public void possiblySyncPreferredTerm(String cls_name, String name, String value) {
if (name.compareTo(NCIEditTab.ALTLABEL) == 0) {
String tn = ComplexPropertyParser.getPtNciTermName(value);
if (tn != null) {
// need to mod preferred name and rdfs:label
OWLNamedClass cls = wrapper.getOWLNamedClass(cls_name);
String pn = wrapper.getPropertyValue(cls, NCIEditTab.PREFLABEL);
String rdl = wrapper.getPropertyValue(cls, "rdfs:label");
wrapper.modifyAnnotationProperty(cls_name, NCIEditTab.PREFLABEL, pn, tn);
wrapper.modifyAnnotationProperty(cls_name, "rdfs:label", rdl, tn);
}
} else if (name.compareTo(NCIEditTab.PREFLABEL) == 0) {
OWLNamedClass cls = wrapper.getOWLNamedClass(cls_name);
ArrayList<String> pvals = wrapper.getPropertyValues(cls, NCIEditTab.ALTLABEL);
for (String s : pvals) {
String tn = ComplexPropertyParser.getPtNciTermName(s);
if (tn != null) {
HashMap<String, String> hm = ComplexPropertyParser.parseXML(s);
String newfspt = ComplexPropertyParser.replaceFullSynValue(hm, "term-name", value);
wrapper.modifyAnnotationProperty(cls_name, NCIEditTab.ALTLABEL, s, newfspt);
}
}
String rdl = wrapper.getPropertyValue(cls, "rdfs:label");
wrapper.modifyAnnotationProperty(cls_name, "rdfs:label", rdl, value);
}
}
public BatchEditTask(NCIEditTab tab, String infile, String outfile) {
super(tab.getBatchProcessPanel());
this.tab = tab;
this.infile = infile;
this.outfile = outfile;
this.owlModel = tab.getOWLModel();
this.wrapper = tab.getWrapper();
supportedRoles = wrapper.getSupportedRoles();
supportedProperties = wrapper.getSupportedAnnotationProperties();
supportedAssociations = wrapper.getSupportedAssociations();
data_vec = getData(infile);
setMax(data_vec.size());
setMessage("Batch Edit processing in progress, please wait ...");
}
public boolean processTask(int taskId) {
String s = (String) data_vec.elementAt(taskId);
super.print("processing: " + s);
try {
Vector<String> w = getTokenStr(s, 9);
String name = (String) w.elementAt(0);
if (super.checkNoErrors(w, taskId)) {
// ok
} else {
return false;
}
String edit = (String) w.elementAt(1);
String attribute = (String) w.elementAt(2);
String attributeName = (String) w.elementAt(3);
String attributeValue = (String) w.elementAt(4);
String newAttributeValue = (String) w.elementAt(5);
owlModel.beginTransaction("BatchEdit. Processing " + s);
// this should be false???
boolean retval = false;
if (edit.compareToIgnoreCase("new") == 0) {
if (attribute.compareToIgnoreCase("property") == 0) {
if (attributeName.compareToIgnoreCase(NCIEditTab.ALTLABEL) == 0) {
OWLNamedClass hostClass = wrapper.getOWLNamedClass(name);
retval =
wrapper.addAnnotationProperty(
hostClass,
NCIEditTab.ALTLABEL,
owlModel.createRDFSLiteral(
attributeValue, owlModel.getSystemFrames().getXmlLiteralType()));
} else {
retval = wrapper.addAnnotationProperty(name, attributeName, attributeValue);
}
} else if (attribute.compareToIgnoreCase("parent") == 0) {
OWLNamedClass hostClass = wrapper.getOWLNamedClass(name);
OWLNamedClass targetClass = wrapper.getOWLNamedClass(attributeName);
retval = wrapper.addDirectSuperclass(hostClass, targetClass);
} else if (attribute.compareToIgnoreCase("association") == 0) {
OWLNamedClass hostClass = wrapper.getOWLNamedClass(name);
retval = wrapper.addObjectProperty(hostClass, attributeName, attributeValue);
} else if (attribute.compareToIgnoreCase("role") == 0) {
int pos = attributeValue.indexOf('|');
String modifier = attributeValue.substring(0, pos);
String value = attributeValue.substring(pos + 1);
retval = wrapper.addRestriction(name, attributeName, value, modifier);
}
} else if (edit.compareToIgnoreCase("delete") == 0) {
if (attribute.compareToIgnoreCase("property") == 0) {
retval = wrapper.removeAnnotationProperty(name, attributeName, attributeValue);
} else if (attribute.compareToIgnoreCase("parent") == 0) {
OWLNamedClass hostClass = wrapper.getOWLNamedClass(name);
OWLNamedClass targetClass = wrapper.getOWLNamedClass(attributeName);
RDFSClass definition = hostClass.getDefinition();
if (definition == null) {
retval = wrapper.removeDirectSuperclass(hostClass, targetClass);
} else {
retval = wrapper.removeEquivalentDefinitionNew(hostClass, targetClass);
}
} else if (attribute.compareToIgnoreCase("association") == 0) {
OWLNamedClass hostClass = wrapper.getOWLNamedClass(name);
retval = wrapper.removeObjectProperty(hostClass, attributeName, attributeValue);
} else if (attribute.compareToIgnoreCase("role") == 0) {
int pos = attributeValue.indexOf('|');
String modifier = attributeValue.substring(0, pos);
String value = attributeValue.substring(pos + 1);
retval = wrapper.removeRestriction(name, attributeName, value, modifier);
}
} else if (edit.compareToIgnoreCase("edit") == 0) {
if (attribute.compareToIgnoreCase("property") == 0) {
retval =
wrapper.modifyAnnotationProperty(
name, attributeName, attributeValue, newAttributeValue);
possiblySyncPreferredTerm(name, attributeName, newAttributeValue);
} else if (attribute.compareToIgnoreCase("role") == 0) {
int pos = attributeValue.indexOf('|');
String modifier = attributeValue.substring(0, pos);
String value = attributeValue.substring(pos + 1);
pos = newAttributeValue.indexOf('|');
String newmodifier = newAttributeValue.substring(0, pos);
String newvalue = newAttributeValue.substring(pos + 1);
retval =
wrapper.modifyRestriction(
name, attributeName, value, modifier, newvalue, newmodifier);
} else if (attribute.compareToIgnoreCase("association") == 0) {
OWLNamedClass hostClass = wrapper.getOWLNamedClass(name);
retval = wrapper.removeObjectProperty(hostClass, attributeName, attributeValue);
retval = wrapper.addObjectProperty(hostClass, attributeName, newAttributeValue);
}
}
// to be implemented
/*
* else if (edit.compareToIgnoreCase("delete-all") == 0) { }
*/
if (retval) {
tab.recordHistory(NCIEditTab.EVSHistoryAction.MODIFY, wrapper.getOWLNamedClass(name), "");
super.print("\t Done.");
} else {
super.print("\t Failed.");
}
owlModel.commitTransaction();
} catch (Exception ex) {
owlModel.rollbackTransaction();
print("Server Error occurred:");
ex.printStackTrace();
super.print(" Failed.");
data_vec.remove(taskId);
this.setMax(max - 1);
return false;
}
return true;
}
public Vector<String> validateData(Vector<String> v) {
// keep a vector or error messages, may be more than one
Vector<String> w = new Vector<String>();
try {
String cls_name = (String) v.elementAt(0);
String action = (String) v.elementAt(1);
String attribute = (String) v.elementAt(2);
String attributename = (String) v.elementAt(3);
String attributevalue_1 = (String) v.elementAt(4);
String attributevalue_2 = (String) v.elementAt(5);
OWLNamedClass hostClass = wrapper.getOWLNamedClass(cls_name);
Vector superclasses = new Vector();
if (hostClass == null) {
String error_msg = " -- concept " + cls_name + " does not exist.";
w.add(error_msg);
} else if (wrapper.isRetired(hostClass)) {
w.add(" -- concept " + cls_name + " is retired, cannot edit");
}
if (action.compareToIgnoreCase("new") != 0
&& action.compareToIgnoreCase("edit") != 0
&& action.compareToIgnoreCase("delete") != 0) {
String error_msg = " -- action " + action + " is not supported.";
w.add(error_msg);
}
if (attribute.compareToIgnoreCase("parent") != 0
&& attribute.compareToIgnoreCase("role") != 0
&& attribute.compareToIgnoreCase("property") != 0
&& attribute.compareToIgnoreCase("association") != 0) {
String error_msg = " -- attribute " + attribute + " is not supported.";
w.add(error_msg);
}
if (action.compareToIgnoreCase("new") == 0) {
if (hostClass != null) {
if (attribute.compareToIgnoreCase("role") == 0) {
if (!supportedRoles.contains(attributename)) {
String error_msg = " -- role " + attributename + " is not identifiable.";
w.add(error_msg);
} else {
int pos = attributevalue_1.indexOf("|");
if (pos == -1) {
String error_msg = " -- missing modifier or filler.";
w.add(error_msg);
} else {
String filler = attributevalue_1.substring(pos + 1, attributevalue_1.length());
OWLNamedClass targetClass = (OWLNamedClass) owlModel.getRDFSNamedClass(filler);
if (targetClass == null) {
String error_msg = " -- concept " + filler + " does not exist.";
w.add(error_msg);
} else {
if (wrapper.hasRole(hostClass, attributename, filler)) {
String error_msg = " -- role already exists.";
w.add(error_msg);
}
}
}
}
} else if (attribute.compareToIgnoreCase("parent") == 0) {
OWLNamedClass superClass = (OWLNamedClass) owlModel.getRDFSNamedClass(attributename);
if (superClass == null) {
String error_msg = " -- superconcept does not exist.";
w.add(error_msg);
} else {
if (wrapper.isPremerged(superClass)
|| wrapper.isPreretired(superClass)
|| wrapper.isRetired(superClass)) {
String error_msg = "superconcept cannot be premerged, preretired, or retired.";
w.add(error_msg);
}
}
} else if (attribute.compareToIgnoreCase("property") == 0) {
if (!supportedProperties.contains(attributename)) {
String error_msg = " -- property " + attributename + " is not identifiable.";
w.add(error_msg);
} else {
if (wrapper.hasProperty(hostClass, attributename, attributevalue_1)) {
String error_msg = " -- property already exists.";
w.add(error_msg);
}
}
if (this.tab.getFilter().checkBatchProperty(attributename, attributevalue_1)
&& this.tab
.getFilter()
.checkBatchPropertyNotFullSynPT(attributename, attributevalue_1)) {
} else {
w.add(tab.getFilter().getErrorMessage());
}
} else if (attribute.compareToIgnoreCase("association") == 0) {
if (!supportedAssociations.contains(attributename)) {
String error_msg = " -- association " + attributename + " is not identifiable.";
w.add(error_msg);
} else {
OWLNamedClass targetClass =
(OWLNamedClass) owlModel.getRDFSNamedClass(attributevalue_1);
if (targetClass == null) {
String error_msg = " -- concept " + attributevalue_1 + " does not exist.";
w.add(error_msg);
} else {
if (wrapper.hasAssociation(hostClass, attributename, attributevalue_1)) {
String error_msg = " -- association already exists.";
w.add(error_msg);
}
}
}
}
}
} else if (action.compareToIgnoreCase("edit") == 0
|| action.compareToIgnoreCase("delete") == 0) {
if (hostClass != null) {
if (attribute.compareToIgnoreCase("parent") == 0) {
if (action.compareToIgnoreCase("delete") == 0) {
OWLNamedClass superClass = (OWLNamedClass) owlModel.getRDFSNamedClass(attributename);
if (superClass == null) {
String error_msg = " -- superconcept " + attributename + " does not exist.";
w.add(error_msg);
} else if (wrapper.getDirectSuperclassNames(hostClass).size() == 1) {
String error_msg = " -- can't delete last superconcept " + attributename;
w.add(error_msg);
}
} else {
String error_msg =
" -- edit parent action is not supported. Use delete and add actions instead.";
w.add(error_msg);
}
} else if (attribute.compareTo("role") == 0) {
if (!supportedRoles.contains(attributename)) {
String error_msg = " -- role " + attributename + " is not identifiable.";
w.add(error_msg);
} else {
int pos = attributevalue_1.indexOf("|");
if (pos == -1) {
String error_msg = " -- missing modifier or filler.";
w.add(error_msg);
} else {
String filler = attributevalue_1.substring(pos + 1, attributevalue_1.length());
OWLNamedClass targetClass = (OWLNamedClass) owlModel.getRDFSNamedClass(filler);
if (targetClass == null) {
String error_msg = " -- concept " + filler + " does not exist.";
w.add(error_msg);
} else {
if (!wrapper.hasRole(hostClass, attributename, filler)) {
String error_msg = " -- role does not exist.";
w.add(error_msg);
}
if (action.compareTo("edit") == 0) {
pos = attributevalue_2.indexOf("|");
if (pos == -1) {
String error_msg = " -- missing modifier or filler.";
w.add(error_msg);
} else {
filler = attributevalue_2.substring(pos + 1, attributevalue_2.length());
targetClass = (OWLNamedClass) owlModel.getRDFSNamedClass(filler);
if (targetClass == null) {
String error_msg = " -- concept " + filler + " does not exist.";
w.add(error_msg);
}
}
}
}
}
}
} else if (attribute.compareToIgnoreCase("property") == 0) {
if (!supportedProperties.contains(attributename)) {
String error_msg = " -- property " + attributename + " is not identifiable.";
w.add(error_msg);
} else {
Boolean editable = wrapper.isReadOnlyProperty(attributename);
if (editable.equals(Boolean.TRUE)) {
String error_msg = " -- property " + attributename + ", it is read-only.";
w.add(error_msg);
}
if (!wrapper.hasProperty(hostClass, attributename, attributevalue_1)) {
String error_msg =
" -- property "
+ "("
+ attributename
+ ", "
+ attributevalue_1
+ ") does not exist.";
w.add(error_msg);
}
if (action.compareToIgnoreCase("edit") == 0) {
if (wrapper.hasProperty(hostClass, attributename, attributevalue_2)) {
String error_msg =
" -- property "
+ "("
+ attributename
+ ", "
+ attributevalue_2
+ ") already exists.";
w.add(error_msg);
} else if (attributevalue_2.equalsIgnoreCase("NA")) {
String error_msg =
" -- property " + "(" + attributename + ") new value is not specified.";
w.add(error_msg);
} else if (this.tab.getFilter().checkBatchProperty(attributename, attributevalue_2)
&& this.tab
.getFilter()
.checkBatchPropertyNotFullSynPT(attributename, attributevalue_2)) {
} else {
w.add(tab.getFilter().getErrorMessage());
}
} else {
if (this.tab.getFilter().checkBatchProperty(attributename, attributevalue_1)) {
} else {
w.add(tab.getFilter().getErrorMessage());
}
}
}
} else if (attribute.compareTo("association") == 0) {
if (!supportedAssociations.contains(attributename)) {
String error_msg = " -- association " + attributename + " is not identifiable.";
w.add(error_msg);
}
if (action.compareToIgnoreCase("delete") == 0) {
OWLNamedClass targetClass =
(OWLNamedClass) owlModel.getRDFSNamedClass(attributevalue_1);
if (targetClass == null) {
String error_msg = " -- concept " + attributevalue_1 + " does not exist.";
w.add(error_msg);
} else {
if (!wrapper.hasAssociation(hostClass, attributename, attributevalue_1)) {
String error_msg = " -- association does not exist.";
w.add(error_msg);
}
}
} else {
String error_msg =
" -- edit association action is not supported. Use delete and add actions instead.";
w.add(error_msg);
}
}
}
}
} catch (Exception e) {
Log.getLogger().log(Level.WARNING, "Exception caught", e);
}
return w;
}