, flattenTableSet, false), c);
y++;
}
} else {
dsTableName = child.getAttributeValue(Resources.get("DSTABLE"));
if (flattenTableSet.contains(dsTableName) && hasFlattenAttribute == false) {
hasFlattenAttribute = true;
Element ptElement =
JDomUtils.searchElementWithCondition(
dsElement,
Resources.get("PARTITIONTABLE"),
Resources.get("DSTABLE"),
dsTableName);
flattendata = JDomUtils.ptElement2Table(ptElement);
}
String oldLabelName = child.getAttributeValue(Resources.get("NAME"));
String labelName = this.renameWithPartitionInfo(oldLabelName, ptTableMap);
// check masked
Element dsTableElement =
JDomUtils.searchElement(dsElement, Resources.get("DSTABLE"), dsTableName);
boolean colMasked = this.isDsColMasked(dsTableElement, oldLabelName);
if (colMasked) continue;
if (child.getName().equals(Resources.get("FILTER"))) {
String ptName = child.getAttributeValue(Resources.get("PARTITIONTABLE"));
if (!hasFlattenAttribute && ptName != null && !ptName.equals("")) {
Element ptElement =
JDomUtils.searchElement(dsElement, Resources.get("PARTITIONTABLE"), ptName);
List<ArrayList<String>> data = JDomUtils.ptElement2Table(ptElement);
PartitionedFilterDropDown pfo = new PartitionedFilterDropDown(data, child, this);
c.gridx = labelx;
c.gridy = y;
if (!colMasked) {
JLabel label = new JLabel(labelName);
this.updateList.put(label, child);
containerPanel.add(label, c);
c.gridx = tfx;
containerPanel.add(pfo, c);
}
} else {
JLabel label = new JLabel(labelName);
c.gridx = labelx;
c.gridy = y;
containerPanel.add(label, c);
this.updateList.put(label, child);
c.gridx = tfx;
JTextField tf = new JTextField(5);
containerPanel.add(tf, c);
}
y++;
} else {
JCheckBox cb = new JCheckBox(labelName);
this.updateList.put(cb, child);
c.gridx = labelx;
c.gridy = y;
containerPanel.add(cb, c);
y++;
}
}
}
if (!clone && hasFlattenAttribute) {
JPanel panel = new JPanel(new GridLayout(0, 1));
containerPanel.setBorder(
new TitledBorder(
new EtchedBorder(), dsTableName + "(" + flattendata.get(0).get(0) + ")"));
panel.add(containerPanel);
for (int i = 1; i < flattendata.size(); i++) {
// get partitiontable name
Element pt =
JDomUtils.searchElementWithCondition(
dsElement, Resources.get("PARTITIONTABLE"), Resources.get("DSTABLE"), dsTableName);
this.ptCurrentIndex.put(pt.getAttributeValue(Resources.get("NAME")), i);
JPanel clonePanel = this.createContainerPanel(e, dsElement, flattenTableSet, true);
clonePanel.setBorder(
new TitledBorder(
new EtchedBorder(), dsTableName + "(" + flattendata.get(i).get(0) + ")"));
panel.add(clonePanel);
}
return panel;
} else return containerPanel;
}
public Connection getConnection() throws SQLException {
// If we are already connected, test to see if we are
// still connected. If not, reset our connection.
if (this.connection != null && this.connection.isClosed())
try {
Log.debug("Closing dead JDBC connection");
this.connection.close();
} catch (final SQLException e) {
// We don't care. Ignore it.
} finally {
this.connection = null;
}
// If we are not connected, we should attempt to (re)connect now.
if (this.connection == null) {
Log.debug("Establishing JDBC connection");
// Start out with no driver at all.
Class loadedDriverClass = null;
// Try the system class loader instead.
try {
loadedDriverClass = Class.forName(this.conObj.getJdbcType().getDriverClassName());
} catch (final ClassNotFoundException e) {
final SQLException e2 = new SQLException();
e2.initCause(e);
throw e2;
}
// Check it really is an instance of Driver.
if (!Driver.class.isAssignableFrom(loadedDriverClass))
throw new ClassCastException(Resources.get("driverClassNotJDBCDriver"));
// Connect!
final Properties properties = new Properties();
properties.setProperty("user", this.conObj.getUserName());
if (!this.conObj.getPassword().equals(""))
properties.setProperty("password", this.conObj.getPassword());
properties.setProperty("nullCatalogMeansCurrent", "false");
/*
* this.connection = DriverManager.getConnection( overrideDataLinkSchema == null ? this.conObj.getJdbcUrl():
* (this.conObj.getJdbcUrl()) .replaceAll(this.getDataLinkSchema(), overrideDataLinkSchema), properties);
*/
this.connection =
DriverManager.getConnection(
this.conObj.getJdbcUrl(), conObj.getUserName(), conObj.getPassword());
// Check the schema name.
final DatabaseMetaData dmd = this.connection.getMetaData();
final String catalog = this.connection.getCatalog();
this.realSchemaName = this.getDataLinkSchema();
ResultSet rs = dmd.getTables(catalog, this.realSchemaName, "%", null);
if (!rs.next()) {
rs = dmd.getTables(catalog, this.realSchemaName.toUpperCase(), "%", null);
if (rs.next()) this.realSchemaName = this.realSchemaName.toUpperCase();
}
if (!rs.next()) {
rs = dmd.getTables(catalog, this.realSchemaName.toLowerCase(), "%", null);
if (rs.next()) this.realSchemaName = this.realSchemaName.toLowerCase();
}
rs.close();
}
// Return the connection.
return this.connection;
}
