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Re: [las_users] Lat/Lon problems
Hi,
I had problems with time axes with units of minutes some time ago, so I
expanded the LASConfig.java file for our internal LAS server. Now we can
use the unit "min" for axes like:
<time_axis type="t" units="min">
<arange start="01-AUG-2006 11:12" step="12" size="1905"
end="17-AUG-2006 08:12"/>
</time_axis>
If you don't fear editing the Java source code you can use it, but have
to change your LASUI.js (in /WebContent/JavaScript/ui/) in line 1524 from:
this.refs.DW = new
DateWidget(this.state.grid.getLo('t'),this.state.grid.getHi('t'));
to:
var scale = 1;
var tUnits = this.state.grid.getUnits('t');
var tDelta = this.state.grid.getDelta('t');
if (tUnits == "hour") {
scale = 60;
if ((24 % tDelta) != 0) {
tDelta = 1;
}
}
else {
if (tDelta == null || tUnits == "day") {
tDelta = 1440;
}
if (tUnits == "min") {
if ((1440 % tDelta) != 0) {
tDelta = 1;
}
}
}
this.refs.DW = new
DateWidget(this.state.grid.getLo('t'),this.state.grid.getHi('t'),(tDelta
* scale));
and replace /gov/noaa/pmel/tmap/las/jdom/LASConfig.java by the attached
LASConfig.java.
You should backup all files first!
I hope it works,
Bastian
On 02/24/2010 05:32 PM, Roland Schweitzer wrote:
> Anton,
>
> Anton Yoel Buenavista wrote:
>> Hello again everyone,
>>
>> For an update on my problem, I was able to display the variables
>> which only depend on lat and lon using the documentation here:
>> http://ferret.pmel.noaa.gov/LAS/documentation/installer-documentation/adding-curvilinear-data/.
>> Thank you Roland for your guidance on that.
>>
>> However, I am faced with a new problem. The remaining variables depend
>> on lat, lon, and a time dimension as well as you can see in the sample
>> variable definition below:
> [...]
>> <time-t-id-01ced4ab23 type="t" units="minute">
>> <arange start="2008-01-23 00:00:00" size="84" step="15" />
>> </time-t-id-01ced4ab23>
>> </axes>
>>
>> I have attached a screenshot of the error being returned when the plot
>> is trying to be loaded. Your kind help on the matter is greatly
>> appreciated!
> Unfortunately the LAS user interface time widget does not understand
> time increments of less than one hour. We'll be working on improving
> that in future versions, but for now you'll need to create your time
> axis by listing each individual time value. I know it's not practical
> for all cases, but it's the only solution for the immediate future. For
> example:
>
> <time-t-id-01ced4ab23 type="t" units="minute">
> <v>2008-01-23 00:00:00</v>
> <v>2008-01-23 00:15:00</v>
> <v>2008-01-23 00:30:00</v>
> <v>2008-01-23 00:45:00</v>
> <v>2008-01-23 01:00:00</v>
>
>
> [...]
>
> </time-t-id-01ced4ab23>
>
> Roland
>
/**
* This software is provided by NOAA for full, free and open release. It is
* understood by the recipient/user that NOAA assumes no liability for any
* errors contained in the code. Although this software is released without
* conditions or restrictions in its use, it is expected that appropriate
* credit be given to its author and to the National Oceanic and Atmospheric
* Administration should the software be included by the recipient as an
* element in other product development.
*/
package gov.noaa.pmel.tmap.las.jdom;
import gov.noaa.pmel.tmap.las.client.CategorySerializable;
import gov.noaa.pmel.tmap.las.client.DatasetSerializable;
import gov.noaa.pmel.tmap.las.client.RPCException;
import gov.noaa.pmel.tmap.las.client.VariableSerializable;
import gov.noaa.pmel.tmap.las.exception.LASException;
import gov.noaa.pmel.tmap.las.filter.AttributeFilter;
import gov.noaa.pmel.tmap.las.filter.CategoryFilter;
import gov.noaa.pmel.tmap.las.ui.state.StateNameValueList;
import gov.noaa.pmel.tmap.las.ui.state.TimeSelector;
import gov.noaa.pmel.tmap.las.util.Category;
import gov.noaa.pmel.tmap.las.util.DataConstraint;
import gov.noaa.pmel.tmap.las.util.Dataset;
import gov.noaa.pmel.tmap.las.util.Grid;
import gov.noaa.pmel.tmap.las.util.Institution;
import gov.noaa.pmel.tmap.las.util.NameValuePair;
import gov.noaa.pmel.tmap.las.util.Operation;
import gov.noaa.pmel.tmap.las.util.Option;
import gov.noaa.pmel.tmap.las.util.Region;
import gov.noaa.pmel.tmap.las.util.TimeAxis;
import gov.noaa.pmel.tmap.las.util.Variable;
import gov.noaa.pmel.tmap.las.util.View;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import org.apache.log4j.LogManager;
import org.apache.log4j.Logger;
import org.jdom.Attribute;
import org.jdom.Element;
import org.jdom.JDOMException;
import org.jdom.xpath.XPath;
import org.joda.time.DateTime;
import org.joda.time.DateTimeZone;
import org.joda.time.Period;
import org.joda.time.format.DateTimeFormat;
import org.joda.time.format.DateTimeFormatter;
/**
* This class is the JDOM instantiation of the "las.xml" file and any entities it references (data stubs and operationsV7.xml).
* @author Roland Schweitzer
*
*/
public class LASConfig extends LASDocument {
private static Logger log = LogManager.getLogger(LASConfig.class.getName());
private static String time_formats[] = {
"yyyy-MM-dd HH:mm:ss",
"yyyy-MM-dd HH:mm",
"yyyy-MM-dd HH",
"yyyy-MM-dd",
"yyy-MM-dd HH:mm:ss",
"yyy-MM-dd HH:mm",
"yyy-MM-dd HH",
"yyy-MM-dd",
"yy-MM-dd HH:mm:ss",
"yy-MM-dd HH:mm",
"yy-MM-dd HH",
"yy-MM-dd",
"y-MM-dd HH:mm:ss",
"y-MM-dd HH:mm",
"y-MM-dd HH",
"y-MM-dd",
"yyyy-M-dd HH:mm:ss",
"yyyy-M-dd HH:mm",
"yyyy-M-dd HH",
"yyyy-M-dd",
"yyy-M-dd HH:mm:ss",
"yyy-M-dd HH:mm",
"yyy-M-dd HH",
"yyy-M-dd",
"yy-M-dd HH:mm:ss",
"yy-M-dd HH:mm",
"yy-M-dd HH",
"yy-M-dd",
"y-M-dd HH:mm:ss",
"y-M-dd HH:mm",
"y-M-dd HH",
"y-M-dd",
"yyyy-MM-d HH:mm:ss",
"yyyy-MM-d HH:mm",
"yyyy-MM-d HH",
"yyyy-MM-d",
"yyy-MM-d HH:mm:ss",
"yyy-MM-d HH:mm",
"yyy-MM-d HH",
"yyy-MM-d",
"yy-MM-d HH:mm:ss",
"yy-MM-d HH:mm",
"yy-MM-d HH",
"yy-MM-d",
"y-MM-d HH:mm:ss",
"y-MM-d HH:mm",
"y-MM-d HH",
"y-MM-d",
"yyyy-M-d HH:mm:ss",
"yyyy-M-d HH:mm",
"yyyy-M-d HH",
"yyyy-M-d",
"yyy-M-d HH:mm:ss",
"yyy-M-d HH:mm",
"yyy-M-d HH",
"yyy-M-d",
"yy-M-d HH:mm:ss",
"yy-M-d HH:mm",
"yy-M-d HH",
"yy-M-d",
"y-M-d HH:mm:ss",
"y-M-d HH:mm",
"y-M-d HH",
"y-M-d",
"dd-MMM-yyyy HH:mm:ss",
"dd-MMM-yyyy HH:mm",
"dd-MMM-yyyy HH",
"dd-MMM-yyyy",
"d-MMM-yyyy HH:mm:ss",
"d-MMM-yyyy HH:mm",
"d-MMM-yyyy HH",
"d-MMM-yyyy",
"dd-MMM-yyy HH:mm:ss",
"dd-MMM-yyy HH:mm",
"dd-MMM-yyy HH",
"dd-MMM-yyy",
"d-MMM-yyy HH:mm:ss",
"d-MMM-yyy HH:mm",
"d-MMM-yyy HH",
"d-MMM-yyy",
"dd-MMM-yy HH:mm:ss",
"dd-MMM-yy HH:mm",
"dd-MMM-yy HH",
"dd-MMM-yy",
"d-MMM-yy HH:mm:ss",
"d-MMM-yy HH:mm",
"d-MMM-yy HH",
"d-MMM-yy",
"dd-MMM-y HH:mm:ss",
"dd-MMM-y HH:mm",
"dd-MMM-y HH",
"dd-MMM-y",
"d-MMM-y HH:mm:ss",
"d-MMM-y HH:mm",
"d-MMM-y HH",
"d-MMM-y"
};
/**.
* Get all the possible combinations of the characters in a string. Combo routines based on code by Robert Sedgewick and Kevin Wayne.
* from their book Introduction to Programming in Java published by Adison Wesley.
* @param s
* @return
*/
private static ArrayList<String> combo(String s) {
return combo("", s);
}
/**
* Get combinations of the characters in a string.
* @param prefix A prefix for the combinations
* @param s the string to scramble
* @return the combinations
*/
private static ArrayList<String> combo(String prefix, String s) {
ArrayList<String> comboList = new ArrayList<String>();
if (!prefix.equals("")) {
comboList.add(prefix);
}
if ( s.equals("") ) {
return comboList;
}
for ( int i = 0; i < s.length(); i++ ) {
comboList.addAll(combo(prefix + s.charAt(i), s.substring(i+1)));
}
return comboList;
}
/**
* Take F-TDS server URL and data directory and build the F-TDS URLs for each variable.
* @param fds_base the base URL of the F-TDS server http://server:port/thredds/dodsC
* @param fds_dir the directory into which the F-TDS journal files will be written
* @throws LASException
* @throws JDOMExcption
* @throws IOFoundException
*/
public void addFDS(String fds_base, String fds_dir) throws LASException, JDOMException, IOException {
File datadir = new File(fds_dir);
if ( !datadir.exists() ) {
boolean success = datadir.mkdirs();
if ( !success ) {
log.warn("No T-FDS directory.");
}
}
datadir = new File(fds_dir+"dynamic");
if ( !datadir.exists() ) {
boolean success = datadir.mkdirs();
if ( !success ) {
log.warn("No T-FDS directory for user defined data.");
}
}
List datasetsElements = getRootElement().getChildren("datasets");
for (Iterator datasetsElementIt = datasetsElements.iterator(); datasetsElementIt.hasNext();) {
Element datasetsE = (Element) datasetsElementIt.next();
List datasets = datasetsE.getChildren("dataset");
for (Iterator datasetIt = datasets.iterator(); datasetIt.hasNext();) {
HashMap<String, String> jnls = new HashMap<String, String>();
Element dataset = (Element) datasetIt.next();
String dsID = dataset.getAttributeValue("ID");
List variablesElements = dataset.getChildren("variables");
for (Iterator variablesEelementsIt = variablesElements.iterator(); variablesEelementsIt.hasNext();) {
Element variablesE = (Element) variablesEelementsIt.next();
List variables = variablesE.getChildren("variable");
for (Iterator varsIt = variables.iterator(); varsIt.hasNext();) {
Element variable = (Element) varsIt.next();
String varID = variable.getAttributeValue("ID");
String var = getVariableName(dsID,varID);
String grid_type = variable.getAttributeValue("grid_type");
if ( grid_type.equals("regular") ) {
datadir = new File(fds_dir+dsID);
if ( !datadir.exists() ) {
boolean success = datadir.mkdirs();
if ( !success ) {
log.warn("No T-FDS directory for "+dsID);
}
}
String url = getDataObjectURL(variable);
String init = getVariablePropertyValue(variable,"ferret","init_script");
String key;
if ( init != null && !init.equals("") ) {
key = url+"_"+init+"_"+var;
} else {
key = url;
}
if ( key.startsWith("http://";) ) {
key = key.substring(6,key.length());
}
key = key.replaceAll("/","_");
key = key.replaceAll(":","_");
if ( key.startsWith("_") ) {
key = key.substring(1,key.length());
}
if ( !jnls.containsKey(key) ) {
StringBuffer jnl = new StringBuffer();
if ( init != null && !init.equals("") ) {
jnl.append("DEFINE SYMBOL data_url \\\""+url+"\\\"\n");
jnl.append("DEFINE SYMBOL data_var "+var+"\n");
jnl.append("GO "+init+"\n");
jnls.put(key, jnl.toString());
} else {
jnl.append("USE \""+url+"\"\n");
jnls.put(key, jnl.toString());
}
}
variable.setAttribute("ftds_url", fds_base+dsID+"/data_"+key+".jnl");
}
}
}
if ( jnls.size() > 0 ) {
int index=0;
for (Iterator jnlsIt = jnls.keySet().iterator(); jnlsIt.hasNext();) {
String key = (String) jnlsIt.next();
File varjnl = new File(fds_dir+dsID+File.separator+"data_"+key+".jnl");
PrintWriter data_script = new PrintWriter(new FileWriter(varjnl));
data_script.println(jnls.get(key));
data_script.close();
index++;
}
}
}
}
}
/**
* Descends the dataset and variable tree and set the grid_type attribute
* if it is not already set.
* @throws LASException
* @throws JDOMException
*/
public void addGridType() throws LASException, JDOMException {
Element root = getRootElement();
String version = root.getAttributeValue("version");
if ( version != null && !version.contains("7.")) {
throw new LASException("XML is not version 7.0 or above. Try convertToSeven() first.");
}
List datasetsElements = root.getChildren("datasets");
for (Iterator dseIt = datasetsElements.iterator(); dseIt.hasNext();) {
Element datasetsE = (Element) dseIt.next();
List datasets = datasetsE.getChildren("dataset");
for (Iterator dsIt = datasets.iterator(); dsIt.hasNext();) {
Element dataset = (Element) dsIt.next();
// In theory there's only 1, but loop to be sure.
List variablesElements = dataset.getChildren("variables");
for (Iterator varseIt = variablesElements.iterator(); varseIt
.hasNext();) {
Element variablesE = (Element) varseIt.next();
List variables = variablesE.getChildren("variable");
for (Iterator varIt = variables.iterator(); varIt.hasNext();) {
Element variable = (Element) varIt.next();
setGridType(variable);
}
}
}
}
}
/**
* Adds attributes to all variables that indicate whether or not the variable
* has a range or a point in the definition of each axis. Must be a version
* 7.0 style document before this method is invoked.
* @throws LASException
* @throws JDOMException
*/
public void addIntervalsAndPoints() throws LASException, JDOMException {
Element root = getRootElement();
String version = root.getAttributeValue("version");
if ( version != null && !version.contains("7.")) {
throw new LASException("XML is not version 7.0 or above. Try convertToSeven() first.");
}
List datasetsElements = root.getChildren("datasets");
for (Iterator dseIt = datasetsElements.iterator(); dseIt.hasNext();) {
Element datasetsE = (Element) dseIt.next();
List datasets = datasetsE.getChildren("dataset");
for (Iterator dsIt = datasets.iterator(); dsIt.hasNext();) {
Element dataset = (Element) dsIt.next();
// In theory there's only 1, but loop to be sure.
List variablesElements = dataset.getChildren("variables");
for (Iterator varseIt = variablesElements.iterator(); varseIt
.hasNext();) {
Element variablesE = (Element) varseIt.next();
List variables = variablesE.getChildren("variable");
for (Iterator varIt = variables.iterator(); varIt.hasNext();) {
Element variable = (Element) varIt.next();
// Get the reference to the grid
Element grid = variable.getChild("grid");
String gridID = grid.getAttributeValue("IDREF");
// Replace it with the actual grid element.
grid = getElementByXPath("/lasdata/grids/grid[@ID='"+gridID+"']");
List axes = grid.getChildren("axis");
String[] intervals = {"","","",""};
String[] points = {"","","",""};
for (Iterator axIt = axes.iterator(); axIt.hasNext();) {
// This is a reference to an axis
Element axis = (Element) axIt.next();
String axisID = axis.getAttributeValue("IDREF");
// Replace it with the actual axis
axis = getElementByXPath("/lasdata/axes/axis[@ID='"+axisID+"']");
String type = axis.getAttributeValue("type");
Element arange = axis.getChild("arange");
int size;
if ( arange != null ) {
size = Integer.valueOf(arange.getAttributeValue("size")).intValue();
} else {
List v = axis.getChildren("v");
size = v.size();
}
// The axis defintions can come in any order but
// we want this string orders XYZT
if ( size == 1 ) {
if ( type.equals("x") ) {
points[0] = type;
} else if ( type.equals("y") ) {
points[1] = type;
} else if ( type.equals("z") ) {
points[2] = type;
} else if ( type.equals("t") ) {
points[3] = type;
}
} else if ( size > 1 ) {
if ( type.equals("x") ) {
points[0] = type;
intervals[0] = type;
} else if ( type.equals("y") ) {
points[1] = type;
intervals[1] = type;
} else if ( type.equals("z") ) {
points[2] = type;
intervals[2] = type;
} else if ( type.equals("t") ) {
points[3] = type;
intervals[3] = type;
}
}
}
String existingPoints = variable.getAttributeValue("points");
String existingIntervals = variable.getAttributeValue("intervals");
// Set them only if they don't already exist in the variable definition.
if ( existingPoints == null ) {
variable.setAttribute("points", points[0]+points[1]+points[2]+points[3]);
}
if ( existingIntervals == null ) {
variable.setAttribute("intervals", intervals[0]+intervals[1]+intervals[2]+intervals[3]);
}
}
}
}
}
}
/**
* Create all the extra fancy attributes for a time axis so the DateWidgets can be initialized.
* @param axis the axis description from this config
* @throws LASException
*/
private void addTimeAxisAttributes(Element axis) throws LASException {
Element arange = axis.getChild("arange");
if (arange == null) {
List v = axis.getChildren("v");
for (Iterator vIt = v.iterator(); vIt.hasNext();) {
Element vE = (Element) vIt.next();
String label = vE.getAttributeValue("label");
if ( label == null ) {
String content = vE.getTextTrim();
vE.setAttribute("label", content);
}
}
Element v0 = (Element) v.get(0);
String tlo = v0.getTextTrim();
Element vN = (Element) v.get(v.size()-1);
String thi = vN.getTextTrim();
axis.setAttribute("lo", tlo);
axis.setAttribute("hi", thi);
axis.setAttribute("display_type", "menu");
} else {
axis.setAttribute("display_type", "widget");
String tlo = arange.getAttributeValue("start");
String units = axis.getAttributeValue("units");
/** by Baschti:
new attribute end for enddate. so size or end can be used in xml file
*****************************************************************************/
String thi = arange.getAttributeValue("end");
double size = 0;
try {
size = Double.valueOf(arange.getAttributeValue("size")).doubleValue();
} catch (Exception e) {}
/** Baschti End **/
double step = Double.valueOf(arange.getAttributeValue("step")).doubleValue();
DateTimeFormatter fmt = null;
DateTime lodt = new DateTime("9000-01-01");
boolean found = false;
for (int i = 0; i < time_formats.length; i++) {
fmt = DateTimeFormat.forPattern(time_formats[i]).withZone(DateTimeZone.UTC);
try {
lodt = fmt.parseDateTime(tlo);
found = true;
} catch ( IllegalArgumentException e ) {
found = false;
}
if (found) break;
}
if ( !found ) {
throw new LASException("Time format for "+tlo+" could not be parsed.");
}
/** by Baschti:
do the same test as for lodt for hidt
*****************************************************************************/
DateTime hidt = new DateTime();
if ( thi != null) {
fmt = null;
hidt = new DateTime("9000-01-01");
found = false;
for (int i = 0; i < time_formats.length; i++) {
fmt = DateTimeFormat.forPattern(time_formats[i]).withZone(DateTimeZone.UTC);
try {
hidt = fmt.parseDateTime(thi);
found = true;
} catch ( IllegalArgumentException e ) {
found = false;
}
if (found) break;
}
if ( !found ) {
throw new LASException("Time format for "+thi+" could not be parsed.");
}
}
/** Baschti End **/
DateTimeFormatter longfmt = DateTimeFormat.forPattern("yyyy-MM-dd HH:mm:ss").withZone(DateTimeZone.UTC);
axis.setAttribute("lo", lodt.toString(longfmt));
/** by Baschti
added min for minutes
*****************************************************************************/
if ( units.contains("min") ) {
axis.setAttribute("hourNeeded", "true");
axis.setAttribute("dayNeeded", "true");
axis.setAttribute("monthNeeded", "true");
axis.setAttribute("yearNeeded", "true");
int minutes = 0;
if (thi == null) {
minutes = (int) Math.round((size-1)*step);
hidt = lodt.plus(Period.minutes(minutes));
}
else {
Period delta = new Period(lodt,hidt);
minutes = (int) (12 * 8017 * 3);
}
int minuteInterval = (int) Math.round(minutes);
axis.setAttribute("minuteInterval", String.valueOf(minuteInterval) );
axis.setAttribute("hi", hidt.toString(longfmt));
/** Baschti End **/
} else if ( units.contains("hour") ) {
axis.setAttribute("hourNeeded", "true");
axis.setAttribute("dayNeeded", "true");
axis.setAttribute("monthNeeded", "true");
axis.setAttribute("yearNeeded", "true");
int hours = (int) Math.round((size-1)*step);
int minuteInterval = (int) Math.round(step*60.);
axis.setAttribute("minuteInterval", String.valueOf(minuteInterval) );
hidt = lodt.plus(Period.hours(hours));
axis.setAttribute("hi", hidt.toString(longfmt));
} else if ( units.contains("day") ) {
axis.setAttribute("hourNeeded", "false");
axis.setAttribute("dayNeeded", "true");
axis.setAttribute("monthNeeded", "true");
axis.setAttribute("yearNeeded", "true");
int days = (int) Math.round((size-1)*step);
hidt = lodt.plus(Period.days(days));
axis.setAttribute("hi", hidt.toString(longfmt));
} else if ( units.contains("month") ) {
axis.setAttribute("hourNeeded", "false");
axis.setAttribute("dayNeeded", "false");
axis.setAttribute("monthNeeded", "true");
axis.setAttribute("yearNeeded", "true");
int months = (int) Math.round((size-1)*step);
hidt = lodt.plus(Period.months(months));
axis.setAttribute("hi", hidt.toString(longfmt));
} else if ( units.contains("year") ) {
axis.setAttribute("hourNeeded", "false");
axis.setAttribute("dayNeeded", "false");
axis.setAttribute("monthNeeded", "false");
axis.setAttribute("yearNeeded", "true");
double start = Double.valueOf(tlo).doubleValue();
int years = (int) Math.round(start + (size-1)*step);
hidt = lodt.plus(Period.years(years));
axis.setAttribute("hi", hidt.toString(longfmt));
}
String modulo = axis.getAttributeValue("modulo");
String climatology = axis.getAttributeValue("climatology");
if ( modulo != null && modulo.equals("true") ) {
axis.setAttribute("yearNeeded", "false");
}
if ( climatology != null && climatology.equals("true") ) {
axis.setAttribute("yearNeeded", "false");
}
}
}
/**
* @param fdsURL
* @param analysis_axes
* @param jsessionid
* @throws JDOMException
* We aren't going to do this here. We're going to keep a session object with the user defined variables.
public void addAnalysisVariables(Variable var, ArrayList<String> analysis_axes, String jsessionid) throws JDOMException {
Grid grid = getGrid(var.getDSID(), var.getAttributeValue("orig_var_id"));
Grid analysis_grid = (Grid) grid.clone();
for (Iterator aaIt = analysis_axes.iterator(); aaIt.hasNext();) {
String analysis_axis_type = (String) aaIt.next();
analysis_grid.removeAxis(analysis_axis_type);
}
analysis_grid.setID( analysis_grid.getID()+"_" +var.getName() + "_" + jsessionid );
var.setGridID(analysis_grid.getID());
if ( !containsVariable( var.getDSID(), var.getID() ) ) {
getDatasetElement(var.getDSID()).getChild("variables").addContent(var.toElement());
}
if ( !containsGrid ( analysis_grid.getID() ) ) {
getRootElement().getChild("grids").addContent(analysis_grid.toElement());
}
System.out.println(this.toString());
} */
/**
* See if this config contains a grid with this ID
* @param id the id to check
* @return true if found; false if not
*/
private boolean containsGrid(String grid_id) {
List gridsElements = getRootElement().getChildren("grids");
for (Iterator gridsIt = gridsElements.iterator(); gridsIt.hasNext();) {
Element gridsE = (Element) gridsIt.next();
List grids = gridsE.getChildren("grid");
for (Iterator gridIt = grids.iterator(); gridIt.hasNext();) {
Element gridE = (Element) gridIt.next();
String ID = gridE.getAttributeValue("ID");
if ( ID.equals(grid_id) ) {
return true;
}
}
}
return false;
}
/**
* Does this config contain this data set and variable?
* @param dsid the data set
* @param id the variable
* @return
* @throws JDOMException
*/
private boolean containsVariable(String dsid, String var_id) throws JDOMException {
// Could be done with getElementByXPath, no?
Element dataset = getDatasetElement(dsid);
List variables = dataset.getChild("variables").getChildren("variable");
for (Iterator varIt = variables.iterator(); varIt.hasNext();) {
Element varE = (Element) varIt.next();
String ID = varE.getAttributeValue("ID");
if ( ID.equals(var_id) ) {
return true;
}
}
return false;
}
/**
* Converts to XML that can be validated against a schema, or returns if it detects that XML is already "Version 7".
*
*/
public void convertToSeven() {
Element root = getRootElement();
String version = root.getAttributeValue("version");
if ( version != null && version.contains("7.")) {
return;
}
root.setAttribute("version", "7.0");
List children = root.getChildren();
for (Iterator childIt = children.iterator(); childIt.hasNext();) {
Element child = (Element) childIt.next();
if (child.getName().equalsIgnoreCase("datasets")) {
List datasets = child.getChildren();
for (Iterator dsIt = datasets.iterator(); dsIt.hasNext();) {
Element dataset = (Element) dsIt.next();
/*
* Rather than look for the element we want we have to ignore the elements
* we don't want (since the "dataset" element names are random.
* If there are other names that must be ignored, the must be
* added here and below...
*/
if ( !dataset.getName().equals("properties") &&
!dataset.getName().equals("documentation") &&
!dataset.getName().equals("contributor")) {
String ID = dataset.getName();
dataset.setName("dataset");
dataset.setAttribute("ID", ID);
// Technically, I think there's only one of these per dataset,
// but you can't be sure so loop over all you can find.
List variablesParents = dataset.getChildren();
for (Iterator varsIt = variablesParents.iterator(); varsIt.hasNext();) {
Element variablesElement = (Element) varsIt.next();
if ( !variablesElement.getName().equals("properties") &&
!variablesElement.getName().equals("documentation") &&
!variablesElement.getName().equals("contributor") ) {
List variables = variablesElement.getChildren();
for (Iterator varIt = variables.iterator(); varIt.hasNext();) {
Element var = (Element) varIt.next();
if ( !var.getName().equals("properties") &&
!var.getName().equals("documentation") &&
!var.getName().equals("contributor")) {
String VID = var.getName();
var.setName("variable");
var.setAttribute("ID", VID);
Element grid = var.getChild("link");
String GID = grid.getAttributeValue("match");
String[] parts = GID.split("/");
GID = parts[3];
grid.setName("grid");
grid.removeAttribute("match");
grid.setAttribute("IDREF", GID);
// Convert any proproperties.
Element vprops = var.getChild("properties");
if (vprops != null) {
vprops.setContent(LASDocument.convertProperties(vprops));
}
} else if ( var.getName().equals("properties") ){
var.setContent(LASDocument.convertProperties(var));
}
}
} else if ( variablesElement.getName().equals("properties") ) {
variablesElement.setContent(LASDocument.convertProperties(variablesElement));
}
}
} else if ( dataset.getName().equals("properties") ) {
dataset.setContent(LASDocument.convertProperties(dataset));
}
}
} else if ( child.getName().equalsIgnoreCase("grids")) {
List grids = child.getChildren();
for (Iterator gridsIt = grids.iterator(); gridsIt.hasNext();) {
Element grid = (Element) gridsIt.next();
String GID = grid.getName();
grid.setName("grid");
grid.setAttribute("ID", GID);
List axesrefs = grid.getChildren();
for (Iterator axisIt = axesrefs.iterator(); axisIt.hasNext();) {
Element axis = (Element) axisIt.next();
String AID = axis.getAttributeValue("match");
axis.setName("axis");
String[] parts = AID.split("/");
AID = parts[3];
axis.setAttribute("IDREF", AID);
axis.removeAttribute("match");
}
}
} else if (child.getName().equalsIgnoreCase("axes")) {
List axes = child.getChildren();
for (Iterator axesIt = axes.iterator(); axesIt.hasNext();) {
Element axis = (Element) axesIt.next();
if ( !axis.getName().equals("properties")) {
String AID = axis.getName();
axis.setName("axis");
axis.setAttribute("ID", AID);
List v = axis.getChildren("v");
boolean warn = false;
if ( v != null && axis.getAttributeValue("type").equals("t") ) {
for (Iterator vIt = v.iterator(); vIt.hasNext();) {
Element ve = (Element) vIt.next();
String value = ve.getTextTrim();
if ( value.equalsIgnoreCase("jan") || value.equalsIgnoreCase("feb") ||
value.equalsIgnoreCase("mar") || value.equalsIgnoreCase("apr") ||
value.equalsIgnoreCase("may") || value.equalsIgnoreCase("jun") ||
value.equalsIgnoreCase("jul") || value.equalsIgnoreCase("aug") ||
value.equalsIgnoreCase("sep") || value.equalsIgnoreCase("oct") ||
value.equalsIgnoreCase("nov") || value.equalsIgnoreCase("dec") ) {
ve.setAttribute("label", value);
ve.setText("15-"+value);
warn = true;
}
}
if ( warn ) {
log.warn("Converted <v>Jan</v> syntax to <v label=\"Jan\">15-Jan</v> syntax for axis "+AID);
}
}
} else if ( axis.getName().equals("properties")) {
axis.setContent(LASDocument.convertProperties(axis));
}
}
} else if ( child.getName().equalsIgnoreCase("properties")) {
child.setContent(LASDocument.convertProperties(child));
} else if ( child.getName().equalsIgnoreCase("las_categories") ) {
List categories = child.getChildren("category");
setID(categories);
}
}
}
/**
* Helper method to recursively extract the options.
* @throws JDOMException
*/
public ArrayList<Option> extractOptions (String optionID) throws JDOMException {
ArrayList<Option> options = new ArrayList<Option>();
Element optiondef = getElementByXPath("/lasdata/lasui/options/optiondef[@name='"+optionID+"']");
List definedOptions = optiondef.getChildren("option");
// Collect the options that are defined inside this optiondef.
Option opB = null;
for (Iterator doIt = definedOptions.iterator(); doIt.hasNext();) {
Element opt = (Element) doIt.next();
opB = new Option((Element)opt.clone());
options.add(opB);
}
// These options are defined by inheritence from other optiondef elements.
String inherit = optiondef.getAttributeValue("inherit");
if ( inherit != null ) {
if ( inherit.contains(",")) {
String[] inheritedOptionsIDs = optiondef.getAttributeValue("inherit").split(",");
for (int i = 0; i < inheritedOptionsIDs.length; i++) {
options.addAll(extractOptions(inheritedOptionsIDs[i].substring(1)));
}
} else {
options.addAll(extractOptions(inherit.substring(1)));
}
}
return options;
}
/**
* A filter to find a category by its ID
* @param catid the ID to find
* @return the category element
* @throws JDOMException
*/
private Element findCategory(String catid) throws JDOMException {
CategoryFilter filter = new CategoryFilter(catid);
Iterator catIt= getRootElement().getDescendants(filter);
return (Element) catIt.next();
}
/**
* Get the base url of this LAS server (the server host, port and context path).
* @return base url of the LAS server family.
* @throws JDOMException
*/
public String getBaseServerURL() throws JDOMException {
Element ops = getElementByXPath("/lasdata/operations");
String server = ops.getAttributeValue("url");
if ( server != null && server.contains("ProductServer.do") ) {
return server.substring(0, server.lastIndexOf("/"));
} else {
throw new JDOMException("No server URL found in the las.xml operations element.");
}
}
/**
* Get any applicable data constraints for a particular data set and variable.
* @param dsID
* @param varID
* @return the list of constraints
* @throws JDOMException
*/
public ArrayList<DataConstraint> getConstraints(String dsID, String varID) throws JDOMException {
String ui_default = getUIDefaultName(dsID, varID);
ui_default = ui_default.substring(ui_default.indexOf("#")+1);
if ( ui_default != null && !ui_default.equals("") ) {
return getConstraints(ui_default, dsID, varID);
} else {
return new ArrayList<DataConstraint>();
}
}
/**
* Get any constraints from the named UI default.
*
* @param ui_default
* @return the constraints
* @throws JDOMException
*/
public ArrayList<DataConstraint> getConstraints(String ui_default, String dsID, String varID) throws JDOMException {
ArrayList<DataConstraint> constraints = new ArrayList<DataConstraint>();
Element def = getUIDefault(ui_default);
Element op = getUIMap(def, "ops");
List cons = op.getChildren("constraint");
for (Iterator consIt = cons.iterator(); consIt.hasNext();) {
// Get the reference to the constraint...
Element constraint = (Element) consIt.next();
String type = constraint.getAttributeValue("type");
String name = constraint.getAttributeValue("name");
String ID = constraint.getAttributeValue("ID");
if ( type.equals("variable") ) {
DataConstraint vc = getVariableConstraint(dsID, varID);
if ( name != null ) {
vc.setName(name);
} else {
vc.setName("variable");
}
if ( ID != null ) {
vc.setID(ID);
}
constraints.add(vc);
} else {
// Build the constraint...
Element full_constraint = new Element("constraint");
if ( name != null ) {
full_constraint.setAttribute("name", name);
}
if ( ID != null ) {
full_constraint.setAttribute("ID", ID);
}
full_constraint.setAttribute("type", "menu");
// First copy the attributes...
List attrs = constraint.getAttributes();
for (Iterator attIt = attrs.iterator(); attIt.hasNext();) {
Attribute attr = (Attribute) attIt.next();
full_constraint.setAttribute(attr.getName(), attr.getValue());
}
// Then follow the references to get the three parts, left-hand side menu, operations, right-hand side menu
List menus = constraint.getChildren("menu");
int it = 0;
for (Iterator menuIt = menus.iterator(); menuIt.hasNext();) {
Element menu_ref = (Element) menuIt.next();
String href = menu_ref.getAttributeValue("href");
href = href.substring(1, href.length());
Element menu = getUIMenu(href);
Element menu_clone = (Element) menu.clone();
if ( it == 0 ) {
menu_clone.setAttribute("position", "lhs");
} else if ( it == 1 ) {
menu_clone.setAttribute("position", "ops");
} else if ( it == 2 ) {
menu_clone.setAttribute("position", "rhs");
}
full_constraint.addContent(menu_clone);
it++;
}
constraints.add(new DataConstraint(full_constraint));
}
}
return constraints;
}
/**
* Build a variable constraint from a particular variable
* @param dsID the data set ID of the variable
* @param varID the variable id
* @return the data constraint for this variable
* @throws JDOMException
*/
public DataConstraint getVariableConstraint(String dsID, String varID) throws JDOMException {
Element constraint = new Element("constraint");
constraint.setAttribute("type", "variable");
ArrayList<Variable> vars = getVariables(dsID);
Element menu = new Element("menu");
menu.setAttribute("position", "lhs");
menu.setAttribute("type", "constraint");
menu.setAttribute("name","variable_"+dsID);
for (Iterator varIt = vars.iterator(); varIt.hasNext();) {
Variable var = (Variable) varIt.next();
Element item = new Element("item");
item.setAttribute("values", var.getID());
item.setText(var.getName());
menu.addContent(item);
}
constraint.addContent(menu);
menu = new Element("menu");
menu.setAttribute("position", "ops");
menu.setAttribute("type", "constraint");
menu.setAttribute("name","variable_"+dsID);
Element item = new Element("item");
item.setAttribute("values",">=");
item.setText(">=");
menu.addContent(item);
item = new Element("item");
item.setAttribute("values",">");
item.setText(">");
menu.addContent(item);
item = new Element("item");
item.setAttribute("values","=");
item.setText("=");
menu.addContent(item);
item = new Element("item");
item.setAttribute("values","!=");
item.setText("!=");
menu.addContent(item);
item = new Element("item");
item.setAttribute("values","<");
item.setText("<");
menu.addContent(item);
item = new Element("item");
item.setAttribute("values","<=");
item.setText("<=");
menu.addContent(item);
constraint.addContent(menu);
return new DataConstraint(constraint);
}
public CategorySerializable[] getCategorySerializable(ArrayList<Category> categories) throws LASException, JDOMException {
CategorySerializable[] cats = new CategorySerializable[categories.size()];
int i=0;
for (Iterator catIt = categories.iterator(); catIt.hasNext();) {
Category cat = (Category) catIt.next();
CategorySerializable wireCat = cat.getCategorySerializable();
if ( wireCat.hasMultipleDatasets() ) {
DatasetSerializable[] ds = wireCat.getDatasetSerializableArray();
for (int j = 0; j < ds.length; j++) {
VariableSerializable[] wireVars = ds[j].getVariablesSerializable();
for (int k = 0; k < wireVars.length; k++) {
VariableSerializable var = wireVars[k];
Grid grid = getGrid(var.getDSID(), var.getID());
var.setGrid(grid.getGridSerializable());
}
}
} else {
if ( wireCat.isVariableChildren() ) {
VariableSerializable[] wireVars = wireCat.getDatasetSerializable().getVariablesSerializable();
for (int j = 0; j < wireVars.length; j++) {
VariableSerializable var = wireVars[j];
Grid grid = getGrid(var.getDSID(), var.getID());
var.setGrid(grid.getGridSerializable());
}
}
}
cats[i] = wireCat;
i++;
}
return cats;
}
/**
* Get the categories directly below this id. If the id is null get the top.
* @param catid
* @return
* @throws JDOMException
*/
public ArrayList<Category> getCategories(String catid) throws JDOMException {
ArrayList<Category> categories = new ArrayList<Category>();
List tops = getRootElement().getChildren("las_categories");
if ( catid == null ) {
// Get the top level categories...
if ( tops != null && tops.size() > 0 ) {
for (Iterator topIt = tops.iterator(); topIt.hasNext();) {
Element las_categoryE = (Element)((Element) topIt.next()).clone();
List cats = (List) las_categoryE.getChildren("category");
for (Iterator catIt = cats.iterator(); catIt.hasNext();) {
Element category = (Element) ((Element) catIt.next()).clone();
Element category_container = new Element("category");
List attributes = category.getAttributes();
for (Iterator attrIt = attributes.iterator(); attrIt.hasNext();) {
Attribute attr = (Attribute) attrIt.next();
category_container.setAttribute(attr.getName(), attr.getValue());
}
// Set the "chidren" attribute to identify what kind of kids it has.
if ( category.getChild("filter") != null ) {
Element filter = category.getChild("filter");
Dataset dataset = getDataset(filter);
if ( dataset != null ) {
category_container.setAttribute("children_dsid", dataset.getAttributeValue("ID"));
}
category_container.setAttribute("children", "variables");
} else {
category_container.setAttribute("children", "categories");
}
categories.add(new Category(category_container));
}
}
} else {
categories = getDatasets();
}
} else {
// There are categories in the config, use them...
if ( tops != null && tops.size() > 0 ) {
// Either the category has other categories as children...
// When a category has categories as children, we need to only include
// the next level down. Therefore we copy the attributes and add
// the child categories without the grandchildren.
Element category = findCategory(catid);
Element category_container = new Element("category");
List attributes = category.getAttributes();
for (Iterator attrIt = attributes.iterator(); attrIt.hasNext();) {
Attribute attr = (Attribute) attrIt.next();
category_container.setAttribute(attr.getName(), attr.getValue());
}
List cats = (List) category.getChildren("category");
if ( cats.size() > 0 ) {
for (Iterator catsIt = cats.iterator(); catsIt.hasNext();) {
Element cat = (Element) catsIt.next();
Element cat_nokids = new Element("category");
List cat_attr = cat.getAttributes();
for (Iterator attrIt = cat_attr.iterator(); attrIt.hasNext();) {
Attribute attr = (Attribute) attrIt.next();
cat_nokids.setAttribute(attr.getName(), attr.getValue());
}
List filters = cat.getChildren("filter");
if ( filters.size() > 0 ) {
Element filter = (Element)filters.get(0);
Dataset dataset = getDataset(filter);
if ( dataset != null ) {
// Add only if the filter returns a dataset. It's possible to create
// a filter that returns an empty list.
cat_nokids.setAttribute("children_dsid", dataset.getAttributeValue("ID"));
}
cat_nokids.setAttribute("children", "variables");
} else {
cat_nokids.setAttribute("children", "categories");
}
categories.add(new Category(cat_nokids));
}
}
// or it has variables...
if ( category.getChild("filter") != null ) {
List filters = category.getChildren("filter");
for (Iterator filterIt = filters.iterator(); filterIt.hasNext();) {
Element filter = (Element) filterIt.next();
/*
* The rules say that all of the variables caught by a filter
* must come from the same dataset. I think the best way to
* represent this collection of information is via a dataset
* element the filtered list of variables. Therefore this
* is a getDataset call...
*/
Dataset dataset = getDataset(filter);
if ( dataset != null ) {
category_container.addContent(dataset.getElement());
}
}
categories.add(new Category(category_container));
}
} else {
// This config has no "categories", just datasets and variables. Use them.
Element dataset = getDatasetElement(catid);
Element container_dataset;
if ( dataset != null ) {
container_dataset = (Element) dataset.clone();
} else {
// send an empty one
container_dataset = new Element("dataset");
}
Element category = new Element("category");
category.addContent(container_dataset);
categories.add(new Category(category));
}
}
return categories;
}
/**
* Get data access URL. If fds is set to true, then the FDS URL will be
* returned in every case. If the fds boolean is set to false, then the
* actual OPeNDAP URL of the remote data set will be returned where available.
* If no remote URL is available, the the FDS URL will be returned.
* @param xpath the XPath of the variable
* @param fds true if FDS URL is required
* @throws JDOMException
* @throws LASException
*/
public String getDataAccessURL(String xpath, boolean fds) throws LASException, JDOMException {
String url = "";
String dataObjectURL = getDataObjectURL(xpath);
if (dataObjectURL == null || dataObjectURL.equals("")) {
return url;
}
// If this is a local data set then fds must be set to true.
if ( !dataObjectURL.startsWith("http:")) {
fds = true;
}
if (fds) {
url = getFTDSURL(xpath);
} else {
url = dataObjectURL;
}
return url;
}
/**
* Get data access URL. If fds is set to true, then the FDS URL will be
* returned in every case. If the fds boolean is set to false, then the
* actual OPeNDAP URL of the remote data set will be returned where available.
* If no remote URL is available, the the FDS URL will be returned.
* @param dsID the Dataset ID
* @param varID the Variable ID
* @param fds true if FDS URL is required
* @throws JDOMException
* @throws LASException
*/
public String getDataAccessURL(String dsID, String varID, boolean fds) throws LASException, JDOMException {
return getDataAccessURL("/lasdata/datasets/dataset[@ID='"+dsID+"']/variables/variable[@ID='"+varID+"']", fds);
}
/**
* Returns the data access URL for a particular variable via the XPath of the variable (strips off the #var)
* @param xpathValue The XPath of the variable
* @return url The access ready URL OPeNDAP URL or filename.
* @throws JDOMException
* @throws LASException
*/
public String getDataObjectURL(Element variable) throws LASException, JDOMException {
String url = getFullDataObjectURL(variable);
if ( url.contains("#")) {
url = url.substring(0,url.indexOf("#"));
}
return url;
}
/**
* Returns the OPeNDAP ready data access URL for a particular variable via the XPath of the variable (strips off the #var)
* @param xpathValue The XPath of the variable
* @return url The access ready URL OPeNDAP URL or filename.
* @throws JDOMException
* @throws LASException
*/
public String getDataObjectURL(String xpathValue) throws LASException, JDOMException {
String url = getFullDataObjectURL(xpathValue);
if ( url.contains("#")) {
url = url.substring(0,url.indexOf("#"));
}
return url;
}
/**
* Return a list of attributes on the given element
* @param xpathValue The XPath to the element
* @return attribute The list of JDOM attributes on this element.
* @throws JDOMException
*/
public List getDataOjectAttributes(String xpathValue) throws JDOMException {
/*
* We know this is a variable XPath. If it's "old style" fix it.
*/
if (!xpathValue.contains("@ID")) {
String[] parts = xpathValue.split("/");
// Throw away index 0 since the string has a leading "/".
xpathValue = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
Element variable = getElementByXPath(xpathValue);
return variable.getAttributes();
}
/**
* Extract data sets based on a <filter> element from the config.
* @param filter A category filter element to be used to select variables from the configuration.
* @return the data set that matches the filter
*/
private Dataset getDataset(Element filter) {
Dataset container_dataset = null;
String action = filter.getAttributeValue("action");
String name_contains = filter.getAttributeValue("contains");
String name_equals = filter.getAttributeValue("equals");
String tag_contains = filter.getAttributeValue("contains-tag");
String tag_equals = filter.getAttributeValue("equals-tag");
if ( action.equals("apply-dataset") ) {
List datasets = getRootElement().getChildren("datasets");
/**
* In this case, we're going to take the first dataset that matches
* and ignore all the rest...
*/
for (Iterator datasetsIt = datasets.iterator(); datasetsIt.hasNext();) {
Element datasetsE = (Element) datasetsIt.next();
List memberDatasets = datasetsE.getChildren("dataset");
// If we found a match quit. I don't like this so much, but it might be a bit more efficient.
if ( container_dataset != null ) {
break;
}
for (Iterator memberDSIt = memberDatasets.iterator(); memberDSIt.hasNext();) {
Element dataset = (Element) memberDSIt.next();
Element container_dataset_element = (Element) dataset.clone();
String name = dataset.getAttributeValue("name");
String ID = dataset.getAttributeValue("ID");
if ( (name_contains != null && name.contains(name_contains)) ||
(name_equals != null && name.equals(name_equals)) ||
(tag_contains != null && ID.contains(tag_contains)) ||
(tag_equals != null && ID.equals(tag_equals)) ) {
// There is nothing to do except create the dataset container and break out.
container_dataset = new Dataset(container_dataset_element);
break; // I don't like this so much, but it might be a bit more efficient.
}
}
}
} else if ( action.equals("apply-variable") ) {
/*
* In this case we need to find the data set that contains the first match,
* filter its member variables to include only the matches.
*/
List datasets = getRootElement().getChildren("datasets");
for (Iterator datasetsIt = datasets.iterator(); datasetsIt.hasNext();) {
if ( container_dataset != null ) {
break; // Ugly loop breaking in the interest of efficiency.
}
Element datasetsE = (Element) datasetsIt.next();
List memberDatasets = datasetsE.getChildren("dataset");
for (Iterator memberDSIt = memberDatasets.iterator(); memberDSIt.hasNext();) {
if ( container_dataset != null ) {
break; // Ugly loop breaking in the interest of efficiency.
}
Element dataset = (Element) memberDSIt.next();
Element container_dataset_element = (Element) dataset.clone();
container_dataset_element.removeChildren("variables");
List memberVariables = dataset.getChild("variables").getChildren("variable");
for (Iterator varIt = memberVariables.iterator(); varIt.hasNext();) {
Element variable = (Element) varIt.next();
Element container_variable = (Element) variable.clone();
String name = variable.getAttributeValue("name");
String ID = variable.getAttributeValue("ID");
if ( (name_contains != null && name.contains(name_contains)) ||
(name_equals != null && name.equals(name_equals)) ||
(tag_contains != null && ID.contains(tag_contains)) ||
(tag_equals != null && ID.equals(tag_equals)) ) {
container_dataset_element.addContent(container_variable);
}
}
container_dataset = new Dataset(container_dataset_element);
}
}
}
return container_dataset;
}
/**
* Get all of the attributes from the parent data set element.
* @param varXPath the variable whose parent data set will be used
* @return the attributes
* @throws JDOMException
*/
public HashMap <String, String> getDatasetAttributes(String varXPath) throws JDOMException {
HashMap<String, String> attrs = new HashMap<String, String>();
if (!varXPath.contains("@ID")) {
String[] parts = varXPath.split("/");
// Throw away index 0 since the string has a leading "/".
varXPath = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
Element variable = getElementByXPath(varXPath);
Element dataset = variable.getParentElement().getParentElement();
List attributes = dataset.getAttributes();
for (Iterator iter = attributes.iterator(); iter.hasNext();) {
Attribute attr = (Attribute) iter.next();
String name = attr.getName();
String value = attr.getValue();
if ( name != null && value != null && !name.equals("") && !value.equals("") ) {
attrs.put(name, value );
}
}
return attrs;
}
/**
* Get the <dataset> element from this config that matches this ID
* @param dsid
* @return
* @throws JDOMException
*/
private Element getDatasetElement(String dsid) throws JDOMException {
String xPath = "/lasdata/datasets/dataset[@ID='"+dsid+"']";
return getElementByXPath(xPath);
}
/**
* Returns all the datasets as gov.noaa.pmel.tmap.las.util.Dataset objects.
* @return ArrayList of dataset objects
*/
public ArrayList<Category> getDatasets() {
ArrayList<Category> datasets = new ArrayList<Category>();
Element datasetsE = getDatasetsAsElement();
List datasetElements = datasetsE.getChildren("dataset");
for (Iterator dsIt = datasetElements.iterator(); dsIt.hasNext();) {
Element dataset = (Element) dsIt.next();
Element ds_novars = (Element)dataset.clone();
ds_novars.setName("category");
/*
* Since we don't want all the children (the variables, composites, etc.)
* we'll remove every things that's not properties. However, we will
* keep the contributor and documentation elements.
*/
List children = ds_novars.getChildren();
ArrayList<String> remove = new ArrayList<String>();
for (Iterator childIt = children.iterator(); childIt.hasNext();) {
Element child = (Element) childIt.next();
if (!child.getName().equals("properties") &&
!child.getName().equals("documentation") &&
!child.getName().equals("contributor") ) {
remove.add(child.getName());
}
}
for (int i=0; i < remove.size(); i++) {
ds_novars.removeChild(remove.get(i));
}
ds_novars.setAttribute("children", "variables");
ds_novars.setAttribute("children_dsid", ds_novars.getAttributeValue("ID"));
Category ds = new Category(ds_novars);
datasets.add(ds);
}
return datasets;
}
/**
* Return all datasets as a single "datasets" element.
*
*/
public Element getDatasetsAsElement() {
Element datasets = new Element("datasets");
List datasetsElements = getRootElement().getChildren("datasets");
for (Iterator dseIt = datasetsElements.iterator(); dseIt.hasNext();) {
Element dsets = (Element) dseIt.next();
List datasetElements = dsets.getChildren("dataset");
for (Iterator dsIt = datasetElements.iterator(); dsIt.hasNext();) {
Element dataset = (Element) dsIt.next();
datasets.addContent((Element)dataset.clone());
}
}
return datasets;
}
/**
* Get a <dataset> element base on the data set id
* @param dsID the id of the dataset
* @return the data set element
* @throws JDOMException
*/
public Dataset getDataset(String dsID) throws JDOMException {
String xpathValue = "/lasdata/datasets/dataset[@ID='"+dsID+"']";
Element ds = getElementByXPath(xpathValue);
if ( ds != null ) {
return new Dataset(ds);
} else {
return null;
}
}
/**
* !!!! returns datasets list This ignores categories for now. Have to fix this.
* Don't need this anymore
* @deprecated
*/
//TODO decide what to do about categories...
public ArrayList<NameValuePair> getDatasetsAsNameValueBeans() {
ArrayList <NameValuePair> datasets = new ArrayList<NameValuePair>();
List datasetsElements = getRootElement().getChildren("datasets");
for (Iterator dseIt = datasetsElements.iterator(); dseIt.hasNext();) {
Element dsets = (Element) dseIt.next();
List datasetElements = dsets.getChildren("dataset");
for (Iterator dsIt = datasetElements.iterator(); dsIt.hasNext();) {
Element dataset = (Element) dsIt.next();
String name = dataset.getAttributeValue("name");
String value = dataset.getAttributeValue("ID");
datasets.add(new NameValuePair(name, value));
}
}
return datasets;
}
/**
* Get first variable from LASConfig.
* @return The XPath of the first variable in the LASConfig (the default)
*/
public String getFirstVariable() {
Element dataset = getRootElement().getChild("datasets").getChild("dataset");
String datasetID = dataset.getAttributeValue("ID");
Element variable = dataset.getChild("variables").getChild("variable");
String variableID = variable.getAttributeValue("ID");
return "/lasdata/datasets/dataset[@ID='"+datasetID+"']/variables/variable[@ID='"+variableID+"']";
}
/**
* Returns the full data URL for a particular variable (as identified by the variable element) including the #var (netCDF variable name convention used by LAS)
* @param variable The variable element of the variable whose data access URL is desired
* @return url The access URL (either a /path/path/filename#var or http://opendap_url#var).
* @throws JDOMException
* @throws LASException
*/
public String getFullDataObjectURL(Element variable) throws LASException, JDOMException {
if ( variable == null ) {
throw new LASException("Variable not found.");
}
Element dataset = variable.getParentElement().getParentElement();
String varURL = variable.getAttributeValue("url");
String dsURL = dataset.getAttributeValue("url");
String url = "";
if ( varURL != null && dsURL != null) {
if ( varURL.startsWith("http://";) || varURL.startsWith("file:///") ) {
url = varURL;
} else {
url = dsURL + varURL;
}
} else if ( varURL != null && dsURL == null ) {
url = varURL;
} else if ( varURL == null && dsURL != null ) {
url = dsURL;
} else if ( varURL == null && dsURL == null ) {
url = null;
}
if (url.startsWith("file://")) {
url = url.substring(6, url.length());
}
if (url.startsWith("file:/")) {
url = url.substring(5, url.length());
}
if (url.startsWith("file:")) {
url = url.substring(5, url.length());
}
return url;
}
/**
* Returns the full data URL for a particular variable (as identified by its XPath) including the #var (netCDF variable name convention used by LAS)
* @param xpathValue The XPath of the variable whose data access URL is desired
* @return url The access URL (either a /path/path/filename#var or http://opendap_url#var).
* @throws JDOMException
* @throws LASException
*/
public String getFullDataObjectURL(String xpathValue) throws LASException, JDOMException {
/*
* We know this is a variable XPath. If it's "old style" fix it.
*/
if (!xpathValue.contains("@ID")) {
String[] parts = xpathValue.split("/");
// Throw away index 0 since the string has a leading "/".
xpathValue = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
Element variable = getElementByXPath(xpathValue);
if ( variable == null ) {
throw new LASException("Variable: "+xpathValue+" not found.");
}
Element dataset = variable.getParentElement().getParentElement();
String varURL = variable.getAttributeValue("url");
String dsURL = dataset.getAttributeValue("url");
String url = "";
if ( varURL != null && dsURL != null) {
if ( varURL.startsWith("http://";) || varURL.startsWith("file:///") ) {
url = varURL;
} else {
url = dsURL + varURL;
}
} else if ( varURL != null && dsURL == null ) {
url = varURL;
} else if ( varURL == null && dsURL != null ) {
url = dsURL;
} else if ( varURL == null && dsURL == null ) {
url = null;
}
if ( url == null ) {
log.warn("URL for "+xpathValue+" is empty.");
url = "none";
}
if (url.startsWith("file://")) {
url = url.substring(6, url.length());
}
if (url.startsWith("file:/")) {
url = url.substring(5, url.length());
}
if (url.startsWith("file:")) {
url = url.substring(5, url.length());
}
return url;
}
/**
* Get the value of a "global" property (a property in the config that is not in any particular data set or variable).
* @param group the name of the property group
* @param name the name of the property
* @return the value of specified property
*/
public String getGlobalPropertyValue(String group, String name) {
String value = "";
Element properties = getRootElement().getChild("properties");
if (properties != null) {
List groups = properties.getChildren("property_group");
for (Iterator groupsIt = groups.iterator(); groupsIt.hasNext();) {
Element property_group = (Element) groupsIt.next();
if ( property_group.getAttributeValue("type").equals(group)) {
List props = property_group.getChildren("property");
for (Iterator propsIt = props.iterator(); propsIt.hasNext();) {
Element property = (Element) propsIt.next();
String pname = property.getChildTextNormalize("name");
String pvalue = property.getChildTextNormalize("value");
if ( pname.equals(name) ) {
return pvalue;
}
}
}
}
}
return value;
}
/**
* Get the grid of a variable from its XPath
* @param varXPath
* @return
* @throws JDOMException
* @throws LASException
*/
public Grid getGrid(String varXPath) throws JDOMException, LASException {
if (!varXPath.contains("@ID")) {
String[] parts = varXPath.split("/");
// Throw away index 0 since the string has a leading "/".
varXPath = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
Element variable = getElementByXPath(varXPath);
ArrayList<Element> axes_list = new ArrayList<Element>();
Element gridE = null;
if (variable != null) {
String ID = variable.getChild("grid").getAttributeValue("IDREF");
gridE = (Element) getElementByXPath("/lasdata/grids/grid[@ID='"+ID+"']").clone();
List axes = gridE.getChildren("axis");
for (Iterator axisIt = axes.iterator(); axisIt.hasNext();) {
Element axis_ref = (Element) axisIt.next();
String axisID = axis_ref.getAttributeValue("IDREF");
Element axisE = (Element) getElementByXPath("/lasdata/axes/axis[@ID='"+axisID+"']").clone();
String type = axisE.getAttributeValue("type");
if ( type.equals("x") || type.equals("y") || type.equals("z") ) {
axes_list.add(axisE);
} else if (type.equals("t") ) {
addTimeAxisAttributes(axisE);
axes_list.add(axisE);
} else if ( type.equals("d") ) {
axes_list.add(axisE);
}
}
}
// Replace the references with the actual axis definition.
if ( gridE != null ) {
gridE.setContent(axes_list);
return new Grid(gridE);
} else {
throw new LASException("The grid was empty.");
}
}
/**
* Get grid for a particular dataset and variable.
*
* @param dsid the id of the desired data set
* @param varid the id if the desired variable
* @return grid the Grid object with up to for Axes
* @throws JDOMException
*/
public Grid getGrid(String dsID, String varID) throws JDOMException, LASException {
return getGrid("/lasdata/datasets/dataset[@ID='"+dsID+"']/variables/variable[@ID='"+varID+"']");
}
/**
* Get the grid_type for the variable (regular, scattered, ...)
* @param dsID
* @param varID
* @throws JDOMException
*/
public String getGridType(String dsID, String varID) throws JDOMException {
String grid_type="";
String varXPath = "/lasdata/datasets/dataset[@ID='"+dsID+"']/variables/variable[@ID='"+varID+"']";
Element var = getElementByXPath(varXPath);
if ( var != null ) {
grid_type = var.getAttributeValue("grid_type");
if ( grid_type == null ) {
grid_type = "";
}
}
return grid_type;
}
/**
* Get hi value for a particular axis type for the specified variable
* @param varpath XPath to the variable
* @param type which axis x,y,z or t
*
*/
public String getHi(String type, String varpath) throws JDOMException {
String hi = null;
/*
* We know this is a variable XPath. If it's "old style" fix it.
*/
if (!varpath.contains("@ID")) {
String[] parts = varpath.split("/");
// Throw away index 0 since the string has a leading "/".
varpath = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
Element variable = getElementByXPath(varpath);
if (variable == null) {
return hi;
}
String gridID = variable.getChild("grid").getAttributeValue("IDREF");
Element grid = getElementByXPath("/lasdata/grids/grid[@ID='"+gridID+"']");
if (grid == null) {
return hi;
}
List axes = grid.getChildren("axis");
for (Iterator axIt = axes.iterator(); axIt.hasNext();) {
Element axis = (Element) axIt.next();
String axisID = axis.getAttributeValue("IDREF");
axis = getElementByXPath("/lasdata/axes/axis[@ID='"+axisID+"']");
String t = axis.getAttributeValue("type");
if ( type.equals(t) ) {
Element arange = axis.getChild("arange");
if (arange == null) {
List v = axis.getChildren("v");
Element vN = (Element) v.get(v.size()-1);
hi = vN.getTextTrim();
} else {
String st = arange.getAttributeValue("start");
double start = Double.valueOf(st).doubleValue();
double step = Double.valueOf(arange.getAttributeValue("step")).doubleValue();
double size = Double.valueOf(arange.getAttributeValue("size")).doubleValue();
double end = start+(size-1)*step;
hi = String.valueOf(end);
}
}
}
return hi;
}
/**
* Get the container with all the information about the institution that installed this LAS.
* @return Institution the information about the place that installed this LAS.
*/
public Institution getInstitution() throws JDOMException {
Element institution = getElementByXPath("/lasdata/institution");
return new Institution(institution);
}
/**
* Get lo value for a particular axis type for the specified variable. If it's
* the T axis you get a string with the low value, but you might want a TimeSelector instead.
* @param varpath XPath to the variable
* @param type which axis x,y,z or t
*
*/
public String getLo(String type, String varpath) throws JDOMException {
String lo = null;
/*
* We know this is a variable XPath. If it's "old style" fix it.
*/
if (!varpath.contains("@ID")) {
String[] parts = varpath.split("/");
// Throw away index 0 since the string has a leading "/".
varpath = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
Element variable = getElementByXPath(varpath);
if (variable == null) {
return lo;
}
String gridID = variable.getChild("grid").getAttributeValue("IDREF");
Element grid = getElementByXPath("/lasdata/grids/grid[@ID='"+gridID+"']");
if (grid == null) {
return lo;
}
List axes = grid.getChildren("axis");
for (Iterator axIt = axes.iterator(); axIt.hasNext();) {
Element axis = (Element) axIt.next();
String axisID = axis.getAttributeValue("IDREF");
axis = getElementByXPath("/lasdata/axes/axis[@ID='"+axisID+"']");
String t = axis.getAttributeValue("type");
// do xyz
if ( type.equals(t) ) {
Element arange = axis.getChild("arange");
if (arange == null) {
List v = axis.getChildren("v");
Element v0 = (Element) v.get(0);
lo = v0.getTextTrim();
} else {
lo = arange.getAttributeValue("start");
}
}
}
return lo;
}
/**
* Given a dataset element merge the properties (probably should be private)
* All properties should have been converted to "V7.0" style properties
* before this code is called.
* @param dsE The dataset element to merge
* @return datasetElement The same element with all of the new properites folded in to each variable.
*/
public Element getMergedProperties(Element dsE) {
// The colleciton is a HashMap of HashMaps.
// TODO these should be lists and loop through the list and combine any
// stray property groups...
Element variablePropsE = dsE.getChild("properties");
// The parent of the variable is <variables> the parent of <variables>
// is the particular <[datasetname]> tag.
Element datasetPropsE = dsE.getParentElement().getParentElement().getChild("properties");
// Same as above, plus the parent of the particular dataset tag is <datasets> and
// the parent of that is <lasdata>
Element globalPropsE = dsE.getParentElement().getParentElement().getParentElement().getParentElement().getChild("properties");
HashMap<String, HashMap<String, String>> propertyGroups = new HashMap<String, HashMap<String, String>>();
if (globalPropsE != null) {
// All children should be elements of the form <property_group type="name">
List propGroups = globalPropsE.getChildren();
for (Iterator pgIt = propGroups.iterator(); pgIt.hasNext();) {
Element propGroupE = (Element) pgIt.next();
// All children should be elements of the form <property><name>thename</name><value>thevalue</value></property>
List props = propGroupE.getChildren();
HashMap<String, String> property = new HashMap<String, String>();
for (Iterator propIt = props.iterator(); propIt.hasNext();) {
Element prop = (Element) propIt.next();
String propName = prop.getChildTextNormalize("name");
String propValue = prop.getChildTextNormalize("value");
property.put(propName, propValue);
}
propertyGroups.put(propGroupE.getAttributeValue("type"), property);
}
}
// If the group already exists any properties from this element
// replace the properites from the "global" properties.
if (datasetPropsE != null) {
List propGroups = datasetPropsE.getChildren();
for (Iterator pgIt = propGroups.iterator(); pgIt.hasNext();) {
Element propGroupE = (Element) pgIt.next();
List props = propGroupE.getChildren();
HashMap<String, String> group = propertyGroups.get(propGroupE.getAttributeValue("type"));
if (group == null) {
group = new HashMap<String, String>();
}
for (Iterator propIt = props.iterator(); propIt.hasNext();) {
Element prop = (Element) propIt.next();
String propName = prop.getChildTextNormalize("name");
String propValue = prop.getChildTextNormalize("value");
String currentValue = group.get(propName);
if (currentValue == null) {
group.put(propName, propValue);
} else if (currentValue.equals("default")) {
group.put(propName, propValue);
}
}
propertyGroups.put(propGroupE.getAttributeValue("type"), group);
}
}
if (variablePropsE != null) {
List propGroups = variablePropsE.getChildren();
for (Iterator pgIt = propGroups.iterator(); pgIt.hasNext();) {
Element propGroupE = (Element) pgIt.next();
List props = propGroupE.getChildren();
HashMap<String, String> group = propertyGroups.get(propGroupE.getAttributeValue("type"));
if (group == null) {
group = new HashMap<String, String>();
}
for (Iterator propIt = props.iterator(); propIt.hasNext();) {
Element prop = (Element) propIt.next();
String propName = prop.getChildTextNormalize("name");
String propValue = prop.getChildTextNormalize("value");
String currentValue = group.get(propName);
if (currentValue == null) {
group.put(propName, propValue);
} else if (currentValue.equals("default")) {
group.put(propName, propValue);
}
}
propertyGroups.put(propGroupE.getAttributeValue("type"), group);
}
}
Element properties = new Element("properties");
Element dsGroupE = null;
for (Iterator propertyGroupKeyIterator = propertyGroups.keySet()
.iterator(); propertyGroupKeyIterator.hasNext();) {
String propertyGroupKey = (String) propertyGroupKeyIterator
.next();
dsGroupE = new Element("property_group");
dsGroupE.setAttribute("type", propertyGroupKey);
HashMap propertyGroup = (HashMap) propertyGroups.get(propertyGroupKey);
for (Iterator keyIt = propertyGroup.keySet().iterator(); keyIt
.hasNext();) {
String key = (String) keyIt.next();
Element property = new Element("property");
Element property_name = new Element("name");
Element property_value = new Element("value");
property_name.addContent(key);
property_value.addContent((String) propertyGroup.get(key));
property.addContent(property_name);
property.addContent(property_value);
dsGroupE.addContent(property);
}
properties.addContent(dsGroupE);
}
return properties;
}
/**
* !! temporarily busted for V7 XML -- Returns the merged properties for a particular (maybe this should be private)
* This /lasdata/datasets/DatasetTagName/variables/VariableTagName path and it
* should be /lasdata/datasets/dataset[@ID='DatasetID']/variables/variable[@ID='VariableID'].
* @deprecated
* @param xpathValue
* @return Element The varaible element with the properties merged into it.
* @throws JDOMException
*/
public Element getMergedProperties(String xpathValue) throws JDOMException {
/*
* We know this is a variable XPath. If it's "old style" fix it.
*/
if (!xpathValue.contains("@ID")) {
String[] parts = xpathValue.split("/");
// Throw away index 0 since the string has a leading "/".
xpathValue = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
return getMergedProperties(getElementByXPath(xpathValue));
}
/**
* Get operations for a data set and variable, either by the associated default or by the interval.
* @throws JDOMException
*/
public ArrayList<Operation> getOperations(String view, String dsID, String varID) throws JDOMException {
ArrayList<Operation> operations = new ArrayList<Operation>();
String grid_type = getGridType(dsID, varID);
String ui_default = getUIDefaultName(dsID, varID);
if ( ui_default != null && !ui_default.equals("") ) {
ui_default = ui_default.substring(ui_default.indexOf("#")+1, ui_default.length());
operations = getOperationsByDefault(view, ui_default);
} else {
operations = getOperationsByIntervalAndGridType(view, grid_type);
}
return operations;
}
/**
* Get the operations that are include with a particular UI default
* @param ui_default
* @return operations JSONObject with the operations that are defined for this "default".
* @throws JDOMException
*/
public ArrayList<Operation> getOperationsByDefault(String view, String ui_default) throws JDOMException {
ArrayList<Operation> operations = new ArrayList<Operation>();
Element def = getUIDefault(ui_default);
if ( def != null ) {
Element map = getUIMap(def, "ops");
if (map != null) {
List ifmenusElements = map.getChildren("ifmenu");
for (Iterator ifmenusIt = ifmenusElements.iterator(); ifmenusIt
.hasNext();) {
Element ifmenu = (Element) ifmenusIt.next();
// An ifmenu is not always controlled by a view.
// Could be the mode as well !!
// TODO handle distinctions for comparison mode
String ifmenu_view = ifmenu.getAttributeValue("view");
if ( ifmenu_view != null ) {
if (ifmenu_view.equals(view)) {
String ops_menu_ref = ifmenu
.getAttributeValue("href");
Element menu = getElementByXPath("/lasdata/lasui/menus/menu[@name='"
+ ops_menu_ref.substring(1) + "']");
List ops = menu.getChildren("item");
for (Iterator opsIt = ops.iterator(); opsIt
.hasNext();) {
Element item = (Element) opsIt.next();
String value = item.getAttributeValue("values");
/* This is pulling out information that was designed to be the values
* of an HTML menu. It's not such a great way to store informaiton that
* is intended to be used to extract further information from the XML.
* Therefore there's a lot of splitting and spitting to get the job done.
* TODO we should re-think the XML at some point... Soon?
*/
String opID = value.substring(0, value
.indexOf(","));
Element opE = getElementByXPath("/lasdata/operations/operation[@ID='"
+ opID + "']");
if ( opE != null ) {
Operation op = new Operation(opE);
operations.add(op);
} else {
log.warn("Operation "+opID+" from default "+ui_default+" not found in configuration.");
}
}
}
}
}
}
}
return operations;
}
/**
* Get the operations based on the axes defined on an interval and the grid type.
* @param view The view to be matched to the interval specifications in the operation config
* @param grid_type the desired grid type
* @return the list of operations
*/
public ArrayList<Operation> getOperationsByIntervalAndGridType(String view, String grid_type) throws JDOMException {
ArrayList<Operation> matchingOperations = new ArrayList<Operation>();
List operationsElements = getRootElement().getChildren("operations");
for (Iterator opsElementsIt = operationsElements.iterator(); opsElementsIt.hasNext();) {
Element opsElement = (Element) opsElementsIt.next();
List opElements = opsElement.getChildren("operation");
for (Iterator opIt = opElements.iterator(); opIt.hasNext(); ) {
boolean grid_type_match = false;
boolean intervals_match = false;
boolean degenerate_match = false;
Element operation = (Element) opIt.next();
Element region = operation.getChild("region");
Element grid_types = operation.getChild("grid_types");
if (region != null && grid_types != null) {
List types = grid_types.getChildren("grid_type");
for (Iterator typeIt = types.iterator(); typeIt.hasNext();) {
Element type = (Element) typeIt.next();
if (type.getAttributeValue("name").equals(
grid_type)) {
grid_type_match = true;
}
}
List intervals = region.getChildren("intervals");
for (Iterator intvIt = intervals.iterator(); intvIt.hasNext();) {
Element intv = (Element) intvIt.next();
if (intv.getAttributeValue("name").equals(view)) {
intervals_match = true;
}
}
Element degenerate = region.getChild("degenerate");
if ( degenerate != null && view.equals("d") ) {
degenerate_match = true;
}
boolean private_op = false;
String private_attr = operation.getAttributeValue("private");
if ( private_attr != null && private_attr.equals("true") ) {
private_op = true;
}
if (grid_type_match && (intervals_match||degenerate_match) && !private_op) {
Operation op = new Operation(operation);
matchingOperations.add(op);
}
}
}
}
return matchingOperations;
}
/**
* Selects operations that use interval inputs on the axes listed in the view
*
* @param view a string containing an ordered subset of xyzt.
* @return operations a list of operation elements that use this view
* @throws JDOMException
* @deprecated
*/
public ArrayList<NameValuePair> getOperationsByView(String view) throws JDOMException {
ArrayList<NameValuePair> ops = new ArrayList<NameValuePair>();
String path = "/lasdata/operations/operation[@intervals='"+view+"']";
XPath xpath = XPath.newInstance(path);
for (Iterator nodes = xpath.selectNodes(this).iterator(); nodes.hasNext(); ) {
Element op = (Element)nodes.next();
ops.add(new NameValuePair(op.getAttributeValue("name"), op.getAttributeValue("ID")));
}
return ops;
}
/**
* Returns the options associated with this option ID
* @param optionID option ID
* @return options the options for this id.
* @throws JDOMException
*/
public ArrayList<Option> getOptions(String optionID) throws JDOMException {
ArrayList<Option> options = new ArrayList<Option>();
// Collect the options from this ID (which is really the name, but nevermind).
options.addAll(extractOptions(optionID));
return options;
}
/**
* Returns the options associated with this operation ID
* @param operationID operation ID
* @return options the options for this operation.
* @throws JDOMException
*/
public ArrayList<Option> getOptionsByOperationID(String operationID) throws JDOMException {
ArrayList<Option> options = new ArrayList<Option>();
// Be sure to make items null for textarea.
Element op = getElementByXPath("/lasdata/operations/operation[@ID='"+operationID+"']");
if ( op != null ) {
Element option = op.getChild("optiondef");
if ( option != null ) {
String optionID = option.getAttributeValue("IDREF");
if ( optionID != null ) {
// Collect the options from this ID (which is really the name, but nevermind).
options.addAll(extractOptions(optionID));
}
}
}
return options;
}
/**
* Get the name of the output directory for this LAS
* @return outputdir The path to the output directory.
*/
public String getOutputDir() {
return this.getRootElement().getChildText("output_dir");
}
/**
* Get xy region for a particular variable
* @param varpath XPath to variable
* @return region ArrayList of NameValueBeans with x_lo, x_hi, y_lo and y_hi
* @throws JDOMException
*/
public ArrayList<NameValuePair> getRangeForXY(String varpath) throws JDOMException {
ArrayList<NameValuePair> region = new ArrayList<NameValuePair>();
/*
* We know this is a variable XPath. If it's "old style" fix it.
*/
if (!varpath.contains("@ID")) {
String[] parts = varpath.split("/");
// Throw away index 0 since the string has a leading "/".
varpath = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
Element variable = getElementByXPath(varpath);
if (variable == null) {
return region;
}
String gridID = variable.getChild("grid").getAttributeValue("IDREF");
Element grid = getElementByXPath("/lasdata/grids/grid[@ID='"+gridID+"']");
if (grid == null) {
return region;
}
List axes = grid.getChildren("axis");
for (Iterator axIt = axes.iterator(); axIt.hasNext();) {
Element axis = (Element) axIt.next();
String axisID = axis.getAttributeValue("IDREF");
axis = getElementByXPath("/lasdata/axes/axis[@ID='"+axisID+"']");
String type = axis.getAttributeValue("type");
if ( type.equals("x") || type.equals("y") ) {
NameValuePair lo=null;
NameValuePair hi=null;
if ( type.equals("x") ) {
lo = new NameValuePair("x_lo", "");
hi = new NameValuePair("x_hi", "");
} else if ( type.equals("y") ) {
lo = new NameValuePair("y_lo", "");
hi = new NameValuePair("y_hi", "");
}
Element arange = axis.getChild("arange");
if (arange == null) {
List v = axis.getChildren("v");
Element v0 = (Element) v.get(0);
Element vN = (Element) v.get(v.size()-1);
lo.setValue(v0.getTextTrim());
hi.setValue(vN.getTextTrim());
} else {
String st = arange.getAttributeValue("start");
lo.setValue(st);
double start = Double.valueOf(st).doubleValue();
long step = Long.valueOf(arange.getAttributeValue("step")).longValue();
double size = Double.valueOf(arange.getAttributeValue("size")).doubleValue();
double end = start+(size-1)*step;
hi.setValue(String.valueOf(end));
}
region.add(lo);
region.add(hi);
}
}
return region;
}
/**
* Get the pre-defined regions, by UI default based on the data set and variable.
* @param dsID
* @param varID
* @return
* @throws JDOMException
*/
public ArrayList<Region> getRegions(String dsID, String varID) throws JDOMException {
ArrayList<Region> regions = new ArrayList<Region>();
Element ui_default = getUIDefault(dsID, varID);
Element livemap = getUIMap(ui_default, "livemap");
if ( livemap != null ) {
Element menu = livemap.getChild("menu");
String href = menu.getAttributeValue("href");
menu = getElementByXPath("/lasdata/lasui/menus/menu[@name='"+href.substring(1)+"']");
List items = menu.getChildren("item");
for (Iterator itemsIt = items.iterator(); itemsIt.hasNext();) {
Element item = (Element) itemsIt.next();
Element region = new Element("region");
String values = item.getAttributeValue("values");
String name = item.getTextTrim();
region.setAttribute("name", name);
region.setAttribute("ID", name);
region.setAttribute("values", values);
String[] corners = values.split(",");
region.setAttribute("xhi", corners[0]);
region.setAttribute("xlo", corners[1]);
region.setAttribute("yhi", corners[2]);
region.setAttribute("ylo", corners[3]);
Region reg = new Region(region);
regions.add(reg);
}
}
return regions;
}
/**
* Get all variables in a data set that are defined on a regular grid
* @param dsID the data set
* @return the list of variables
* @throws JDOMException
*/
public ArrayList<NameValuePair> getRegularVariables(String dsID) throws JDOMException {
ArrayList<NameValuePair> variables = new ArrayList<NameValuePair>();
Element dataset = getElementByXPath("/lasdata/datasets/dataset[@ID='"+dsID+"']");
List variablesElements = dataset.getChildren("variables");
for (Iterator vseIt = variablesElements.iterator(); vseIt.hasNext();) {
Element variablesElement = (Element) vseIt.next();
List vars = variablesElement.getChildren("variable");
for (Iterator varIt = vars.iterator(); varIt.hasNext();) {
Element variable = (Element) varIt.next();
String grid_type = variable.getAttributeValue("grid_type");
if (grid_type.equals("regular")) {
String name = variable.getAttributeValue("name");
String value = variable.getAttributeValue("ID");
variables.add(new NameValuePair(name, value));
}
}
}
return variables;
}
/**
* Get the URL of the product server. This URL should be correct even if the
* server is being proxied through Apache.
* @throws JDOMException
*/
public String getServerURL() throws JDOMException {
String server = "";
Element ops = getElementByXPath("/lasdata/operations");
server = ops.getAttributeValue("url");
return server;
}
/**
* Get the name of the service based on the operation ID.
* @param opID the ID of the operation
* @return service the name of the service associated with this operation
* @throws JDOMException
*/
public String getService(String opID) throws JDOMException {
String service = null;
Element op = getElementByXPath("/lasdata/operations/operation[@ID='"+opID+"']");
if ( op != null ) {
Element serviceE = op.getChild("service");
if ( serviceE != null ) {
return serviceE.getTextNormalize();
}
}
return service;
}
/**
* Get time selector object the specified variable
* @param varpath XPath to the variable
* @throws JDOMException
*
*/
public TimeSelector getT(String varpath) throws JDOMException {
TimeSelector t = new TimeSelector();
/*
* We know this is a variable XPath. If it's "old style" fix it.
*/
if (!varpath.contains("@ID")) {
String[] parts = varpath.split("/");
// Throw away index 0 since the string has a leading "/".
varpath = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
Element variable = getElementByXPath(varpath);
if (variable == null) {
return t;
}
String gridID = variable.getChild("grid").getAttributeValue("IDREF");
Element grid = getElementByXPath("/lasdata/grids/grid[@ID='"+gridID+"']");
if (grid == null) {
return t;
}
List axes = grid.getChildren("axis");
for (Iterator axIt = axes.iterator(); axIt.hasNext();) {
Element axis = (Element) axIt.next();
String axisID = axis.getAttributeValue("IDREF");
axis = getElementByXPath("/lasdata/axes/axis[@ID='"+axisID+"']");
String type = axis.getAttributeValue("type");
if ( type.equals("t") ) {
String default_display = axis.getAttributeValue("default");
Element arange = axis.getChild("arange");
if (arange == null) {
t.setType("menu");
List v = axis.getChildren("v");
Element v0 = (Element) v.get(0);
String tlo = v0.getTextTrim();
Element vN = (Element) v.get(v.size()-1);
String thi = vN.getTextTrim();
t.setLo(tlo);
t.setCurrent_lo(tlo);
if ( default_display != null && default_display.equals("last") ) {
t.setCurrent_hi(thi);
} else {
t.setCurrent_hi(tlo);
}
StateNameValueList vs = new StateNameValueList();
for (Iterator vIt = v.iterator(); vIt.hasNext();) {
Element vElement = (Element) vIt.next();
vs.add(new NameValuePair(vElement.getTextNormalize(), vElement.getTextNormalize()));
}
t.setLo_items(vs);
t.setHi_items(vs);
if (default_display != null && default_display.equals("last") ) {
t.getHi_items().setCurrent(thi);
}
} else {
t.setType("widget");
String tlo = arange.getAttributeValue("start");
String units = axis.getAttributeValue("units");
double size = Double.valueOf(arange.getAttributeValue("size")).doubleValue();
double step = Double.valueOf(arange.getAttributeValue("step")).doubleValue();
DateTimeFormatter fmt = DateTimeFormat.forPattern("yyyy-MM-dd HH").withZone(DateTimeZone.UTC);
DateTimeFormatter zfmt = DateTimeFormat.forPattern("yyyy-MM-dd").withZone(DateTimeZone.UTC);
DateTimeFormatter longfmt = DateTimeFormat.forPattern("yyyy-MM-dd HH:mm:ss").withZone(DateTimeZone.UTC);
DateTime lodt;
if ( tlo.length() == 10 ) {
lodt = zfmt.parseDateTime(tlo);
} else {
lodt = fmt.parseDateTime(tlo);
}
t.setLo(lodt.toString(longfmt));
t.setCurrent_lo(t.getLo());
DateTime hidt = new DateTime();
if ( units.contains("hour") ) {
t.setHourNeeded(true);
t.setDayNeeded(true);
t.setMonthNeeded(true);
t.setYearNeeded(true);
int hours = (int) Math.round((size-1)*step);
int minuteInterval = (int) Math.round(step*60.);
t.setMinuteInterval(minuteInterval);
hidt = lodt.plus(Period.hours(hours));
t.setHi(hidt.toString(longfmt));
} else if ( units.contains("day") ) {
t.setHourNeeded(false);
t.setDayNeeded(true);
t.setMonthNeeded(true);
t.setYearNeeded(true);
int days = (int) Math.round((size-1)*step);
hidt = lodt.plus(Period.days(days));
t.setHi(hidt.toString(longfmt));
} else if ( units.contains("month") ) {
t.setHourNeeded(false);
t.setDayNeeded(false);
t.setMonthNeeded(true);
t.setYearNeeded(true);
int months = (int) Math.round((size-1)*step);
hidt = lodt.plus(Period.months(months));
t.setHi(hidt.toString(longfmt));
} else if ( units.contains("year") ) {
t.setHourNeeded(false);
t.setDayNeeded(false);
t.setMonthNeeded(false);
t.setYearNeeded(true);
double start = Double.valueOf(tlo).doubleValue();
int years = (int) Math.round(start + (size-1)*step);
hidt = lodt.plus(Period.years(years));
t.setHi(hidt.toString(longfmt));
}
if ( default_display != null && default_display.equals("last") ) {
t.setCurrent_hi(hidt.toString(longfmt));
} else {
t.setCurrent_hi(lodt.toString(longfmt));
}
}
}
}
return t;
}
/**
* Given the XPath to an operation return the output template that should be processed for this product
* @param XPath The path to the operation element
* @return output_template The name of the template (which will be resolve using the class loader and the backend config information)
* @throws JDOMException
*/
public String getTemplateByXPath(String XPath) throws JDOMException {
Element opE = getElementByXPath(XPath);
if (opE != null) {
return opE.getAttributeValue("output_template");
} else {
//TODO configurable default output_template.
return "output";
}
}
/**
* Get the F-TDS URL for this variable
* @param variable the variable element
* @return the F-TDS URL
* @throws JDOMException
*/
public String getFTDSURL(Element variable) {
String ftds_url = variable.getAttributeValue("ftds_url");
if ( ftds_url != null ) {
return ftds_url;
} else {
return "";
}
}
/**
* Get the F-TDS URL for the variable specified by the XPath
* @param varXPath the XPath of the variable
* @return the F-TDS URL
* @throws JDOMException
*/
public String getFTDSURL(String varXPath) throws JDOMException {
if (!varXPath.contains("@ID")) {
String[] parts = varXPath.split("/");
// Throw away index 0 since the string has a leading "/".
varXPath = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
Element variable = getElementByXPath(varXPath);
return getFTDSURL(variable);
}
/**
* Get the F-TDS URL for the variable specified by the dsID and varID
* @param dsID of the variable
* @param varID of the variable
* @return the F-TDS URL
* @throws JDOMException
*/
public String getFTDSURL(String dsID, String varID) throws JDOMException {
String varXPath = "/lasdata/datasets/dataset[@ID='"+dsID+"']/"+"variables/variable[@ID='"+varID+"']";
Element variable = getElementByXPath(varXPath);
return getFTDSURL(variable);
}
/**
* Create a time axis with all the info needed for the DateWidgets
* @param variable the variable whose time axis will be built
* @return the time axis specification
* @throws JDOMException
* @throws LASException
*/
public TimeAxis getTime(Element variable) throws JDOMException, LASException {
TimeAxis t = null;
if (variable == null) {
return t;
}
String gridID = variable.getChild("grid").getAttributeValue("IDREF");
Element grid = getElementByXPath("/lasdata/grids/grid[@ID='"+gridID+"']");
if (grid == null) {
return t;
}
List axes = grid.getChildren("axis");
for (Iterator axIt = axes.iterator(); axIt.hasNext();) {
Element axis = (Element) axIt.next();
String axisID = axis.getAttributeValue("IDREF");
axis = getElementByXPath("/lasdata/axes/axis[@ID='"+axisID+"']");
String type = axis.getAttributeValue("type");
if ( type.equals("t") ) {
Element arange = axis.getChild("arange");
if (arange == null) {
List v = axis.getChildren("v");
Element v0 = (Element) v.get(0);
String tlo = v0.getTextTrim();
Element vN = (Element) v.get(v.size()-1);
String thi = vN.getTextTrim();
ArrayList<NameValuePair> vs = new ArrayList<NameValuePair>();
for (Iterator vIt = v.iterator(); vIt.hasNext();) {
Element vElement = (Element) vIt.next();
String label = vElement.getAttributeValue("label");
if ( label == null ) {
label = vElement.getTextNormalize();
}
vs.add(new NameValuePair(label, vElement.getTextNormalize()));
}
t = new TimeAxis(axis);
t.setLo(tlo);
t.setHi(thi);
t.setDisplay_type("menu");
} else {
t = new TimeAxis(axis);
t.setDisplay_type("widget");
String tlo = arange.getAttributeValue("start");
String units = axis.getAttributeValue("units");
double size = Double.valueOf(arange.getAttributeValue("size")).doubleValue();
double step = Double.valueOf(arange.getAttributeValue("step")).doubleValue();
DateTimeFormatter fmt = null;
DateTime lodt = new DateTime("9000-01-01");
boolean found = false;
for (int i = 0; i < time_formats.length; i++) {
fmt = DateTimeFormat.forPattern(time_formats[i]).withZone(DateTimeZone.UTC);
try {
lodt = fmt.parseDateTime(tlo);
found = true;
} catch ( IllegalArgumentException e ) {
found = false;
}
if (found) break;
}
if ( !found ) {
throw new LASException("Time format for "+tlo+" could not be parsed.");
}
t.setLo(lodt.toString(fmt));
DateTime hidt = new DateTime();
if ( units.contains("hour") ) {
t.setHourNeeded(true);
t.setDayNeeded(true);
t.setMonthNeeded(true);
t.setYearNeeded(true);
int hours = (int) Math.round((size-1)*step);
int minuteInterval = (int) Math.round(step*60.);
t.setMinuteInterval(minuteInterval);
hidt = lodt.plus(Period.hours(hours));
t.setHi(hidt.toString(fmt));
} else if ( units.contains("day") ) {
t.setHourNeeded(false);
t.setDayNeeded(true);
t.setMonthNeeded(true);
t.setYearNeeded(true);
int days = (int) Math.round((size-1)*step);
hidt = lodt.plus(Period.days(days));
t.setHi(hidt.toString(fmt));
} else if ( units.contains("month") ) {
t.setHourNeeded(false);
t.setDayNeeded(false);
t.setMonthNeeded(true);
t.setYearNeeded(true);
int months = (int) Math.round((size-1)*step);
hidt = lodt.plus(Period.months(months));
t.setHi(hidt.toString(fmt));
} else if ( units.contains("year") ) {
t.setHourNeeded(false);
t.setDayNeeded(false);
t.setMonthNeeded(false);
t.setYearNeeded(true);
double start = Double.valueOf(tlo).doubleValue();
int years = (int) Math.round(start + (size-1)*step);
hidt = lodt.plus(Period.years(years));
t.setHi(hidt.toString(fmt));
}
}
}
}
return t;
}
/**
* Get time selector object the specified variable
* @param varpath XPath to the variable
* @throws LASException
*
*/
public TimeAxis getTime(String varpath) throws JDOMException, LASException {
/*
* We know this is a variable XPath. If it's "old style" fix it.
*/
if (!varpath.contains("@ID")) {
String[] parts = varpath.split("/");
// Throw away index 0 since the string has a leading "/".
varpath = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
Element variable = getElementByXPath(varpath);
return getTime(variable);
}
/**
* Extracts the LAS title from the configuration
* @return title The title of this LAS
* @throws JDOMException
*/
public String getTitle() throws JDOMException {
String title = "";
Element ui = getElementByXPath("/lasdata/lasui");
if ( ui != null ) {
title = ui.getAttributeValue("title");
if ( title == null ) {
title="";
}
}
return title;
}
/**
* Get the name of the UI Default associated with this variable.
* @param dsID the data set
* @param varID the variable
* @return the UI Default name; can be null
* @throws JDOMException
*/
public String getUIDefaultName(String dsID, String varID) throws JDOMException {
return getVariablePropertyValue("/lasdata/datasets/dataset[@ID='"+dsID+"']/variables/variable[@ID='"+varID+"']","ui", "default");
}
/**
* Get the actual UI Default element
* @param dsID the data set
* @param varID the variable
* @return the default element (can be null)
* @throws JDOMException
*/
public Element getUIDefault(String dsID, String varID) throws JDOMException {
return getUIDefault(getUIDefaultName(dsID, varID));
}
/**
* Get the default element based on its name
* @param ui_default the name of the desired default
* @return the default element (can be null)
*/
public Element getUIDefault(String ui_default) {
List defaultsElements = getRootElement().getChild("lasui").getChildren("defaults");
for (Iterator defsIt = defaultsElements.iterator(); defsIt.hasNext();) {
Element defaultsE = (Element) defsIt.next();
List defaults = defaultsE.getChildren("default");
for (Iterator defIt = defaults.iterator(); defIt.hasNext();) {
Element def = (Element) defIt.next();
String name = def.getAttributeValue("name");
// The default default has no name...
if ( name != null ) {
if ( name.equals(ui_default) ) {
return def;
}
} else {
// The default "default" has no name so the input is null and the match is null.
if ( ui_default == null || ui_default.equals("") ) {
return def;
}
}
}
}
return null;
}
public Element getUIMap(Element def, String intype) throws JDOMException {
List maps = def.getChildren("map");
for (Iterator mapIt = maps.iterator(); mapIt.hasNext();) {
Element map_ref = (Element) mapIt.next();
String ref = map_ref.getAttributeValue("href");
Element map = getElementByXPath("/lasdata/lasui/maps/map[@name='"+ref.substring(1)+"']");
String type = map.getAttributeValue("type");
if ( type.equals(intype)) {
return map;
}
}
return null;
}
public Element getUIMenu (String href) throws JDOMException {
return getElementByXPath("/lasdata/lasui/menus/menu[@name='"+href+"']");
}
/**
* Extracts of list of known LAS UI Clients for this product server.
* @return ui_url_list a list of URLs of known LAS UI Clients for this server
* @throws JDOMException
*/
public ArrayList<String> getUIs() {
ArrayList<String> uis = new ArrayList<String>();
List uiElements = getRootElement().getChild("lasui").getChildren("ui");
for (Iterator uiIt = uiElements.iterator(); uiIt.hasNext();) {
Element ui = (Element) uiIt.next();
uis.add(ui.getAttributeValue("url"));
}
return uis;
}
public Variable getVariableByXPath(String xpath) throws JDOMException {
String dsid;
if (!xpath.contains("@ID")) {
String[] parts = xpath.split("/");
// Throw away index 0 since the string has a leading "/".
xpath = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
dsid = parts[3];
} else {
dsid = xpath.substring(xpath.indexOf("dataset[@ID='")+13,xpath.indexOf("']"));
}
Element variable = getElementByXPath(xpath);
if ( variable != null ) {
return new Variable(variable, dsid);
} else {
return null;
}
}
public String getVariableIntervals(String xpath) throws JDOMException {
Element variable = getElementByXPath(xpath);
return variable.getAttributeValue("intervals");
}
/**
* !!! does not work with V7 XML...Returns the netCDF variable name from the variable's XPath (the #var or the variable ID)
* @param xpathValue The XPath of the variable
* @return var The netCDF variable name
* @throws JDOMException
*/
public String getVariableName(String xpathValue) throws LASException, JDOMException {
String url = getFullDataObjectURL(xpathValue);
if ( url.contains("#")) {
return url.substring(url.indexOf("#")+1, url.length());
} else {
/*
* We know this is a variable XPath. If it's "old style" fix it.
*/
if (!xpathValue.contains("@ID")) {
String[] parts = xpathValue.split("/");
// Throw away index 0 since the string has a leading "/".
xpathValue = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
Element var = getElementByXPath(xpathValue);
if ( var.getAttributeValue("ID") != null ) {
return var.getAttributeValue("ID");
} else {
return var.getName();
}
}
}
public String getVariableName(String dsID, String varID) throws JDOMException, LASException {
return getVariableName("/lasdata/datasets/dataset[@ID='"+dsID+"']/variables/variable[@ID='"+varID+"']");
}
public String getVariablePoints(String xpath) throws JDOMException {
Element variable = getElementByXPath(xpath);
return variable.getAttributeValue("points");
}
/**
* Extract the properties group from a variable given its JDOM Element
* container as an Array List of NameValueBeans
* @param variable Element an XML variable element
* @param group the name of the property group to extract
* @return properties The an array list of properties.
*
*/
public HashMap getVariableProperties(Element variable, String group) throws JDOMException {
HashMap<String, String> propMap = new HashMap<String, String>();
List propGroups = variable.getChild("properties").getChildren("property_group");
for (Iterator pgIt = propGroups.iterator(); pgIt.hasNext();) {
Element propGroupE = (Element) pgIt.next();
if ( propGroupE.getAttributeValue("type").equals(group)) {
List props = propGroupE.getChildren("property");
for (Iterator pIt = props.iterator(); pIt.hasNext();) {
Element prop = (Element) pIt.next();
String name = prop.getChildText("name");
String value = prop.getChildText("value");
propMap.put(name, value);
}
}
}
return propMap;
}
/**
* Extract the properties element from a variable given its XPath
* @param xpathValue The XPath of the variable to find.
* @return properties The properties element.
*
*/
public Element getVariableProperties(String xpathValue) throws JDOMException {
/*
* We know this is a variable XPath. If it's "old style" fix it.
*/
if (!xpathValue.contains("@ID")) {
String[] parts = xpathValue.split("/");
// Throw away index 0 since the string has a leading "/".
xpathValue = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
Element variable = getElementByXPath(xpathValue);
return variable.getChild("properties");
}
/**
* Extract the properties group from a variable given its XPath as an
* Array List of NameValueBeans
* @param xpathValue The XPath of the variable to find.
* @return properties The an array list of properties.
*
*/
public HashMap getVariableProperties(String xpathValue, String group) throws JDOMException {
/*
* We know this is a variable XPath. If it's "old style" fix it.
*/
HashMap<String, String> theProps = new HashMap<String, String>();
if (!xpathValue.contains("@ID")) {
String[] parts = xpathValue.split("/");
// Throw away index 0 since the string has a leading "/".
xpathValue = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
Element variable = getElementByXPath(xpathValue);
List propGroups = variable.getChild("properties").getChildren("property_group");
for (Iterator pgIt = propGroups.iterator(); pgIt.hasNext();) {
Element propGroupE = (Element) pgIt.next();
List props = propGroupE.getChildren("property");
for (Iterator pIt = props.iterator(); pIt.hasNext();) {
Element prop = (Element) pIt.next();
String name = prop.getChildText("name");
String value = prop.getChildText("value");
theProps.put(name, value);
}
}
return theProps;
}
/**
* Extract a property value from a variable element
* Array List of NameValueBeans
* @param xpathValue The XPath of the variable to find.
* @return value the property value
*
*/
public String getVariablePropertyValue(Element variable, String group, String property) throws JDOMException {
if ( variable != null ) {
List propGroups = variable.getChild("properties").getChildren("property_group");
for (Iterator pgIt = propGroups.iterator(); pgIt.hasNext();) {
Element propGroupE = (Element) pgIt.next();
if ( propGroupE.getAttributeValue("type").equals(group )) {
List props = propGroupE.getChildren("property");
for (Iterator pIt = props.iterator(); pIt.hasNext();) {
Element prop = (Element) pIt.next();
String name = prop.getChildText("name");
String value = prop.getChildText("value");
if (name.equals(property)) {
return value;
}
}
}
}
}
return "";
}
/**
* Extract a property value from a variable given its XPath as an
* Array List of NameValueBeans
* @param xpathValue The XPath of the variable to find.
* @return value the property value
*
*/
public String getVariablePropertyValue(String xpathValue, String group, String property) throws JDOMException {
/*
* We know this is a variable XPath. If it's "old style" fix it.
*/
if (!xpathValue.contains("@ID")) {
String[] parts = xpathValue.split("/");
// Throw away index 0 since the string has a leading "/".
xpathValue = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
Element variable = getElementByXPath(xpathValue);
if ( variable != null ) {
List propGroups = variable.getChild("properties").getChildren("property_group");
for (Iterator pgIt = propGroups.iterator(); pgIt.hasNext();) {
Element propGroupE = (Element) pgIt.next();
if ( propGroupE.getAttributeValue("type").equals(group )) {
List props = propGroupE.getChildren("property");
for (Iterator pIt = props.iterator(); pIt.hasNext();) {
Element prop = (Element) pIt.next();
String name = prop.getChildText("name");
String value = prop.getChildText("value");
if (name.equals(property)) {
return value;
}
}
}
}
}
return "";
}
/**
* Returns a Variable object from a LAS XML variable Element.
* @param variable - the varible element
* @return var - the variable object
*
* Probably won't need this method!!
*
*
*
public Variable getVariable(Element variable) {
List attributes = variable.getAttributes();
Variable var = new Variable();
String dsid = variable.getParentElement().getParentElement().getAttributeValue("ID");
var.setDSID(dsid);
ArrayList<NameValuePair> exattrs = new ArrayList<NameValuePair>();
for (Iterator atIt = attributes.iterator(); atIt.hasNext();) {
Attribute attr = (Attribute) atIt.next();
if ( attr.getName().equals("name") ) {
var.setName(attr.getValue());
} else if ( attr.getName().equals("ID")) {
var.setID(attr.getValue());
} else {
exattrs.add(new NameValuePair(attr.getName(), attr.getValue()));
}
}
var.setAttributes(exattrs);
Element propertiesE = variable.getChild("properties");
if ( propertiesE != null ) {
List groups = propertiesE.getChildren("property_group");
HashMap<String, ArrayList<NameValuePair>> props = new HashMap<String, ArrayList<NameValuePair>>();
for (Iterator grpsIt = groups.iterator(); grpsIt.hasNext();) {
Element group = (Element) grpsIt.next();
String group_name = group.getAttributeValue("type");
List properties = group.getChildren("property");
ArrayList<NameValuePair> group_props = new ArrayList<NameValuePair>();
for (Iterator propIt = properties.iterator(); propIt
.hasNext();) {
Element property = (Element) propIt.next();
NameValuePair prop = new NameValuePair(property
.getChildText("name"), property
.getChildText("value"));
group_props.add(prop);
}
props.put(group_name, group_props);
}
var.setProperties(props);
}
Element grid = variable.getChild("grid");
var.setGridID(grid.getAttributeValue("IDREF"));
return var;
}
*/
/**
* Returns list of variables in given a dataset as pmel.tmap.las.util.Dataset objects.
* @param dsID ID of the dataset for which variables should be listed.
* @return variables Array list of variables
*/
public ArrayList<Variable> getVariables(String dsID) throws JDOMException {
ArrayList<Variable> variables = new ArrayList<Variable>();
Element dataset = getElementByXPath("/lasdata/datasets/dataset[@ID='"+dsID+"']");
if ( dataset != null ) {
List variablesElements = dataset.getChildren("variables");
for (Iterator vseIt = variablesElements.iterator(); vseIt.hasNext();) {
Element variablesElement = (Element) vseIt.next();
List vars = variablesElement.getChildren("variable");
for (Iterator varIt = vars.iterator(); varIt.hasNext();) {
Element variable = (Element) varIt.next();
Variable var = new Variable(variable, dsID);
variables.add(var);
}
}
}
return variables;
}
/**
* Returns a single variable from a given a dataset as a pmel.tmap.las.util.Variable object.
* @param dsID ID of the dataset that contains the variable
* @param varID ID of the variable
* @return variable Variable object
*/
public Variable getVariable(String dsID, String varID) throws JDOMException {
String variableXPath = "/lasdata/datasets/dataset[@ID='"+dsID+"']/variables/variable[@ID='"+varID+"']";
return getVariableByXPath(variableXPath);
}
/**
* Returns list of variables give a dataset
* @param dsID ID of the dataset for which variables should be listed.
* @return variables Array list of variables
*/
public ArrayList<NameValuePair> getVariablesAsNameValueBeans(String dsID) throws JDOMException {
ArrayList<NameValuePair> variables = new ArrayList<NameValuePair>();
Element dataset = getElementByXPath("/lasdata/datasets/dataset[@ID='"+dsID+"']");
List variablesElements = dataset.getChildren("variables");
for (Iterator vseIt = variablesElements.iterator(); vseIt.hasNext();) {
Element variablesElement = (Element) vseIt.next();
List vars = variablesElement.getChildren("variable");
for (Iterator varIt = vars.iterator(); varIt.hasNext();) {
Element variable = (Element) varIt.next();
String name = variable.getAttributeValue("name");
String value = variable.getAttributeValue("ID");
variables.add(new NameValuePair(name, value));
}
}
return variables;
}
/**
* Extract the supposedly human interesting title of a variable
* @param xpathValue The XPath of the variable
* @return title The title of the variable (Not to quibble but, it's actually the name attibute)
* @throws JDOMException
*/
public String getVariableTitle(String xpathValue) throws JDOMException {
/*
* We know this is a variable XPath. If it's "old style" fix it.
*/
if (!xpathValue.contains("@ID")) {
String[] parts = xpathValue.split("/");
// Throw away index 0 since the string has a leading "/".
xpathValue = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
return getElementByXPath(xpathValue).getAttributeValue("name");
}
public ArrayList<View> getViewsByDatasetAndVariable(String dsID, String varID) throws JDOMException {
String variableXPath = "/lasdata/datasets/dataset[@ID='"+dsID+"']/variables/variable[@ID='"+varID+"']";
String ui_default = "";
ui_default = getVariablePropertyValue(variableXPath,"ui", "default");
ArrayList<View> views = new ArrayList<View>();
if ( ui_default != null && !ui_default.equals("") ) {
// This will be a list of views determined by the installer. This list
// will not be modified. The installer is responsible for picking sensible
// views for the data.
ui_default = ui_default.substring(ui_default.indexOf("#")+1, ui_default.length());
views = getViewsByDefault(ui_default);
} else {
// This returns all possible views.
ui_default = null;
ArrayList<View> allViews = getViewsByDefault(ui_default);
// Now filter them according to the places where the data variable
// is defined on an interval.
String intervals = getVariableIntervals(variableXPath);
// Create an ArrayList with all combinations
ArrayList<String> combos = combo(intervals);
for (Iterator viewIt = allViews.iterator(); viewIt.hasNext();) {
View view = (View) viewIt.next();
String view_value = view.getValue();
// If the combination of interval axes matches one of the
// views add it to the collection of acceptable views.
for (Iterator comboIt = combos.iterator(); comboIt.hasNext();) {
String combo = (String) comboIt.next();
if ( combo.equals(view_value) ) {
views.add(view);
}
}
}
}
return views;
}
/**
* @param ui_default
* @return
*/
public ArrayList<View> getViewsByDefault(String ui_default) throws JDOMException {
ArrayList <View> views = new ArrayList<View>();
Element def = getUIDefault(ui_default);
if ( def != null ) {
Element map = getUIMap(def, "views");
if ( map != null ) {
Element menu = map.getChild("menu");
String href = menu.getAttributeValue("href");
menu = getElementByXPath("/lasdata/lasui/menus/menu[@name='"+href.substring(1)+"']");
List ifmenusElements = menu.getChildren("ifitem");
for (Iterator ifItemIt = ifmenusElements.iterator(); ifItemIt.hasNext();) {
Element ifitem = (Element) ifItemIt.next();
Element view = new Element("view");
view.setAttribute("name", ifitem.getTextNormalize());
view.setAttribute("value", ifitem.getAttributeValue("view"));
List attributes = ifitem.getAttributes();
for (Iterator attrIt = attributes.iterator(); attrIt.hasNext();) {
Attribute attr = (Attribute) attrIt.next();
// TODO this really implies we need to rework the XML so that these are expressed with XML that matches
// what we want it to look like in the end.
if (!attr.getName().equals("value") && !attr.getName().equals("values") && !attr.getName().equals("view") ) {
view.setAttribute((Attribute) attr.clone());
}
}
views.add(new View(view));
}
}
}
return views;
}
/**
* Returns true if a T axis is defined for this variable.
* @param varpath XPath of the variable to check
* @return hasZ boolean
*/
public boolean hasT(String varpath) throws JDOMException {
/*
* We know this is a variable XPath. If it's "old style" fix it.
*/
if (!varpath.contains("@ID")) {
String[] parts = varpath.split("/");
// Throw away index 0 since the string has a leading "/".
varpath = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
Element variable = getElementByXPath(varpath);
if (variable == null) {
return false;
}
String gridID = variable.getChild("grid").getAttributeValue("IDREF");
Element grid = getElementByXPath("/lasdata/grids/grid[@ID='"+gridID+"']");
if (grid == null) {
return false;
}
List axes = grid.getChildren("axis");
for (Iterator axIt = axes.iterator(); axIt.hasNext();) {
Element axis = (Element) axIt.next();
String axisID = axis.getAttributeValue("IDREF");
axis = getElementByXPath("/lasdata/axes/axis[@ID='"+axisID+"']");
String type = axis.getAttributeValue("type");
if (type.equals("t")) {
return true;
}
}
return false;
}
/**
* Returns true if a T axis is defined for this variable.
* @param dsID ID of the dataset to check
* @param varID ID of the variable to check
* @return hasZ boolean
*/
public boolean hasT(String dsID, String varID) throws JDOMException {
String varpath = "/lasdata/datasets/dataset[@ID='"+dsID+"']/variables/variable[@ID='"+varID+"']";
return hasT(varpath);
}
/**
* Returns true if a Z axis is defined for this variable.
* @param varpath XPath of the variable to check
* @return hasZ boolean
* @throws JDOMException
*/
public boolean hasZ(String varpath) throws JDOMException {
/*
* We know this is a variable XPath. If it's "old style" fix it.
*/
if (!varpath.contains("@ID")) {
String[] parts = varpath.split("/");
// Throw away index 0 since the string has a leading "/".
varpath = "/"+parts[1]+"/"+parts[2]+"/dataset[@ID='"+parts[3]+"']/"+parts[4]+"/variable[@ID='"+parts[5]+"']";
}
Element variable = getElementByXPath(varpath);
if (variable == null) {
return false;
}
String gridID = variable.getChild("grid").getAttributeValue("IDREF");
Element grid = getElementByXPath("/lasdata/grids/grid[@ID='"+gridID+"']");
if (grid == null) {
return false;
}
List axes = grid.getChildren("axis");
for (Iterator axIt = axes.iterator(); axIt.hasNext();) {
Element axis = (Element) axIt.next();
String axisID = axis.getAttributeValue("IDREF");
axis = getElementByXPath("/lasdata/axes/axis[@ID='"+axisID+"']");
String type = axis.getAttributeValue("type");
if (type.equals("z")) {
return true;
}
}
return false;
}
/**
* Returns true if a Z axis is defined for this variable.
* @param dsID ID of the dataset to check
* @param varID ID of the variable to check
* @return hasZ boolean
*/
public boolean hasZ(String dsID, String varID) throws JDOMException {
String varpath = "/lasdata/datasets/dataset[@ID='"+dsID+"']/variables/variable[@ID='"+varID+"']";
return hasZ(varpath);
}
public boolean isRegular(String dsID, String varID) throws JDOMException {
boolean reg = false;
Element variable = getElementByXPath("/lasdata/datasets/dataset[@ID='"+dsID+"']"+"/variables/variable"+"[@ID='"+varID+"']");
String grid_type = variable.getAttributeValue("grid_type");
if ( grid_type.equals("regular")) {
reg = true;
}
return reg;
}
/**
* Merge all of the variable, dataset and global properties for each variable. Variable properties override dataset
* properties which in turn override "global" properties (those defined under the /lasdata element).
*
*/
public void mergeProperites() {
List dsTags = this.getRootElement().getChildren("datasets");
for (Iterator dsTagIt = dsTags.iterator(); dsTagIt.hasNext();) {
Element dsTag = (Element) dsTagIt.next();
List datasets = dsTag.getChildren();
for (Iterator dsIt = datasets.iterator(); dsIt.hasNext();) {
Element dataset = (Element) dsIt.next();
List varTags = dataset.getChildren("variables");
for (Iterator varTagsIt = varTags.iterator(); varTagsIt.hasNext();) {
Element varTag = (Element)varTagsIt.next();
List variables = varTag.getChildren();
for (Iterator varsIt = variables.iterator(); varsIt.hasNext();) {
Element var = (Element) varsIt.next();
Element properties = var.getChild("properties");
if ( properties != null ) {
var.setContent(var.indexOf(properties), getMergedProperties(var));
} else {
var.addContent(getMergedProperties(var));
}
}
}
}
}
}
/**
* Descends the dataset and variable tree and set the grid_type attribute
* if it is not already set.
* @throws JDOMException
*/
public void setGridType(Element variable) throws JDOMException {
String grid_type = variable.getAttributeValue("grid_type");
if ( grid_type == null || grid_type.equals("") ) {
HashMap<String, String> propMap = getVariableProperties(variable, "database_access");
if ( propMap.size() > 0 ) {
variable.setAttribute("grid_type","scattered");
} else {
variable.setAttribute("grid_type", "regular");
}
}
}
private void setID(List categories) {
for (Iterator catIt = categories.iterator(); catIt.hasNext();) {
Element category = (Element) catIt.next();
String ID = category.getAttributeValue("ID");
if ( ID == null ) {
String name = category.getAttributeValue("name");
try {
ID = JDOMUtils.MD5Encode(name+String.valueOf(Math.random()));
} catch (UnsupportedEncodingException e) {
ID = String.valueOf(Math.random());
}
category.setAttribute("ID", ID);
}
List subcategories = category.getChildren("category");
if ( subcategories.size() > 0 ) {
setID(subcategories);
}
}
}
/**
* Helper method to set the output directory if need be
* @param dir The path to the directory
*/
public void setOutputDir(String dir) {
Element output_dir = this.getRootElement().getChild("output_dir");
if (output_dir == null) {
output_dir = new Element("output_dir");
this.getRootElement().addContent(output_dir);
}
output_dir.setText(dir);
}
public ArrayList<Category> getTimeSeriesDatasets() throws LASException {
ArrayList<Category> time_series = new ArrayList<Category>();
if (hasCategories()) {
AttributeFilter attribute_filter = new AttributeFilter("category", "group_type", "time_series");
Iterator catIt = getRootElement().getDescendants(attribute_filter);
while( catIt.hasNext() ) {
Element category = (Element) ((Element)catIt.next()).clone();
Element category_container = new Element("category");
List attributes = category.getAttributes();
for (Iterator attrIt = attributes.iterator(); attrIt.hasNext();) {
Attribute attr = (Attribute) attrIt.next();
category_container.setAttribute(attr.getName(), attr.getValue());
}
List filters = category.getChildren("filter");
for (Iterator filterIt = filters.iterator(); filterIt.hasNext();) {
Element filter = (Element) filterIt.next();
List<Dataset> group_list = getDatasets(filter);
for (Iterator groupIt = group_list.iterator(); groupIt
.hasNext();) {
Dataset dataset = (Dataset) groupIt.next();
category_container.addContent(dataset.getElement());
}
}
time_series.add(new Category(category_container));
}
} else {
AttributeFilter filter = new AttributeFilter("dataset", "group_type", "time_series");
Iterator dsIt= getRootElement().getDescendants(filter);
HashMap<String, ArrayList<Dataset>> time_series_groups = new HashMap<String, ArrayList<Dataset>>();
while (dsIt.hasNext()) {
Element dataset = (Element)((Element) dsIt.next()).clone();
String ts_id = dataset.getAttributeValue("group_id");
ArrayList<Dataset> members = time_series_groups.get(ts_id);
if ( members == null) {
members = new ArrayList<Dataset>();
time_series_groups.put(ts_id, members);
}
members.add(new Dataset(dataset));
}
for (Iterator gIt = time_series_groups.keySet().iterator(); gIt.hasNext();) {
String group = (String) gIt.next();
ArrayList<Dataset> members = time_series_groups.get(group);
Element category = new Element("category");
category.setAttribute("id", group);
for (Iterator memIt = members.iterator(); memIt.hasNext();) {
Dataset member = (Dataset) memIt.next();
category.addContent(member.getElement());
category.setAttribute("name", member.getAttributeValue("group_name"));
category.setAttribute("ID", member.getAttributeValue("group_id"));
}
time_series.add(new Category(category));
}
}
return time_series;
}
/**
* Extract data sets based on a <filter> element from the config, used for group_type="time_series" and group_type="ensemble" categories.
* @param filter A category filter element to be used to select variables from the configuration.
* @return the data set that matches the filter
* @throws LASException
*/
private List<Dataset> getDatasets(Element filter) throws LASException {
List<Dataset> container_datasets = new ArrayList<Dataset>();
String action = filter.getAttributeValue("action");
String name_contains = filter.getAttributeValue("contains");
String name_equals = filter.getAttributeValue("equals");
String tag_contains = filter.getAttributeValue("contains-tag");
String tag_equals = filter.getAttributeValue("equals-tag");
if ( action.equals("apply-dataset") ) {
List datasets = getRootElement().getChildren("datasets");
for (Iterator datasetsIt = datasets.iterator(); datasetsIt.hasNext();) {
Element datasetsE = (Element) datasetsIt.next();
List memberDatasets = datasetsE.getChildren("dataset");
for (Iterator memberDSIt = memberDatasets.iterator(); memberDSIt.hasNext();) {
Element dataset = (Element) memberDSIt.next();
Element container_dataset_element = (Element) dataset.clone();
String name = dataset.getAttributeValue("name");
String ID = dataset.getAttributeValue("ID");
if ( (name_contains != null && name.contains(name_contains)) ||
(name_equals != null && name.equals(name_equals)) ||
(tag_contains != null && ID.contains(tag_contains)) ||
(tag_equals != null && ID.equals(tag_equals)) ) {
container_datasets.add(new Dataset(container_dataset_element));
}
}
}
} else if ( action.equals("apply-variable") ) {
throw new LASException("Should not try to filter groups using an 'apply-variable' filter.");
}
return container_datasets;
}
public boolean hasCategories() {
List tops = getRootElement().getChildren("las_categories");
if ( tops != null && tops.size() > 0 ) {
return true;
} else {
return false;
}
}
}
begin:vcard
fn:Bastian Kern
n:Kern;Bastian
org:Max Planck Institute for Chemistry;Atmospheric Chemistry Department
adr:;;Johann-Joachim Becher Weg 27;Mainz;;55128;Germany
email;internet:bastian.kern@xxxxxxx
title:Dipl.-Met.
tel;work:+49 6131 305452
tel;fax:+49 6131 305436
url:www.atmosphere.mpg.de
version:2.1
end:vcard
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