private String chooserQuery() {
Random r = new Random();
File experimentFile = new File(queryFile);
SAXBuilder sb = new SAXBuilder();
Document d = null;
try {
d = sb.build(experimentFile);
} catch (JDOMException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
List<String> queries = new ArrayList<String>();
Element jpameterTag = d.getRootElement();
Element queriesTag = jpameterTag.getChild("queries");
List<Element> query = queriesTag.getChildren();
for (Element e : query) {
Element type = e.getChild("type");
if (Integer.parseInt(type.getValue()) == typeQuery + 1) {
Element sql = e.getChild("sql");
queries.add(sql.getValue());
}
}
if (queries.size() > 0) return queries.get(r.nextInt(queries.size()));
else return null;
}
@Test
public void test_setCommands() {
Map<String, Command> expected = new HashMap<String, Command>();
for (Element tmp : expected_commands) {
expected.put(
tmp.getValue(),
new Command(
tmp.getValue(),
Integer.parseInt(tmp.getAttributeValue("id")),
tmp.getAttributeValue("type")));
}
Assert.assertEquals(expected, this.commands.getMapOfCommand());
}
private String get(XMLProperty p) {
final Element child = getElement(p);
if (child == null) {
return "";
}
return child.getValue();
}
/**
* get start and end elemnt form parent element
*
* @param elem _more_
* @param ns _more_
* @return list of times
*/
public List<String> readSelectTime(Element elem, Namespace ns) {
// look for stations
Element region = elem.getChild("TimeSpan", ns);
java.util.List regionInfo = region.getChildren();
// lat, lon
Element start = region.getChild("start", ns);
String sv = start.getValue();
Element end = region.getChild("end", ns);
String ev = end.getValue();
List<String> ll = new ArrayList<String>();
ll.add(sv);
ll.add(ev);
return ll;
}
/**
* Load all the deals in this element
*
* @param e an element that contains messages in XML format.
*/
protected void loadDeals(Element e) {
Element root = StringToElement.getElementFromString(e.getValue(), e.getName());
for (Element d : root.getChildren()) {
String owner = d.getChildText("owner");
Element deal = d.getChild("Deal");
addDeal(owner, new Contrat(deal));
}
}
/**
* get region from parent element
*
* @param elem _more_
* @param ns _more_
* @return _more_
*/
public LatLonRect readSelectRegion(Element elem, Namespace ns) {
Element region = elem.getChild("LatLonBox", ns);
// lat, lon
Element north = region.getChild("north", ns);
String nv = north.getValue();
Element south = region.getChild("south", ns);
String sv = south.getValue();
Element east = region.getChild("east", ns);
String ev = east.getValue();
Element west = region.getChild("west", ns);
String wv = west.getValue();
LatLonPointImpl p1 = new LatLonPointImpl(Double.valueOf(sv), Double.valueOf(wv));
LatLonPointImpl p2 = new LatLonPointImpl(Double.valueOf(nv), Double.valueOf(ev));
LatLonRect llr = new LatLonRect(p1, p2);
return llr;
}
public List<String> getLocaleDirectories() throws JDOMException {
List<Element> langAddedList = ((List<Element>) XPath.selectNodes(loopDoc, "//langAdded"));
List<String> stringLocaleDirectories = new ArrayList<String>();
List<Element> localeDirectories = new ArrayList<Element>();
for (Element langAdded : langAddedList) {
localeDirectories = langAdded.getChildren("language");
for (Element localeDirectory : localeDirectories) {
stringLocaleDirectories.add(localeDirectory.getValue());
}
}
return stringLocaleDirectories;
}
static void loadNXParams(NXFrame nxFrame, Element elem) {
if (elem == null) {
return;
}
nxFrame.setVisible(false);
Element e = elem.getChild("maxspeed");
if (e != null) {
try {
nxFrame.setMaxSpeed(Float.valueOf(e.getValue()));
} catch (NumberFormatException nfe) {
log.error("NXWarrant MaxSpeed; " + nfe);
}
}
e = elem.getChild("haltstart");
if (e != null) {
if (e.getValue().equals("yes")) {
nxFrame.setStartHalt(true);
} else {
nxFrame.setStartHalt(false);
}
}
}
/**
* get station object from parent element
*
* @param elem _more_
* @return stationImpl
*/
private Station readStation(Element elem) {
// look for stations
String name = elem.getAttributeValue("id");
// latitude
Element desc = elem.getChild("name");
String descv = desc.getValue();
Element lat = elem.getChild("latitude");
String latv = lat.getValue();
Element lon = elem.getChild("longitude");
String lonv = lon.getValue();
Element alt = elem.getChild("elevation");
String altv = alt.getValue();
StationImpl station =
new StationImpl(
name,
descv,
"",
Double.parseDouble(latv),
Double.parseDouble(lonv),
Double.parseDouble(altv));
return station;
}
/**
* remove parts from this.nonSpecificParts if parts start a sentence in the description. for
* example "Body ellipsoidal" suggests that the organism has one body, and it is not a unspecific
* part of some other organ.
*
* @param text
* @return
*/
private String removeNonSpecificPartsIfFirstWord(Element description) {
String result = this.nonSpecificParts;
for (Element statement : description.getChildren("statement")) {
String sentence = statement.getValue().toLowerCase().trim();
if (sentence != null && sentence.matches("^[A-Z].*")) { // record parentorgan
String word1 = sentence.toLowerCase();
if (sentence.indexOf(" ") > 0)
word1 = sentence.substring(0, sentence.indexOf(" ")).toLowerCase();
result =
this.nonSpecificParts
.replaceFirst("(^|\\|)" + word1 + "(\\||$)", "|")
.replaceFirst("(^\\||\\|$)", "");
}
}
return result;
}
@Override
public void transform(Document document) {
for (Element description : this.descriptionXpath.evaluate(document)) {
String nonSpecificParts = removeNonSpecificPartsIfFirstWord(description);
String parentOrgan = null;
Element biologicalEntityA = null;
for (Element statement : description.getChildren("statement")) {
List<Element> biologicalEntities = statement.getChildren("biological_entity");
Element textElement = statement.getChild("text");
String text = textElement.getValue();
if (text != null && text.matches("^[A-Z].*")) { // record parentorgan
if (!biologicalEntities.isEmpty()) {
biologicalEntityA = biologicalEntities.get(0);
// attach parent organ to other structures in this statement, return parentorgan used.
parentOrgan =
attachParentOrganToOtherBiologicalEntities(
document, description, statement, biologicalEntityA, "", nonSpecificParts);
}
} else {
// sentences not starting with a capitalized structure names => those structures after ';'
if (parentOrgan != null) {
if (!biologicalEntities.isEmpty()) {
// then apply parentorgan to the first structure
biologicalEntityA = biologicalEntities.get(0);
// apply parentorgan + localpo(struct) to other structures in the statement
attachParentOrganToOtherBiologicalEntities(
document,
description,
statement,
biologicalEntityA,
parentOrgan,
nonSpecificParts);
handlePartOfOrganOfOrgan(document, description, biologicalEntityA, parentOrgan);
}
}
}
}
}
}
/**
* This constructor is not intended for usage.
*
* @param xml An XML string
* @throws JDOMException Is thrown when the xml string is invalid
* @throws IOException Is thrown when the xml string is invalid
*/
public LolStatus(String xml) throws JDOMException, IOException {
outputter.setFormat(outputter.getFormat().setExpandEmptyElements(false));
final SAXBuilder saxBuilder = new SAXBuilder();
doc = saxBuilder.build(new StringReader(xml));
for (final Element e : doc.getRootElement().getChildren()) {
boolean found = false;
for (final XMLProperty p : XMLProperty.values()) {
if (p.name().equals(e.getName())) {
found = true;
}
}
if (!found) {
System.err.println(
"XMLProperty \""
+ e.getName()
+ "\" value: \""
+ e.getValue()
+ "\" not implemented yet!");
}
}
}
/**
* get document from parent element
*
* @param elem _more_
* @param ns _more_
* @return _more_
*/
private String readSelectDocument(Element elem, Namespace ns) {
Element doc = elem.getChild("documentation", ns);
return doc.getValue();
}