public TableConfig readConfigXML(
String fileLocation, FeatureType wantFeatureType, NetcdfDataset ds, Formatter errlog)
throws IOException {
org.jdom2.Document doc;
try {
SAXBuilder builder = new SAXBuilder(false);
if (debugURL) System.out.println(" PointConfig URL = <" + fileLocation + ">");
doc = builder.build(fileLocation);
} catch (JDOMException e) {
throw new IOException(e.getMessage());
}
if (debugXML) System.out.println(" SAXBuilder done");
if (showParsedXML) {
XMLOutputter xmlOut = new XMLOutputter();
System.out.println(
"*** PointConfig/showParsedXML = \n" + xmlOut.outputString(doc) + "\n*******");
}
Element configElem = doc.getRootElement();
String featureType = configElem.getAttributeValue("featureType");
Element tableElem = configElem.getChild("table");
TableConfig tc = parseTableConfig(ds, tableElem, null);
tc.featureType = FeatureType.valueOf(featureType);
return tc;
}
public TableConfig readConfigXMLfromResource(
String resourceLocation, FeatureType wantFeatureType, NetcdfDataset ds, Formatter errlog)
throws IOException {
ClassLoader cl = this.getClass().getClassLoader();
try (InputStream is = cl.getResourceAsStream(resourceLocation)) {
if (is == null) throw new FileNotFoundException(resourceLocation);
if (debugXML) {
System.out.println(" PointConfig URL = <" + resourceLocation + ">");
try (InputStream is2 = cl.getResourceAsStream(resourceLocation)) {
System.out.println(" contents=\n" + IO.readContents(is2));
}
}
org.jdom2.Document doc;
try {
SAXBuilder builder = new SAXBuilder(false);
if (debugURL) System.out.println(" PointConfig URL = <" + resourceLocation + ">");
doc = builder.build(is);
} catch (JDOMException e) {
throw new IOException(e.getMessage());
}
if (debugXML) System.out.println(" SAXBuilder done");
if (showParsedXML) {
XMLOutputter xmlOut = new XMLOutputter();
System.out.println(
"*** PointConfig/showParsedXML = \n" + xmlOut.outputString(doc) + "\n*******");
}
Element configElem = doc.getRootElement();
String featureType = configElem.getAttributeValue("featureType");
Element tableElem = configElem.getChild("table");
assert tableElem != null;
TableConfig tc = parseTableConfig(ds, tableElem, null);
tc.featureType = FeatureType.valueOf(featureType);
return tc;
}
}
/**
* Amend the given NetcdfFile with metadata from HDF-EOS structMetadata
*
* @param ncfile Amend this file
* @param structMetadata structMetadata as String
* @throws IOException on read error
*/
private void amendFromODL(NetcdfFile ncfile, String structMetadata) throws IOException {
Group rootg = ncfile.getRootGroup();
ODLparser parser = new ODLparser();
Element root = parser.parseFromString(structMetadata); // now we have the ODL in JDOM elements
FeatureType featureType = null;
// SWATH
Element swathStructure = root.getChild("SwathStructure");
if (swathStructure != null) {
List<Element> swaths = swathStructure.getChildren();
for (Element elemSwath : swaths) {
Element swathNameElem = elemSwath.getChild("SwathName");
if (swathNameElem == null) {
log.warn("No SwathName element in {} {} ", elemSwath.getName(), ncfile.getLocation());
continue;
}
String swathName = NetcdfFile.makeValidCdmObjectName(swathNameElem.getText().trim());
Group swathGroup = findGroupNested(rootg, swathName);
// if (swathGroup == null)
// swathGroup = findGroupNested(rootg, H4header.createValidObjectName(swathName));
if (swathGroup != null) {
featureType = amendSwath(ncfile, elemSwath, swathGroup);
} else {
log.warn("Cant find swath group {} {}", swathName, ncfile.getLocation());
}
}
}
// GRID
Element gridStructure = root.getChild("GridStructure");
if (gridStructure != null) {
List<Element> grids = gridStructure.getChildren();
for (Element elemGrid : grids) {
Element gridNameElem = elemGrid.getChild("GridName");
if (gridNameElem == null) {
log.warn("No GridName element in {} {} ", elemGrid.getName(), ncfile.getLocation());
continue;
}
String gridName = NetcdfFile.makeValidCdmObjectName(gridNameElem.getText().trim());
Group gridGroup = findGroupNested(rootg, gridName);
// if (gridGroup == null)
// gridGroup = findGroupNested(rootg, H4header.createValidObjectName(gridName));
if (gridGroup != null) {
featureType = amendGrid(elemGrid, ncfile, gridGroup, ncfile.getLocation());
} else {
log.warn("Cant find Grid group {} {}", gridName, ncfile.getLocation());
}
}
}
// POINT - NOT DONE YET
Element pointStructure = root.getChild("PointStructure");
if (pointStructure != null) {
List<Element> pts = pointStructure.getChildren();
for (Element elem : pts) {
Element nameElem = elem.getChild("PointName");
if (nameElem == null) {
log.warn("No PointName element in {} {}", elem.getName(), ncfile.getLocation());
continue;
}
String name = nameElem.getText().trim();
Group ptGroup = findGroupNested(rootg, name);
// if (ptGroup == null)
// ptGroup = findGroupNested(rootg, H4header.createValidObjectName(name));
if (ptGroup != null) {
featureType = FeatureType.POINT;
} else {
log.warn("Cant find Point group {} {}", name, ncfile.getLocation());
}
}
}
if (featureType != null) {
if (showWork) System.out.println("***EOS featureType= " + featureType.toString());
rootg.addAttribute(new Attribute(CF.FEATURE_TYPE, featureType.toString()));
// rootg.addAttribute(new Attribute(CDM.CONVENTIONS, "HDFEOS"));
}
}
public static void read(org.jdom2.Element root, StringBuilder errlog) {
List children = root.getChildren();
for (int i = 0; i < children.size(); i++) {
Element elem = (Element) children.get(i);
if (elem.getName().equals("ioServiceProvider")) {
String className = elem.getAttributeValue("class");
try {
ucar.nc2.NetcdfFile.registerIOProvider(className);
} catch (ClassNotFoundException e) {
errlog.append(
"CoordSysBuilder class not found= " + className + "; check your classpath\n");
} catch (Exception e) {
errlog.append("IOServiceProvider " + className + " failed= " + e.getMessage() + "\n");
}
} else if (elem.getName().equals("coordSysBuilder")) {
String conventionName = elem.getAttributeValue("convention");
String className = elem.getAttributeValue("class");
try {
ucar.nc2.dataset.CoordSysBuilder.registerConvention(conventionName, className);
} catch (ClassNotFoundException e) {
errlog.append(
"CoordSysBuilder class not found= " + className + "; check your classpath\n");
} catch (Exception e) {
errlog.append("CoordSysBuilder " + className + " failed= " + e.getMessage() + "\n");
}
} else if (elem.getName().equals("coordTransBuilder")) {
String transformName = elem.getAttributeValue("name");
String className = elem.getAttributeValue("class");
try {
ucar.nc2.dataset.CoordTransBuilder.registerTransform(transformName, className);
} catch (ClassNotFoundException e) {
errlog.append(
"CoordSysBuilder class not found= " + className + "; check your classpath\n");
} catch (Exception e) {
errlog.append("CoordTransBuilder " + className + " failed= " + e.getMessage() + "\n");
}
} else if (elem.getName().equals("typedDatasetFactory")) {
String typeName = elem.getAttributeValue("datatype");
String className = elem.getAttributeValue("class");
FeatureType datatype = FeatureType.valueOf(typeName.toUpperCase());
if (null == datatype) {
errlog.append(
"TypedDatasetFactory " + className + " unknown datatype= " + typeName + "\n");
continue;
}
try {
ucar.nc2.dt.TypedDatasetFactory.registerFactory(datatype, className);
} catch (ClassNotFoundException e) {
errlog.append(
"CoordSysBuilder class not found= " + className + "; check your classpath\n");
} catch (Exception e) {
errlog.append("TypedDatasetFactory " + className + " failed= " + e.getMessage() + "\n");
}
} else if (elem.getName().equals("gribParameterTable")) {
String editionS = elem.getAttributeValue("edition");
String centerS = elem.getAttributeValue("center");
String subcenterS = elem.getAttributeValue("subcenter");
String versionS = elem.getAttributeValue("version");
String filename = elem.getText();
if ((centerS == null) || (versionS == null) || (filename == null)) {
errlog.append("table element must center, version and filename attributes\n");
continue;
}
// Grib1ParamTables.addParameterTable(int center, int subcenter, int tableVersion, String
// filename) {
// use reflection to decouple from the grib package
try {
int center = Integer.parseInt(centerS);
int subcenter = (subcenterS == null) ? -1 : Integer.parseInt(subcenterS);
int version = Integer.parseInt(versionS);
// ucar.nc2.grib.grib1.tables.Grib1ParamTables.addParameterTable(int center, int
// subcenter, int tableVersion, String tableFilename)
Class c =
RuntimeConfigParser.class
.getClassLoader()
.loadClass("ucar.nc2.grib.grib1.tables.Grib1ParamTables");
Method m =
c.getMethod("addParameterTable", int.class, int.class, int.class, String.class);
m.invoke(null, center, subcenter, version, filename);
} catch (Exception e) {
e.printStackTrace();
}
String strictS = elem.getAttributeValue("strict");
if (strictS != null) {
boolean notStrict = strictS.equalsIgnoreCase("false");
try {
Class c =
RuntimeConfigParser.class
.getClassLoader()
.loadClass("ucar.grib.grib1.tables.Grib1ParamTables");
Method m = c.getMethod("setStrict", boolean.class);
m.invoke(null, !notStrict);
} catch (Exception e) {
e.printStackTrace();
}
continue;
}
} else if (elem.getName().equals("gribParameterTableLookup")) {
String editionS = elem.getAttributeValue("edition");
String filename = elem.getText();
// ucar.nc2.grib.grib1.tables.Grib1ParamTables.addParameterTableLookup(String
// lookupFilename)
try {
Class c =
RuntimeConfigParser.class
.getClassLoader()
.loadClass("ucar.nc2.grib.grib1.tables.Grib1ParamTables");
Method m = c.getMethod("addParameterTableLookup", String.class);
m.invoke(null, filename);
} catch (Exception e) {
e.printStackTrace();
}
} else if (elem.getName().equals("table")) {
String type = elem.getAttributeValue("type");
String filename = elem.getAttributeValue("filename");
if ((type == null) || (filename == null)) {
errlog.append("table element must have both type and filename attributes\n");
continue;
}
try {
if (type.equalsIgnoreCase("GRIB1")) {
// ucar.grib.grib1.GribPDSParamTable.addParameterUserLookup( filename);
// use reflection instead to decouple from the grib package
try {
Class c =
RuntimeConfigParser.class
.getClassLoader()
.loadClass("ucar.grib.grib1.GribPDSParamTable");
Method m = c.getMethod("addParameterUserLookup", String.class);
m.invoke(null, filename);
} catch (ClassNotFoundException e) {
e.printStackTrace();
} catch (NoSuchMethodException e) {
e.printStackTrace();
} catch (InvocationTargetException e) {
e.printStackTrace();
} catch (IllegalAccessException e) {
e.printStackTrace();
}
} else if (type.equalsIgnoreCase("GRIB2")) {
// ucar.grib.grib2.ParameterTable.addParametersUser( filename);
try {
Class c =
RuntimeConfigParser.class
.getClassLoader()
.loadClass(" ucar.grib.grib2.ParameterTable");
Method m = c.getMethod("addParametersUser", String.class);
m.invoke(null, filename);
} catch (Exception e) {
e.printStackTrace();
}
} else {
errlog.append("Unknown table type " + type + "\n");
continue;
}
} catch (Exception e) {
errlog.append("table read failed on " + filename + " = " + e.getMessage() + "\n");
}
} else if (elem.getName().equals("bufrtable")) {
String filename = elem.getAttributeValue("filename");
if (filename == null) {
errlog.append("bufrtable must have filename attribute\n");
continue;
}
// reflection is used to decouple optional jars
Class bufrTablesClass;
try {
bufrTablesClass =
RuntimeConfigParser.class
.getClassLoader()
.loadClass(
"ucar.nc2.iosp.bufr.tables.BufrTables"); // only load if bufr.jar is present
java.lang.Class[] params = new Class[1];
params[0] = String.class;
Method method = bufrTablesClass.getMethod("addLookupFile", params);
Object[] args = new Object[1];
args[0] = filename;
method.invoke(null, args); // static method has null for object
} catch (Throwable e) {
if (e instanceof FileNotFoundException)
errlog.append("bufrtable read failed on " + filename + " = " + e.getMessage() + "\n");
else errlog.append("bufr.jar is not on classpath\n");
}
} else if (elem.getName().equals("Netcdf4Clibrary")) {
// cdm does not have a dependency on netcdf4 (and we don't want to introduce one),
// so we cannot refer to the Nc4Iosp.class object.
String nc4IospClassName = "ucar.nc2.jni.netcdf.Nc4Iosp";
/*
<Netcdf4Clibrary>
<libraryPath>/usr/local/lib</libraryPath>
<libraryName>netcdf</libraryName>
<useForReading>false</useForReading>
</Netcdf4Clibrary>
*/
String path = elem.getChildText("libraryPath");
String name = elem.getChildText("libraryName");
if (path != null && name != null) {
// reflection is used to decouple optional jars
try {
Class nc4IospClass =
RuntimeConfigParser.class.getClassLoader().loadClass(nc4IospClassName);
Method method =
nc4IospClass.getMethod(
"setLibraryAndPath", new Class[] {String.class, String.class});
method.invoke(null, path, name); // static method has null for object
} catch (Throwable e) {
errlog.append(nc4IospClassName + " is not on classpath\n");
}
}
boolean useForReading = Boolean.parseBoolean(elem.getChildText("useForReading"));
if (useForReading) {
try {
// Registers Nc4Iosp in front of all the other IOSPs already registered in
// NetcdfFile.<clinit>().
// Crucially, this means that we'll try to open a file with Nc4Iosp before we try it
// with H5iosp.
NetcdfFile.registerIOProvider(nc4IospClassName);
} catch (IllegalAccessException | InstantiationException | ClassNotFoundException e) {
errlog.append(
String.format(
"Could not register IOSP '%s': %s%n", nc4IospClassName, e.getMessage()));
}
}
}
}
}
public DatasetEditor() {
JTabbedPane tabs = new JTabbedPane();
metadataPP = new PrefPanel("Edit Catalog Dataset", null, null);
tabs.add("metadata", metadataPP);
int row = 0;
metadataPP.addHeading("Basic", row++);
// row 0
metadataPP.addTextField(NAME, "Name", "", 0, row++, "8,1");
// row 1
metadataPP.addTextField(ID, "ID", "", 0, row, null);
addPopups(metadataPP.addTextField(AUTHORITY, "Authority", "", 2, row, null));
addPopups(metadataPP.addTextField(SERVICE_NAME, "Service", "", 4, row, null));
row++;
// row 2
addPopups(
metadataPP.addEnumComboField(
FORMAT_TYPE, "Data format", DataFormatType.getAllTypes(), true, 0, row, null));
addPopups(
metadataPP.addEnumComboField(
DATA_TYPE, "Data type", Arrays.asList(FeatureType.values()), true, 2, row, null));
metadataPP.addEnumComboField(
COLLECTION_TYPE, "Collection type", CollectionType.getAllTypes(), true, 4, row++, null);
////////////
metadataPP.addHeading("GeoSpatial Coverage", row++);
// addCheckBoxField("localMetadata.geospatialCoverage.global", "Global", false, 0, row);
gc_type = metadataPP.addEnumComboField(GC_TYPE, "type", inherit_types, false, 0, row, null);
gc_type.addPropertyChangeListener(
new PropertyChangeListener() {
public void propertyChange(PropertyChangeEvent evt) {
String mode = (String) gc_type.getValue();
setGCmode(getMode(mode));
}
});
extractGCButton = makeButton("Extract Geospatial");
extractGCButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
extractGeospatial();
}
});
metadataPP.addComponent(extractGCButton, 2, row, "left, center");
metadataPP.addCheckBoxField(ZPOSITIVE_UP, "Z positive up", false, 4, row);
row++;
/* JPanel geoPanel = new JPanel();
Field.CheckBox global = new Field.CheckBox( "localMetadata.geospatialCoverage.global", "Global", false, persBean);
geoPanel.add( new JLabel("Global: "));
geoPanel.add( global.getEditComponent());
geoPanel.add( new JButton("Read Dataset"));
pp.addComponent(geoPanel, 0, row++, "left, center"); */
// 4 columns in 3 rows
metadataPP.addDoubleField(LAT_START, "Starting Latitude", 0.0, 5, 0, row, null);
metadataPP.addDoubleField(LAT_EXTENT, "Size", 0.0, 5, 2, row, null);
metadataPP.addDoubleField(LAT_RESOLUTION, "Resolution", 0.0, 5, 4, row, null);
metadataPP.addTextField(LAT_UNITS, "Units", "", 6, row, null);
metadataPP.addDoubleField(LON_START, "Starting Longitude", 0.0, 5, 0, row + 1, null);
metadataPP.addDoubleField(LON_EXTENT, "Size", 0.0, 5, 2, row + 1, null);
metadataPP.addDoubleField(LON_RESOLUTION, "Resolution", 0.0, 5, 4, row + 1, null);
metadataPP.addTextField(LON_UNITS, "Units", "", 6, row + 1, null);
metadataPP.addDoubleField(HEIGHT_START, "Starting Height", 0.0, 5, 0, row + 2, null);
metadataPP.addDoubleField(HEIGHT_EXTENT, "Size", 0.0, 5, 2, row + 2, null);
metadataPP.addDoubleField(HEIGHT_RESOLUTION, "Resolution", 0.0, 5, 4, row + 2, null);
metadataPP.addTextField(HEIGHT_UNITS, "Units", "", 6, row + 2, null);
// addTextField("localMetadata.geospatialCoverage.ZPositive", "Z is Positive", "up", 6, row+3,
// null);
row += 3;
//////
metadataPP.addHeading("Temporal Coverage", row++);
tc_type = metadataPP.addEnumComboField(TC_TYPE, "type", inherit_types, false, 0, row++, null);
tc_type.addPropertyChangeListener(
new PropertyChangeListener() {
public void propertyChange(PropertyChangeEvent evt) {
String mode = (String) tc_type.getValue();
setTCmode(getMode(mode));
}
});
DateRange range = null;
try {
range = new DateRange();
} catch (Exception e) {
e
.printStackTrace(); // To change body of catch statement use File | Settings | File
// Templates.
}
dateRangeSelector = new RangeDateSelector("", range, false, false, null, false, false);
DateField minDateField = dateRangeSelector.getMinDateField();
DateField maxDateField = dateRangeSelector.getMaxDateField();
DurationField durationField = dateRangeSelector.getDurationField();
DurationField resolutionField = dateRangeSelector.getResolutionField();
metadataPP.addField(minDateField, 0, row, null);
metadataPP.addField(maxDateField, 2, row, null);
metadataPP.addField(durationField, 4, row, null);
metadataPP.addField(resolutionField, 6, row++, null);
////
metadataPP.addHeading("Digital Library Info", row++);
metadataPP.addCheckBoxField(HARVEST, "Harvest", false, 0, row++);
addPopups(metadataPP.addTextAreaField(SUMMARY, "Summary", null, 7, 0, row, "3,1"));
addPopups(metadataPP.addTextAreaField(RIGHTS, "Rights", null, 2, 0, row + 1, "3,1"));
addPopups(metadataPP.addTextAreaField(HISTORY, "History", null, 7, 4, row, "3,1"));
addPopups(metadataPP.addTextAreaField(PROCESSING, "Process", null, 2, 4, row + 1, "3,1"));
row += 2;
metadataPP.addEmptyRow(row++, 10);
JTabbedPane tabPane = new JTabbedPane();
metadataPP.addComponent(tabPane, 0, row, "8,1");
ArrayList<Field.BeanTableField> tables = new ArrayList<>();
tabPane.addTab("Variables", makeVariablesPanel());
tables.add(variablesFld);
creatorsFld =
new Field.BeanTableField(
CREATORS, "Creators", null, ThreddsMetadata.Source.class, null, null);
tabPane.addTab("Creators", creatorsFld.getEditComponent());
tables.add(creatorsFld);
publishersFld =
new Field.BeanTableField(
PUBLISHERS, "Publishers", null, ThreddsMetadata.Source.class, null, null);
tabPane.addTab("Publishers", publishersFld.getEditComponent());
tables.add(publishersFld);
projectsFld =
new Field.BeanTableField(
PROJECTS, "Projects", null, ThreddsMetadata.Vocab.class, null, null);
tabPane.addTab("Projects", projectsFld.getEditComponent());
tables.add(projectsFld);
keywordsFld =
new Field.BeanTableField(
KEYWORDS, "Keywords", null, ThreddsMetadata.Vocab.class, null, null);
tabPane.addTab("Keywords", keywordsFld.getEditComponent());
tables.add(keywordsFld);
datesFld = new Field.BeanTableField(DATES, "Dates", null, DateType.class, null, null);
tabPane.addTab("Dates", datesFld.getEditComponent());
tables.add(datesFld);
contributorsFld =
new Field.BeanTableField(
CONTRIBUTORS, "Contributors", null, ThreddsMetadata.Contributor.class, null, null);
tabPane.addTab("Contributors", contributorsFld.getEditComponent());
tables.add(contributorsFld);
docsFld =
new Field.BeanTableField(
DOCUMENTATION, "Documentation", null, InvDocumentation.class, null, null);
tabPane.addTab("Documentation", docsFld.getEditComponent());
tables.add(docsFld);
for (Field.BeanTableField table : tables) addPopups(table);
metadataPP.finish(false);
makeDscanPanel();
tabs.add("datasetScan", dscanPP);
setLayout(new BorderLayout());
add(tabs, BorderLayout.CENTER);
}