package org.autoplot.pds; import gov.nasa.pds.ppi.label.PDSLabel; import java.io.File; import java.io.FileInputStream; import java.io.IOException; import java.io.InputStream; import java.net.URI; import java.net.URL; import java.util.ArrayList; import java.util.LinkedHashMap; import java.util.LinkedList; import java.util.List; import java.util.Map; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; import javax.xml.parsers.ParserConfigurationException; import javax.xml.xpath.XPath; import javax.xml.xpath.XPathConstants; import javax.xml.xpath.XPathExpression; import javax.xml.xpath.XPathExpressionException; import javax.xml.xpath.XPathFactory; import org.autoplot.datasource.AbstractDataSource; import org.autoplot.datasource.DataSetURI; import org.autoplot.datasource.DataSource; import org.autoplot.datasource.URISplit; import org.das2.datum.Units; import org.das2.qds.MutablePropertyDataSet; import org.das2.qds.QDataSet; import org.das2.qds.ops.Ops; import org.das2.util.monitor.NullProgressMonitor; import org.das2.util.monitor.ProgressMonitor; import org.w3c.dom.Document; import org.w3c.dom.Node; import org.w3c.dom.NodeList; import org.xml.sax.InputSource; import org.xml.sax.SAXException; /** * PDS4 file source. This is pointed at PDS4 xml files and will return data * they describe. * @author jbf */ public class Pds3DataSource extends AbstractDataSource { public Pds3DataSource(URI uri) { super(uri); } /** * Read the XML file into a document. * @param f the file * @return the document object * @throws IOException * @throws SAXException */ public static Document readXML( File f ) throws IOException, SAXException { DocumentBuilder builder= null; try { builder = DocumentBuilderFactory.newInstance().newDocumentBuilder(); } catch (ParserConfigurationException ex) { throw new RuntimeException(ex); } Document document; try (InputStream in = new FileInputStream(f)) { InputSource source = new InputSource( in ); document = builder.parse(source); } return document; } private static void addAxisArray( Node n, Map axisNames ) throws XPathExpressionException { XPathFactory factory= XPathFactory.newInstance(); XPath xpath= factory.newXPath(); String name = (String)xpath.evaluate( "axis_name", n, XPathConstants.STRING ); Double sequence_number = (Double)xpath.evaluate( "sequence_number", n, XPathConstants.NUMBER ); axisNames.put( sequence_number.intValue(), name ); } /** * return the name of the independent parameter that works in this axis. * This currently assumes the first node with this axisName is the * independent axis. * * For example, with https://space.physics.uiowa.edu/voyager/data/voyager-2-pws-wf/data/1987/vg2_pws_wf_1987-04-21T17_v1.0.xml, * if axisName=='time' then the result will be "Epoch" * * This shows where this logic fails: * https://pds-ppi.igpp.ucla.edu/data/maven-swea-calibrated/data/arc_pad/2016/03/mvn_swe_l2_arcpad_20160316_v04_r01.xml * For this file, I had to kludge in a test for the pitch angles. * * @param doc the xml document * @param axisName the axis name * @return null or the independent variable for the axis. * @throws javax.xml.xpath.XPathExpressionException */ public static String resolveIndependentAxis( Document doc, String axisName ) throws XPathExpressionException { XPathFactory factory= XPathFactory.newInstance(); XPath xpath= factory.newXPath(); String s= "Product_Observational/File_Area_Observational/Array[Axis_Array/axis_name='"+axisName +"']"; NodeList oo= (NodeList) xpath.evaluate( s, doc, XPathConstants.NODESET ); // jbf: I don't see how one can resolve the independent parameter properly. // I'll go through and find the lowest rank data with the axis. // "pitch angle" -> "pa" if ( oo.getLength()>0 ) { int best=0; for ( int i=0; i seekDependencies( Document doc, List depend ) throws XPathExpressionException { if ( depend.size()==1 ) { // always will have one element. XPathFactory factory= XPathFactory.newInstance(); XPath xpath= factory.newXPath(); String name= depend.get(0); Map axisNames= new LinkedHashMap<>(); NodeList oo= (NodeList) xpath.evaluate( "//Product_Observational/File_Area_Observational/Array[name='"+name+"']/Axis_Array", doc, XPathConstants.NODESET ); for ( int i=0; i(depend); depend.add(0,n1); if ( n2!=null && !n2.equals(name) ) { depend.add(1,n2); } } else if ( axisNames.get(1)!=null ) { String n1= resolveIndependentAxis( doc, axisNames.get(1) ); depend= new LinkedList<>(depend); if ( !n1.equals(name) ) { depend.add(0,n1); } } } return depend; } /** * given the bundle, figure out which files should be loaded to implement the time range. This will call recursively * into this code for each item. This unimplemented stub returns an empty dataset. * //TODO: implement me * @param doc the xml document * @param mon progress monitor * @return rank 0 stub * @throws Exception */ public org.das2.qds.QDataSet getDataSetFromBundle(Document doc,ProgressMonitor mon) throws Exception { XPathExpression xp= XPathFactory.newInstance().newXPath().compile( "//Product_Bundle/Bundle_Member_Entry/lidvid_reference/text()"); String lidvid= (String)xp.evaluate( doc, XPathConstants.STRING ); if ( lidvid.trim().length()==0 ) { throw new IllegalArgumentException("lidvid is empty or not found at "+ "//Product_Bundle/Bundle_Member_Entry/lidvid_reference/text()"); } return Ops.dataset(lidvid,Units.nominal()); } /** * given the collection, figure out which files should be loaded to implement the time range. This will call recursively * into this code for each item. This unimplemented stub returns an empty dataset. * //TODO: implement me * @param doc the xml document * @param mon progress monitor * @return rank 0 stub * @throws Exception */ public org.das2.qds.QDataSet getDataSetFromCollection(Document doc,ProgressMonitor mon) throws Exception { XPathExpression xp= XPathFactory.newInstance().newXPath().compile( "//Product_Collection/File_Area_Inventory/File/file_name/text()"); String csvfile= (String)xp.evaluate( doc, XPathConstants.STRING ); if ( csvfile.trim().length()==0 ) { throw new IllegalArgumentException("file name is empty or not found at "+ "//Product_Collection/File_Area_Inventory/File/file_name/text()"); } return Ops.dataset(csvfile,Units.nominal()); } @Override public Map getMetadata(ProgressMonitor mon) throws Exception { URISplit split= URISplit.parse( getURI() ); File lblfile = DataSetURI.getFile( split.resourceUri.toURL() ,new NullProgressMonitor()); String name= getParam("arg_0",""); return Pds3DataSourceFactory.getDataObjectPds3( lblfile.toURL(), name ).getMetadata(); } @Override public org.das2.qds.QDataSet getDataSet(ProgressMonitor mon) throws Exception { String name= getParam("arg_0",""); URISplit split= URISplit.parse( getURI() ); URL labelUrl= split.resourceUri.toURL(); File xmlfile = DataSetURI.getFile( labelUrl,new NullProgressMonitor()); Document doc= Pds3DataSourceFactory.getDocumentWithImports( xmlfile.toURI().toURL() ); PDSLabel label= new PDSLabel(); // we need to parse this twice because it contains the name of the data file as well. if ( !label.parse( xmlfile.getPath() ) ) { throw new IllegalArgumentException("unable to use file "+labelUrl); } List names= new ArrayList<>(); String X= getParam("X",""); if ( !X.equals("") ) { names.add(X); } String Y= getParam("Y",""); if ( !Y.equals("") ) { names.add(Y); } String Z= getParam("Z",""); if ( !Z.equals("") ) { names.add(Z); } if ( !name.equals("") ) { names.add(name); } names= seekDependencies(doc, names ); QDataSet result=null; QDataSet[] results= new QDataSet[names.size()]; XPathFactory factory = XPathFactory.newInstance(); XPath xpath = factory.newXPath(); String datafile = (String) xpath.evaluate("/LABEL/POINTER[@object=\"ASCII_TABLE\"]",doc,XPathConstants.STRING); if ( datafile.length()==0 ) { datafile = (String) xpath.evaluate("/LABEL/POINTER[@object=\"BINARY_TABLE\"]",doc,XPathConstants.STRING); } if ( datafile.length()==0 ) { datafile = (String) xpath.evaluate("/LABEL/POINTER[@object=\"TABLE\"]",doc,XPathConstants.STRING); } FilePointer fp= new FilePointer(labelUrl, datafile ); for ( int i=0; i