/** Recursively save all child elements and then call ObjBase to save itself. */
@Override
public synchronized boolean save(ClothoConnection conn) {
System.out.println("============ Starting plasmidSample save");
if (!isChanged()) {
System.out.println("plasmidSample didn't require saving");
return true;
}
if (Collector.isLocal(_pSampleDatum._plasmidUUID)) {
Plasmid plas = getPlasmid();
if (!plas.isInDatabase()) {
if (!plas.save(conn)) {
return false;
}
}
}
if (Collector.isLocal(_pSampleDatum._sourceStrainUUID)) {
Strain st = getSourceStrain();
if (!st.isInDatabase()) {
if (!st.save(conn)) {
return false;
}
}
}
return super.save(conn);
}
@Override
protected HashMap<String, HashMap<String, Object>> generateXml(
HashMap<String, HashMap<String, Object>> allObjects) {
// If the hash already has the object, skip adding anything
if (allObjects.containsKey(getUUID())) {
return allObjects;
}
// Fill in the individual fields
HashMap<String, Object> datahash = new HashMap<String, Object>();
datahash.put("objType", getType().toString());
datahash.put("uuid", _plateDatum.uuid);
datahash.put("name", _plateDatum.name);
datahash.put("_dateCreated", getDateCreatedAsString());
datahash.put("_lastModified", getLastModifiedAsString());
datahash.put("_barcode", _plateDatum._barcode);
datahash.put("_location", _plateDatum._location);
datahash.put("_authorUUID", _plateDatum._authorUUID);
datahash.put("_plateTypeUUID", _plateDatum._plateTypeUUID);
datahash.put("numRows", Integer.toString(getNumRows()));
datahash.put("numCols", Integer.toString(getNumCols()));
ArrayList<String> containerlist = new ArrayList<String>();
for (int i = 0; i < this.getNumRows(); i++) {
for (int j = 0; j < this.getNumCols(); j++) {
String conuuid = _plateDatum.myWells[i][j];
Container acon = Collector.getContainer(conuuid);
if (acon != null) {
String aline = acon.getUUID() + "," + i + "," + j;
containerlist.add(aline);
}
}
}
datahash.put("containers", containerlist);
// Add the HashMap to the list
allObjects.put(getUUID(), datahash);
// Recursively gather the objects linked to this object
allObjects = getPlateType().generateXml(allObjects);
allObjects = getAuthor().generateXml(allObjects);
for (int i = 0; i < this.getNumRows(); i++) {
for (int j = 0; j < this.getNumCols(); j++) {
String conuuid = _plateDatum.myWells[i][j];
Container acon = Collector.getContainer(conuuid);
if (acon != null) {
allObjects = acon.generateXml(allObjects);
}
}
}
// Return the datahash
return allObjects;
}
/** Recursively save all child elements and then call ObjBase to save itself. */
@Override
public synchronized boolean save(ClothoConnection conn) {
System.out.println("============ Starting plate save of " + getUUID());
if (!isChanged()) {
System.out.println("Collection didn't require saving");
return true;
}
if (Collector.isLocal(this._plateDatum._authorUUID)) {
if (!getAuthor().saveDefault()) {
return false;
}
}
if (!Collector.getCurrentUser().getUUID().equals(this.getAuthor().getUUID())) {
if (!Collector.getCurrentUser().isAdmin()) {
System.out.println(
"Current user "
+ this.getAuthor().getDisplayName()
+ " does not have permission to modify "
+ this.getName());
return false;
}
}
if (!super.save(conn)) {
return false;
}
for (int row = 0; row < getNumRows(); row++) {
for (int col = 0; col < getNumCols(); col++) {
String containerref = this.getContainerRefAt(row, col);
if (!Collector.isLocal(containerref)) {
continue;
}
Container acon = Collector.getContainer(containerref);
System.out.println("plate about to save " + acon.getName());
System.out.println(acon.getUUID());
System.out.println(acon.getName());
System.out.println(acon.getDateCreated());
System.out.println(acon.getLastModified());
System.out.println(acon.getRowAsInt());
System.out.println(acon.getCol());
System.out.println(acon.getBarcode());
System.out.println(acon.isFixed());
System.out.println(acon.getPlateLink());
if (!acon.save(conn)) {
return false;
}
}
}
return true;
}
/**
* returns the Container present in a well of the Plate as a Container object
*
* @param i
* @param j
* @return
*/
public Container getContainerAt(int i, int j) {
System.out.println("Plate retrieving row " + i + " col " + j);
String containerref = getContainerRefAt(i, j);
System.out.println("containerref is: " + containerref);
if (containerref.equals("") || containerref.equals("null")) {
return null;
}
return Collector.getContainer(containerref);
}
private void makePlateActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_makePlateActionPerformed
// TODO add your handling code here:
platetypeList = Collector.getAllLinksOf(ObjType.PLATE_TYPE);
authorList = Collector.getAllLinksOf(ObjType.PERSON);
int authorSelect = this.jComboBoxAuthor.getSelectedIndex();
int plateTypeSelect = this.jComboBoxPlateType.getSelectedIndex();
ObjLink plateLink = platetypeList.get(plateTypeSelect);
ObjLink personLink = authorList.get(authorSelect);
Person testPerson = Collector.getPerson(personLink.uuid);
PlateType testType = Collector.getPlateType(plateLink.uuid);
Plate testPlate = new Plate(this.plateName.getText(), testType, testPerson);
if (this.location.getText() != null) {
testPlate.setLocation(this.location.getText());
}
if (this.barCode.getText() != null) testPlate.setBarcode(this.barCode.getText());
boolean didWork = testPlate.saveDefault();
System.out.println("write plate to DB:" + didWork);
this.parentFrame.setVisible(false);
frame aframe = new frame(testPlate);
hub.guis.add(new WeakReference(aframe));
} // GEN-LAST:event_makePlateActionPerformed
private void addPlateType() {
platetypeList = Collector.getAllLinksOf(ObjType.PLATE_TYPE);
Iterator i = platetypeList.iterator();
while (i.hasNext()) this.jComboBoxPlateType.addItem(i.next());
}
private void addAuthor() {
authorList = Collector.getAllLinksOf(ObjType.PERSON);
Iterator i = authorList.iterator();
while (i.hasNext()) this.jComboBoxAuthor.addItem(i.next());
}
public Person getAuthor() {
return Collector.getPerson(_plateDatum._authorUUID);
}
public PlateType getPlateType() {
return (PlateType) Collector.get(ObjType.PLATE_TYPE, _plateDatum._plateTypeUUID);
}
public Strain getSourceStrain() {
return Collector.getStrain(_pSampleDatum._sourceStrainUUID);
}
public Plasmid getPlasmid() {
return Collector.getPlasmid(_pSampleDatum._plasmidUUID);
}
public SequenceViewPartExport(SequenceView sv, JTextPane jtp) {
initComponents();
_sv = sv;
// addWindowListener(new WindowAdapter(){
// @Override
// public void windowClosing(WindowEvent we){
// ClothoDialogBox db = new ClothoDialogBox("Clotho: Exit Check", "Are you sure you
// want to close the packager?");
//
// if(db.show_optionDialog(javax.swing.JOptionPane.YES_NO_OPTION,
// javax.swing.JOptionPane.QUESTION_MESSAGE) == javax.swing.JOptionPane.YES_OPTION)
// dispose();
// }
// });
dataTextPane.setText(jtp.getText());
if (jtp.getSelectedText() != null) {
intervalRadioButton.setSelected(true);
fromTextField.setText(Integer.toString(jtp.getSelectionStart()));
fromTextField.getDocument().addDocumentListener(new SelectionListener());
toTextField.setText(Integer.toString(jtp.getSelectionEnd()));
toTextField.getDocument().addDocumentListener(new SelectionListener());
try {
// dataTextPane.grabFocus();
dataTextPane.select(jtp.getSelectionStart(), jtp.getSelectionEnd());
dataTextPane
.getHighlighter()
.addHighlight(
jtp.getSelectionStart(),
jtp.getSelectionEnd(),
new javax.swing.text.DefaultHighlighter.DefaultHighlightPainter(
dataTextPane.getSelectionColor()));
} catch (Exception e) {
}
} else {
try {
// dataTextPane.grabFocus();
dataTextPane.selectAll();
dataTextPane
.getHighlighter()
.addHighlight(
0,
dataTextPane.getText().length(),
new javax.swing.text.DefaultHighlighter.DefaultHighlightPainter(
dataTextPane.getSelectionColor()));
} catch (Exception ex) {
Exceptions.printStackTrace(ex);
}
fromTextField.setText("0");
toTextField.setText(Integer.toString(jtp.getText().length()));
wsRadioButton.setSelected(true);
try {
dataTextPane
.getHighlighter()
.addHighlight(
0,
dataTextPane.getText().length(),
new javax.swing.text.DefaultHighlighter.DefaultHighlightPainter(
dataTextPane.getSelectionColor()));
dataTextPane.grabFocus();
dataTextPane.selectAll();
} catch (Exception ex) {
Exceptions.printStackTrace(ex);
}
}
ArrayList<ObjLink> collectionLinks = Collector.getAllLinksOf(ObjType.COLLECTION);
collectionComboBox.removeAllItems();
for (ObjLink oj : collectionLinks) {
collectionComboBox.addItem(oj);
}
collectionComboBox.setSelectedIndex(-1);
formatComboBox.removeAllItems();
ArrayList<ObjLink> formatLinks = Collector.getAllLinksOf(ObjType.FORMAT);
for (ObjLink oj : formatLinks) {
formatComboBox.addItem(oj);
}
formatComboBox.setSelectedIndex(-1);
objectTypeComboBox.removeAllItems();
objectTypeComboBox.addItem("Feature");
objectTypeComboBox.addItem("Oligo");
objectTypeComboBox.addItem("Part");
objectTypeComboBox.addItem("Vector");
objectTypeComboBox.setSelectedIndex(-1);
formatComboBox.setEnabled(false);
formatLabel.setEnabled(false);
this.setVisible(true);
}
private void saveButtonActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_saveButtonActionPerformed
String desc = _sv.getSequenceView().getOutputTextArea().getText();
if (desc == null) {
desc = "";
}
String name = nameTextField.getText();
String seq = null;
System.out.println("saving: " + name);
if (intervalRadioButton.isSelected()) {
try {
if (dataTextPane.getText() != null) {
seq =
dataTextPane
.getText()
.substring(
Integer.parseInt(fromTextField.getText()),
Integer.parseInt(toTextField.getText()));
}
} catch (NumberFormatException e) {
System.out.println("tried to use invalid sequence interval to generate Clotho object");
return;
}
} else {
seq = dataTextPane.getText();
}
Format form = null;
Collection coll = null;
if (objectTypeComboBox.getSelectedIndex() != 1 && objectTypeComboBox.getSelectedIndex() != 0) {
if (formatComboBox.getSelectedIndex() == -1) {
statusLabel.setText("Warning: format not set");
return;
}
form = Collector.getFormat(((ObjLink) formatComboBox.getSelectedItem()).uuid);
}
if (collectionComboBox.getSelectedIndex() != -1) {
coll = Collector.getCollection(((ObjLink) collectionComboBox.getSelectedItem()).uuid);
} else {
statusLabel.setText("Warning: collection not selected");
return;
}
if (objectTypeComboBox.getSelectedIndex() == -1) {
statusLabel.setText("Warning: object Type not set");
return;
}
Boolean saved = false;
ObjBase newObject = null;
if (coll != null) {
if (objectTypeComboBox.getSelectedIndex() == 0) {
// feature
if (seq.toUpperCase().indexOf("ATG") != -1) {
newObject = Feature.generateFeature(name, seq, Collector.getCurrentUser(), true);
} else {
newObject = Feature.generateFeature(name, seq, Collector.getCurrentUser(), false);
}
} else if (objectTypeComboBox.getSelectedIndex() == 1) {
newObject = new Oligo(name, desc, Collector.getCurrentUser(), seq);
} else if (form != null && objectTypeComboBox.getSelectedIndex() == 2) {
// part
newObject = Part.generateBasic(name, desc, seq, form, Collector.getCurrentUser());
} else if (form != null && objectTypeComboBox.getSelectedIndex() == 3) {
Vector.generateVector(name, desc, seq, form, Collector.getCurrentUser());
} else {
statusLabel.setText("error saving new Clotho object, check selected fields");
return;
}
} else {
statusLabel.setText("Not all fields are filled");
return;
}
if (newObject != null) {
statusLabel.setText("saving: " + newObject.getName());
}
saved = newObject.saveDefault();
coll.addObject(newObject);
coll.saveDefault();
Collector.add(newObject);
if (saved) {
statusLabel.setText("Successful save!");
NucSeq.refreshFeatureTable();
this.dispose();
}
} // GEN-LAST:event_saveButtonActionPerformed
