public static ArrayList<String> getUsedFqnFromHits(String xmlResultInString) {
ArrayList<String> usedFqns = new ArrayList<String>();
Document doc = XMLParser.parse(xmlResultInString);
NodeList _arrs = doc.getElementsByTagName("arr");
for (int i = 0; i < _arrs.getLength(); i++) {
Node _arr = _arrs.item(i);
NamedNodeMap _nnm = _arr.getAttributes();
if (_nnm != null) {
Node _nameNode = _nnm.getNamedItem("name");
if (_nameNode != null) {
String _nodeType = _nameNode.getNodeValue();
if (_nodeType.equals("lib_use_fqn_full")
|| _nodeType.equals("jdk_use_fqn_full")
|| _nodeType.equals("local_use_fqn_full")) {
NodeList _fqns = _arr.getChildNodes();
for (int j = 0; j < _fqns.getLength(); j++) {
Node _fqn = _fqns.item(j);
if (_fqn.getNodeName().equals("str")) {
String _usedFqn = _fqn.getFirstChild().getNodeValue();
usedFqns.add(_usedFqn);
}
}
}
}
}
}
return usedFqns;
}
public void onResponseReceived(Request request, Response response) {
try {
String s = Utils.getXmlNodeValue(XMLParser.parse(response.getText()), TAG_BLOBSTORE);
blobstore = "true".equalsIgnoreCase(s);
// with blobstore status does not make sense
if (blobstore) {
updateStatusTimer.setInterval(5000);
}
uploadForm.setAction(session.getServletPath());
uploadForm.submit();
} catch (Exception e) {
String message =
e.getMessage().contains("error:")
? i18nStrs.uploaderServerUnavailable()
+ " (3) "
+ getServletPath()
+ "\n\n"
+ i18nStrs.uploaderServerError()
+ "\nAction: "
+ getServletPath()
+ "\nException: "
+ e.getMessage()
+ response.getText()
: i18nStrs.submitError();
cancelUpload(message);
}
}
public static ArrayList<String> getHitEidsFromHits(String xmlResultInString) {
ArrayList<String> _hitEids = new ArrayList<String>();
Document doc = XMLParser.parse(xmlResultInString);
NodeList hits = doc.getElementsByTagName("doc");
for (int i = 0; i < hits.getLength(); i++) {
Node hit = hits.item(i);
NodeList hitDocChildNodes = hit.getChildNodes();
String entity_id = "";
for (int j = 0; j < hitDocChildNodes.getLength(); j++) {
Node hitDocChildNode = hitDocChildNodes.item(j);
NamedNodeMap attrs = hitDocChildNode.getAttributes();
Node _attributeNode = null;
_attributeNode = attrs.getNamedItem("name");
if (_attributeNode != null) {
if (_attributeNode.getNodeValue().equals("entity_id")) {
entity_id = hitDocChildNode.getFirstChild().getNodeValue();
}
}
}
_hitEids.add(entity_id);
}
return _hitEids;
}
public void onSubmitComplete(SubmitCompleteEvent event) {
updateStatusTimer.cancel();
onSubmitComplete = true;
serverRawResponse = event.getResults();
if (serverRawResponse != null) {
serverRawResponse =
serverRawResponse.replaceFirst(
".*" + TAG_MSG_START + "([\\s\\S]*?)" + TAG_MSG_END + ".*", "$1");
serverRawResponse =
serverRawResponse
.replace(TAG_MSG_LT, "<")
.replace(TAG_MSG_GT, ">")
.replace("<", "<")
.replaceAll(">", ">")
.replaceAll(" ", " ");
}
try {
// Parse the xml and extract UploadedInfos
Document doc = XMLParser.parse(serverRawResponse);
// If the server response is a valid xml
parseAjaxResponse(serverRawResponse);
} catch (Exception e) {
log("onSubmitComplete exception parsing response (Check CORS and XML syntax): ", e);
// Otherwise force an ajax request so as we have not to wait to the timer schedule
// updateStatusTimer.run(); // how could the upload server response be corrupted ?? This
// causes an error loop in my project with firefox
}
}
private void parseXml(String messageXml) {
try {
Document messageDom = XMLParser.parse(messageXml);
Node customerNode = messageDom.getElementsByTagName("customer").item(0);
String id = ((Element) customerNode).getAttribute("id");
idField.setText(id);
String name =
messageDom.getElementsByTagName("fullname").item(0).getFirstChild().getNodeValue();
nameField.setText(name);
String street =
messageDom.getElementsByTagName("street").item(0).getFirstChild().getNodeValue();
streetField.setText(street);
String city = messageDom.getElementsByTagName("city").item(0).getFirstChild().getNodeValue();
cityField.setText(city);
String state =
messageDom.getElementsByTagName("state").item(0).getFirstChild().getNodeValue();
stateField.setText(state);
String zip = messageDom.getElementsByTagName("zip").item(0).getFirstChild().getNodeValue();
zipField.setText(zip);
} catch (DOMException e) {
Window.alert("Could not parse XML document.");
}
}
private Element getXMLDoc() {
Document d = XMLParser.createDocument();
Element root = d.createElement("PedEx");
PelicanPerson[] people = getAllPeople();
for (int i = 0; i < people.length; i++) {
root.appendChild(people[i].save());
}
return root;
}
public void onResponseReceived(Request request, Response response) {
String text = response.getText();
String url = null;
Document document = null;
String bpath = "<" + TAG_BLOBSTORE_PATH + ">";
String sbpath = "</" + TAG_BLOBSTORE_PATH + ">";
if (text.contains(bpath)) {
try {
document = XMLParser.parse(text);
url = Utils.getXmlNodeValue(document, TAG_BLOBSTORE_PATH);
} catch (Exception e) {
cancelUpload(
i18nStrs.uploaderBlobstoreError() + "\n>>>\n" + e.getMessage() + "\n>>>>\n" + e);
return;
}
if (url == null) {
url =
text.replaceAll("[\r\n]+", "")
.replaceAll("^.*" + bpath + "\\s*", "")
.replaceAll("\\s*" + sbpath + ".*$", "");
}
}
if (url != null && url.length() > 0 && !"null".equalsIgnoreCase(url)) {
if (session.getServletPath().startsWith("http")) {
url = session.getServletPath().replaceFirst("(https?://[^/]+).*", "$1") + url;
}
uploadForm.setAction(url);
} else {
uploadForm.setAction(session.getServletPath());
}
removeHiddens();
if (document != null) {
String name = Utils.getXmlNodeValue(document, TAG_BLOBSTORE_NAME);
if (name != null) {
fileInput.setName(name);
}
NodeList list = document.getElementsByTagName(TAG_BLOBSTORE_PARAM);
for (int i = 0; i < list.getLength(); i++) {
Node node = list.item(i);
String value = Utils.getXmlNodeValue(node);
if (value != null) {
Node attribute = node.getAttributes().getNamedItem(ATTR_BLOBSTORE_PARAM_NAME);
if (attribute != null) {
String paramName = attribute.getNodeValue();
if (paramName != null) {
addHidden(paramName, value);
}
}
}
}
}
receivedBlobPath = true;
uploadForm.submit();
}
@Override
public Document decode(JSONValue value) throws DecodingException {
if (value == null || value.isNull() != null) {
return null;
}
JSONString str = value.isString();
if (str == null) {
throw new DecodingException("Expected a json string, but was given: " + value);
}
return XMLParser.parse(str.stringValue());
}
public static Payload parseMessage(String message) {
final Payload payload = new Payload();
Document messageDom = XMLParser.parse(message);
NodeList statements = messageDom.getElementsByTagName("com.freedomotic.reactions.Statement");
for (int i = 0; i < statements.getLength(); i++) {
Element statement = (Element) statements.item(i);
payload.enqueueStatement(parseStatement(statement));
}
return payload;
}
public void loadQueryDef(String xml) {
Document doc = XMLParser.parse(xml);
Element rootNode = doc.getDocumentElement();
if (!rootNode.getNodeName().equalsIgnoreCase(XmlBuilder.NODE_NAME_QUERYDEF)) return;
HashMap<String, DisplayColumnWidget> displayCols = new HashMap<String, DisplayColumnWidget>();
NodeList nodes = rootNode.getElementsByTagName(XmlBuilder.NODE_NAME_DISPLAY_FIELDS);
if (nodes != null && nodes.getLength() > 0)
loadDisplayFields((Element) nodes.item(0), displayCols);
nodes = rootNode.getElementsByTagName(XmlBuilder.NODE_NAME_SORT_FIELDS);
if (nodes != null && nodes.getLength() > 0)
loadSortFields((Element) nodes.item(0), displayCols);
}
public static List<HitFqnEntityId> getUsedApisFromFacetedHits(
String xmlResultInString, EntityCategory c) {
// if (c.equals(EntityCategory.LOCAL))
// throw new IllegalArgumentException("only jdk or lib");
List<HitFqnEntityId> apis = new LinkedList<HitFqnEntityId>();
Document doc = XMLParser.parse(xmlResultInString);
NodeList apisNodes = doc.getElementsByTagName("lst");
String nodeName;
if (c.equals(EntityCategory.JDK)) nodeName = "jdk_use_fqn_full";
else if (c.equals(EntityCategory.LIB)) nodeName = "lib_use_fqn_full";
else return apis;
for (int i = 0; i < apisNodes.getLength(); i++) {
Node apiNode = apisNodes.item(i);
NamedNodeMap attrs = apiNode.getAttributes();
Node _attributeNode = null;
_attributeNode = attrs.getNamedItem("name");
if (_attributeNode != null) {
if (_attributeNode.getNodeValue().equals(nodeName)) {
// iterate through int nodes
NodeList fqnNodes = apiNode.getChildNodes();
for (int j = 0; j < fqnNodes.getLength(); j++) {
Node fqnNode = fqnNodes.item(j);
if (fqnNode.getNodeName().equals("int")) {
String fqn = getAttributeValue(fqnNode, "name");
if (fqn != null) {
String count = fqnNode.getFirstChild().getNodeValue();
HitFqnEntityId _apiFqn = new HitFqnEntityId(fqn, "-1", count);
apis.add(_apiFqn);
}
}
}
}
}
}
return apis;
}
/**
* Converts a form definition object to an XHTML document object.
*
* @param formDef the form definition object.
* @return the xhtml document object.
*/
public static Document fromFormDef2XhtmlDoc(FormDef formDef) {
Document prevdoc = formDef.getDoc();
Document doc = XMLParser.createDocument();
doc.appendChild(doc.createProcessingInstruction("xml", "version=\"1.0\" encoding=\"UTF-8\""));
Element htmlNode = doc.createElement("h:html");
// formDef.setXformsNode(htmlNode);
htmlNode.setAttribute("xmlns:h", "http://www.w3.org/1999/xhtml");
htmlNode.setAttribute("xmlns:jr", "http://openrosa.org/javarosa");
htmlNode.setAttribute(
XformConstants
.XML_NAMESPACE /*XformConstants.XML_NAMESPACE_PREFIX+XformConstants.PREFIX_XFORMS*/,
XformConstants.NAMESPACE_XFORMS);
htmlNode.setAttribute(
XformConstants.XML_NAMESPACE_PREFIX + XformConstants.PREFIX_XML_SCHEMA,
XformConstants.NAMESPACE_XML_SCHEMA);
doc.appendChild(htmlNode);
// add head
Element headNode = doc.createElement("h:head");
htmlNode.appendChild(headNode);
// add title
Element titleNode = doc.createElement("h:title");
titleNode.appendChild(doc.createTextNode(formDef.getName()));
headNode.appendChild(titleNode);
// add body
Element bodyNode = doc.createElement("h:body");
htmlNode.appendChild(bodyNode);
// add model
Element modelNode = doc.createElement(XformConstants.NODE_NAME_MODEL);
headNode.appendChild(modelNode);
// we do not want to lose anything that the model could have had which we do not build when
// creating an xform from scratch
XformBuilder.buildXform(formDef, doc, bodyNode, modelNode);
XformUtil.copyModel(prevdoc, doc);
return doc;
}
private static Node getResponseNode(String xmlResultInString) {
Document doc = XMLParser.parse(xmlResultInString);
NodeList results = doc.getElementsByTagName("result");
for (int i = 0; i < results.getLength(); i++) {
Node result = results.item(i);
NamedNodeMap attrs = result.getAttributes();
Node _attributeNode = null;
_attributeNode = attrs.getNamedItem("name");
if (_attributeNode != null) {
if (_attributeNode.getNodeValue().equals("response")) {
return result;
}
}
}
return null;
}
private void parseAjaxResponse(String responseTxt) {
if (responseTxt == null) {
return;
}
String error = null;
Document doc = null;
try {
doc = XMLParser.parse(responseTxt);
error = Utils.getXmlNodeValue(doc, "error");
if (error == null) {
// Response brings uploaded files info in either:
// POST response or FINISHED status
String msg = Utils.getXmlNodeValue(doc, TAG_MESSAGE);
serverMessage.setMessage(msg);
String fld = Utils.getXmlNodeValue(doc, TAG_FIELD);
NodeList list = doc.getElementsByTagName(TAG_FILE);
for (int i = 0, l = list.getLength(); i < l; i++) {
UploadedInfo info = new UploadedInfo();
info.setField(getInputName() + "-" + i);
info.setName(Utils.getXmlNodeValue(doc, TAG_NAME, i));
info.setCtype(Utils.getXmlNodeValue(doc, TAG_CTYPE, i));
// TODO: test
info.setKey(Utils.getXmlNodeValue(doc, TAG_KEY, i));
// TODO: remove
info.message = msg;
String url = session.composeURL(PARAM_SHOW + "=" + info.getField());
if (info.getKey() != null) {
url += "&" + PARAM_BLOBKEY + "=" + info.getKey();
}
info.setFileUrl(url);
String size = Utils.getXmlNodeValue(doc, TAG_SIZE, i);
if (size != null) {
info.setSize(Integer.parseInt(size));
}
serverMessage.getUploadedInfos().add(info);
}
}
} catch (Exception e) {
if (responseTxt.toLowerCase().matches("error")) {
error =
i18nStrs.uploaderServerError()
+ "\nAction: "
+ getServletPath()
+ "\nException: "
+ e.getMessage()
+ responseTxt;
}
}
if (error != null) {
successful = false;
cancelUpload(error);
return;
} else if (Utils.getXmlNodeValue(doc, TAG_WAIT) != null) {
if (serverRawResponse != null) {
log(
"server response received, cancelling the upload "
+ getFileNames()
+ " "
+ serverRawResponse,
null);
successful = true;
uploadFinished();
}
} else if (Utils.getXmlNodeValue(doc, TAG_CANCELED) != null) {
log("server response is: canceled " + getFileNames(), null);
successful = false;
canceled = true;
uploadFinished();
return;
} else if (Utils.getXmlNodeValue(doc, TAG_FINISHED) != null) {
log("server response is: finished " + serverMessage.getUploadedFileNames(), null);
successful = true;
if (onSubmitComplete) {
log("POST response from server has been received", null);
uploadFinished();
}
return;
} else if (Utils.getXmlNodeValue(doc, TAG_PERCENT) != null) {
lastData = now();
long transferredKB = Long.valueOf(Utils.getXmlNodeValue(doc, TAG_CURRENT_BYTES)) / 1024;
long totalKB = Long.valueOf(Utils.getXmlNodeValue(doc, TAG_TOTAL_BYTES)) / 1024;
statusWidget.setProgress(transferredKB, totalKB);
log(
"server response transferred " + transferredKB + "/" + totalKB + " " + getFileNames(),
null);
if (onSubmitComplete) {
successful = true; // why suppose an error here in this case ?
String msg = i18nStrs.uploaderBadServerResponse() + "\n" + serverRawResponse;
if (blobstore) {
msg += "\n" + i18nStrs.uploaderBlobstoreBilling();
} else {
msg += "\n" + i18nStrs.uploaderBadParsing();
}
msg += "\n\n" + responseTxt;
log(msg, null); // keep log message anyway
// statusWidget.setError(msg); // disable the user visible error message
uploadFinished();
}
return;
} else {
log("incorrect response: " + getFileNames() + " " + responseTxt, null);
}
if (uploadTimeout > 0 && now() - lastData > uploadTimeout) {
successful = false;
cancelUpload(i18nStrs.uploaderTimeout());
try {
sendAjaxRequestToCancelCurrentUpload();
} catch (Exception e) {
}
}
}
public String getGrade() {
Document d = XMLParser.createDocument();
Element root = d.createElement("Grade");
// first, some specifications of the pedigree
int numMales = 0;
int numFemales = 0;
int numAffectedMales = 0;
int numAffectedFemales = 0;
PelicanPerson[] people = getAllPeople();
for (int i = 0; i < people.length; i++) {
PelicanPerson p = people[i];
if (p.sex == PelicanPerson.male) {
numMales++;
if (p.affection == PelicanPerson.affected) {
numAffectedMales++;
}
} else {
numFemales++;
if (p.affection == PelicanPerson.affected) {
numAffectedFemales++;
}
}
}
Element e = d.createElement("Counts");
Element M = d.createElement("M");
M.appendChild(d.createTextNode(String.valueOf(numMales)));
e.appendChild(M);
Element F = d.createElement("F");
F.appendChild(d.createTextNode(String.valueOf(numFemales)));
e.appendChild(F);
Element aM = d.createElement("aM");
aM.appendChild(d.createTextNode(String.valueOf(numAffectedMales)));
e.appendChild(aM);
Element aF = d.createElement("aF");
aF.appendChild(d.createTextNode(String.valueOf(numAffectedFemales)));
e.appendChild(aF);
root.appendChild(e);
// now, the analysis results
renumberAll();
updateDisplay();
String integrity = checkIntegrity(history.lastElement());
if (integrity.equals("")) {
PedigreeSolver ps = new PedigreeSolver(getAllPeople(), getMatingList());
PedigreeSolution sol = ps.solve();
e = d.createElement("Analysis");
GenotypeSet[] results = sol.getResults();
Element AR = d.createElement("AR");
if (results[0].getAll().size() > 0) {
AR.appendChild(d.createTextNode("Y"));
} else {
AR.appendChild(d.createTextNode("N"));
}
e.appendChild(AR);
Element AD = d.createElement("AD");
if (results[1].getAll().size() > 0) {
AD.appendChild(d.createTextNode("Y"));
} else {
AD.appendChild(d.createTextNode("N"));
}
e.appendChild(AD);
Element SR = d.createElement("SR");
if (results[2].getAll().size() > 0) {
SR.appendChild(d.createTextNode("Y"));
} else {
SR.appendChild(d.createTextNode("N"));
}
e.appendChild(SR);
Element SD = d.createElement("SD");
if (results[3].getAll().size() > 0) {
SD.appendChild(d.createTextNode("Y"));
} else {
SD.appendChild(d.createTextNode("N"));
}
e.appendChild(SD);
}
root.appendChild(e);
return root.toString();
}
public void setState(String state) {
// read in this pedigree from the xml
Vector<PelicanPerson> newPedigree = new Vector<PelicanPerson>();
int pedSize = 0;
Vector<Integer> pidList = new Vector<Integer>();
Vector<Integer> midList = new Vector<Integer>();
HashMap<Integer, Integer> idMap = new HashMap<Integer, Integer>();
Document doc = XMLParser.parse(state);
NodeList people = doc.getDocumentElement().getChildNodes();
for (int i = 0; i < people.getLength(); i++) {
Element e = (Element) people.item(i);
if (e.getTagName().equals("Person")) {
int id = Integer.parseInt(e.getAttribute("Id"));
int sex = Integer.parseInt(e.getAttribute("Sex"));
int affection = Integer.parseInt(e.getAttribute("Affection"));
String[] genotype = new String[2];
genotype[0] = "?";
genotype[1] = "?";
PelicanPerson person =
new PelicanPerson(this, id, null, null, sex, affection, "", 0, genotype);
newPedigree.add(person);
int father = Integer.parseInt(e.getAttribute("Father"));
pidList.add(new Integer(father));
int mother = Integer.parseInt(e.getAttribute("Mother"));
midList.add(new Integer(mother));
idMap.put(new Integer(id), new Integer(pedSize++));
}
}
for (int i = 0; i < newPedigree.size(); i++) {
PelicanPerson person = (PelicanPerson) newPedigree.elementAt(i);
// gww if (((Integer)pidList.elementAt(i)).intValue()!=PelicanPerson.unknown) {
if ((Integer) pidList.elementAt(i) != PelicanPerson.unknownID) {
if (!idMap.containsKey(pidList.elementAt(i)))
// gww throw(new Error("Father of subject "+String.valueOf(person.id)+" is
// missing"));
throw (new Error("Father of subject " + person.id + " is missing"));
person.father =
(PelicanPerson)
newPedigree.elementAt(((Integer) idMap.get(pidList.elementAt(i))).intValue());
}
// gww if (((Integer)midList.elementAt(i)).intValue()!=PelicanPerson.unknown) {
if ((Integer) midList.elementAt(i) != PelicanPerson.unknownID) {
if (!idMap.containsKey(midList.elementAt(i)))
// gww throw(new Error("Mother of subject "+String.valueOf(person.id)+" is
// missing"));
throw (new Error("Mother of subject " + person.id + " is missing"));
person.mother =
(PelicanPerson)
newPedigree.elementAt(((Integer) idMap.get(midList.elementAt(i))).intValue());
}
}
// figure out the generations
((PelicanPerson) newPedigree.elementAt(0)).laidOut = true;
boolean someChange = true;
int nperson = newPedigree.size();
// repeatedly pass through the pedigree all subjects laid out
while (someChange) {
someChange = false;
for (int i = 0; i < nperson; i++) {
PelicanPerson p = (PelicanPerson) newPedigree.elementAt(i);
if (!p.laidOut) {
// try to get it from the parents
for (int j = 0; j < nperson; j++) {
PelicanPerson parent = (PelicanPerson) newPedigree.elementAt(j);
if (parent == p.father && parent.laidOut) {
p.generation = parent.generation + 1;
p.laidOut = true;
someChange = true;
}
if (parent == p.mother && parent.laidOut) {
p.generation = parent.generation + 1;
p.laidOut = true;
someChange = true;
}
}
}
if (p.laidOut) {
// assign parents generation
for (int j = 0; j < nperson; j++) {
PelicanPerson parent = (PelicanPerson) newPedigree.elementAt(j);
if (parent == p.father && !parent.laidOut) {
parent.generation = p.generation - 1;
parent.laidOut = true;
someChange = true;
}
if (parent == p.mother && !parent.laidOut) {
parent.generation = p.generation - 1;
parent.laidOut = true;
someChange = true;
}
}
}
}
}
if (!checkIntegrity(newPedigree).equals("")) {
return;
}
// end
clear();
currentId = 0;
for (int i = 0; i < nperson; i++) {
PelicanPerson p = (PelicanPerson) newPedigree.elementAt(i);
add(p);
// gww need to add in check for valid integer ID else ignore updating of currentId
if (p.id > 0) {
// gww if (i==0 || p.id>currentId) currentId=p.id;
if (i == 0 || p.id > currentId) currentId = p.id;
}
}
currentId++;
newPedigree.removeAllElements();
updateDisplay();
}
