package org.autoplot.hapi;
import java.awt.Color;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
import java.net.URLDecoder;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import java.nio.channels.FileChannel;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.concurrent.ConcurrentHashMap;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.regex.PatternSyntaxException;
import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream;
import org.das2.qds.buffer.BufferDataSet;
import org.das2.dataset.NoDataInIntervalException;
import org.das2.datum.CacheTag;
import org.das2.datum.Datum;
import org.das2.datum.DatumRange;
import org.das2.datum.DatumRangeUtil;
import org.das2.datum.EnumerationUnits;
import org.das2.datum.Units;
import org.das2.datum.UnitsUtil;
import org.das2.util.LoggerManager;
import org.das2.util.filesystem.FileSystemUtil;
import org.das2.util.filesystem.HttpUtil;
import org.das2.util.monitor.NullProgressMonitor;
import org.das2.util.monitor.ProgressMonitor;
import org.json.JSONArray;
import org.json.JSONException;
import org.json.JSONObject;
import org.das2.qds.ArrayDataSet;
import org.das2.qds.DDataSet;
import org.das2.qds.DataSetUtil;
import org.das2.qds.MutablePropertyDataSet;
import org.das2.qds.QDataSet;
import org.das2.qds.SemanticOps;
import org.das2.qds.SparseDataSetBuilder;
import org.autoplot.datasource.AbstractDataSource;
import org.autoplot.datasource.AutoplotSettings;
import org.autoplot.datasource.DefaultTimeSeriesBrowse;
import org.autoplot.datasource.URISplit;
import org.autoplot.datasource.capability.Caching;
import org.autoplot.datasource.capability.TimeSeriesBrowse;
import static org.autoplot.hapi.HapiServer.readFromURL;
import org.das2.datum.TimeParser;
import org.das2.datum.TimeUtil;
import org.das2.fsm.FileStorageModel;
import org.das2.graph.ColorUtil;
import org.das2.qds.IDataSet;
import org.das2.qds.ops.Ops;
import org.das2.qds.util.DataSetBuilder;
import org.das2.qstream.TransferType;
import org.das2.util.filesystem.FileSystem;
import org.das2.util.monitor.CancelledOperationException;
/**
* HAPI data source uses transactions with HAPI servers to collect data.
* @author jbf
*/
public final class HapiDataSource extends AbstractDataSource {
protected final static Logger logger= LoggerManager.getLogger("apdss.hapi");
/**
* this logger is for opening connections to remote sites.
*/
protected static final Logger loggerUrl= org.das2.util.LoggerManager.getLogger( "das2.url" );
private static final String WARNING_TIME_MALFORMED= "time malformed";
private static final String WARNING_TIME_ORDER= "time out-of-order";
TimeSeriesBrowse tsb;
public HapiDataSource(URI uri) {
super(uri);
tsb= new DefaultTimeSeriesBrowse();
String str= params.get( URISplit.PARAM_TIME_RANGE );
if ( str!=null ) {
try {
tsb.setURI(uri.toString());
} catch (ParseException ex) {
logger.log(Level.SEVERE, ex.getMessage(), ex);
}
}
addCapability( TimeSeriesBrowse.class, tsb );
addCapability( Caching.class, new Caching() {
@Override
public boolean satisfies(String surl) {
return false;
}
@Override
public void resetURI(String surl) {
}
@Override
public void reset() {
logger.fine("reset cache");
HapiDataSource.csvCache.clear();
}
});
}
private static QDataSet getJSONBins( JSONObject binsObject ) throws JSONException {
boolean foundTimeVarying= false;
JSONArray bins=null;
if ( binsObject.has("values") ) {
logger.fine("using deprecated bins");
bins= binsObject.getJSONArray("values");
} else if ( binsObject.has("centers") ) {
bins= binsObject.optJSONArray("centers");
if ( bins==null ) {
logger.info("time-varying centers are not supported, yet");
foundTimeVarying= true;
}
}
JSONArray ranges= null;
if ( binsObject.has("ranges") ) {
ranges= binsObject.optJSONArray("ranges");
if ( ranges==null ) {
logger.info("time-varying ranges are not supported, yet");
foundTimeVarying= true;
}
}
int len;
if ( ranges==null && bins==null ) {
if ( foundTimeVarying ) {
logger.info("time-varying detected, not supported yet");
return null;
}
throw new IllegalArgumentException("ranges or centers must be specified");
} else {
len= ranges==null ? bins.length() : ranges.length();
}
DDataSet result= DDataSet.createRank1(len);
DDataSet max= DDataSet.createRank1(len);
DDataSet min= DDataSet.createRank1(len);
boolean hasMin= false;
boolean hasMax= false;
boolean hasCenter= false;
if ( len==0 ) {
throw new IllegalArgumentException("bins must have ranges or centers specified");
} else {
if ( bins!=null ) {
hasCenter= true;
Object o= bins.get(0);
if ( o instanceof Number ) {
for ( int j=0; j<len; j++ ) {
result.putValue( j, bins.getDouble(j) );
}
} else if ( o instanceof JSONObject ) {
for ( int j=0; j<len; j++ ) {
JSONObject jo= bins.getJSONObject(j);
result.putValue(j,jo.getDouble("center"));
if ( hasMin || jo.has("min") ) {
hasMin= true;
min.putValue(j,jo.getDouble("min"));
}
if ( hasMax || jo.has("max") ) {
hasMax= true;
max.putValue(j,jo.getDouble("max"));
}
}
}
}
if ( ranges!=null ) {
for ( int j=0; j<len; j++ ) {
JSONArray ja1= ranges.getJSONArray(j);
hasMax= true;
hasMin= true;
min.putValue(j,ja1.getDouble(0));
max.putValue(j,ja1.getDouble(1));
}
}
}
if ( binsObject.has(HapiUtil.KEY_UNITS) ) {
Object uo= binsObject.get(HapiUtil.KEY_UNITS);
if ( uo instanceof String ) {
String sunits= (String)uo;
Units u= Units.lookupUnits(sunits);
result.putProperty( QDataSet.UNITS, u );
if ( hasMin && hasMax ) {
min.putProperty( QDataSet.UNITS, u );
max.putProperty( QDataSet.UNITS, u );
}
}
}
if ( hasCenter ) {
if ( hasMin && hasMax ) {
result.putProperty( QDataSet.BIN_MIN, min );
result.putProperty( QDataSet.BIN_MAX, max );
} else if ( hasMin || hasMax ) {
logger.warning("need both min and max for bins.");
}
} else {
result= (DDataSet)ArrayDataSet.copy( double.class, Ops.bundle( min, max ) );
result.putProperty( QDataSet.BINS_1, QDataSet.VALUE_BINS_MIN_MAX );
result.putProperty( QDataSet.UNITS, min.property(QDataSet.UNITS) );
}
if ( binsObject.has("name") ) {
result.putProperty( QDataSet.NAME, binsObject.getString("name") );
}
if ( binsObject.has("description") ) {
result.putProperty( QDataSet.TITLE, binsObject.getString("description") );
result.putProperty( QDataSet.LABEL, binsObject.getString("description") );
}
return result;
}
public static final double FILL_VALUE= -1e38;
/**
* returns the info for the object to use, or null.
* @return
*/
private JSONObject maybeGetDiffResolutionInfo(String id) {
try {
URL url= HapiServer.createURL( this.resourceURI.toURL(), "semantics");
String s= readFromURL( url, "json" );
JSONObject o= new JSONObject(s);
JSONArray a= o.optJSONArray("cadenceVariants");
if ( a!=null ) {
for ( int i=0; i<a.length(); i++ ) {
Object o1= a.get(i);
if ( o1 instanceof JSONObject ) {
JSONObject jo2= (JSONObject)o1;
if ( jo2.optString("groupId","").equals(id) ) {
String sourceId= jo2.getString("sourceId");
return getInfo( sourceId );
}
}
}
}
return null;
} catch (JSONException ex) {
Logger.getLogger(HapiDataSource.class.getName()).log(Level.SEVERE, null, ex);
} catch (IOException ex) {
Logger.getLogger(HapiDataSource.class.getName()).log(Level.SEVERE, null, ex);
}
return null;
}
private JSONObject getInfo( String id ) throws MalformedURLException, IOException, JSONException {
URI server = this.resourceURI;
if ( id.equals("") ) throw new IllegalArgumentException("missing id");
id = URLDecoder.decode(id,"UTF-8");
JSONArray jo= HapiServer.getCatalog(server.toURL());
for ( int i=0; i<jo.length(); i++ ) {
JSONObject jo1= jo.getJSONObject(i);
if ( jo1.get("id").equals(id) ) {
return HapiServer.getInfo(server.toURL(), id);
}
}
JSONObject r = maybeGetDiffResolutionInfo(id);
if ( r==null ) {
throw new IllegalArgumentException("Bad id: "+id );
} else {
return r;
}
}
/**
* reformat the URL with the new timerange.
* @param url the URL containing time.min and time.max parameters.
* @param tr the new timerange
* @param vers the HAPI server version
* @return the URL with time.min and time.max replaced.
*/
private static URL replaceTimeRangeURL(URL url, DatumRange tr, String vers ) {
try {
URISplit split= URISplit.parse(url.toURI());
Map<String,String> params= URISplit.parseParams(split.params);
String smin= tr.min().toString();
String smax= tr.max().toString();
if ( smin.endsWith("00:00:00.000Z") ) smin= smin.substring(0,smin.length()-14) + "T00:00Z";
if ( smax.endsWith("00:00:00.000Z") ) smax= smax.substring(0,smax.length()-14) + "T00:00Z";
if ( vers.startsWith("1.") || vers.startsWith("2.")) {
params.put("time.min",smin);
params.put("time.max",smax);
} else {
params.put("start",smin);
params.put("stop",smax);
}
split.params= URISplit.formatParams(params);
String surl= URISplit.format(split);
url= new URL(surl);
return url;
} catch (URISyntaxException | MalformedURLException ex) {
throw new RuntimeException(ex);
}
}
public static class ParamDescription {
boolean hasFill= false;
double fillValue= -1e38;
Units units= Units.dimensionless;
String name= "";
String description= "";
String label="";
String[] labels=null;
String type= "";
/**
* number of indices in each index.
*/
int[] size= new int[0];
/**
* total number of fields
*/
int nFields= 1;
/**
* length in bytes when transferring with binary.
*/
int length= 0;
QDataSet[] depend= null;
/**
* for time-varying depend1 (not in HAPI1.1)
*/
String[] dependName= null;
/**
* date the parameter was last modified, or 0 if not known.
*/
long modifiedDateMillis= 0;
JSONObject parameter = null;
/**
* may contain hint for renderer, such as nnspectrogram
*/
String renderType=null;
private ParamDescription( String name ) {
this.name= name;
}
@Override
public String toString() {
return this.name;
}
}
private static final Map<String,Datum> lastRecordFound= new HashMap<>();
private static String[] cacheFilesFor( URL url, ParamDescription[] pp, Datum xx ) {
String s= AutoplotSettings.settings().resolveProperty(AutoplotSettings.PROP_FSCACHE);
if ( s.endsWith("/") ) s= s.substring(0,s.length()-1);
StringBuilder ub= new StringBuilder( url.getProtocol() + "/" + url.getHost() + "/" + url.getPath() );
if ( url.getQuery()!=null ) {
String[] querys= url.getQuery().split("\\&");
Pattern p= Pattern.compile("id=(.+)");
for ( String q : querys ) {
Matcher m= p.matcher(q);
if ( m.matches() ) {
ub.append("/").append(m.group(1));
break;
}
}
} else {
throw new IllegalArgumentException("query must be specified, implementation error");
}
TimeParser tp= TimeParser.create( "$Y/$m/$Y$m$d" );
String sxx= tp.format(xx);
String u= ub.toString();
String[] result= new String[pp.length];
for ( int i=0; i<pp.length; i++ ){
result[i]= s + "/" + u + "/" + sxx + "." + pp[0].name + ".csv";
}
return result;
}
private static final Map<String,ArrayList<ByteBuffer>> binaryCache= new ConcurrentHashMap<>();
private static final Map<String,ArrayList<String>> csvCache= new ConcurrentHashMap<>();
/**
* print the cache stats.
* @see https://sourceforge.net/p/autoplot/bugs/1996/
*/
public static void printCacheStats() {
if ( csvCache==null || csvCache.isEmpty() ) {
System.err.println( "(cache is empty)" );
} else {
for ( Entry<String,ArrayList<String>> s: csvCache.entrySet() ) {
System.err.println( "" + s.getKey() +": "+s.getValue().size()+" records");
}
}
if ( binaryCache==null || binaryCache.isEmpty() ) {
System.err.println( "(cache is empty)" );
} else {
for ( Entry<String,ArrayList<ByteBuffer>> s: binaryCache.entrySet() ) {
System.err.println( "" + s.getKey() +": "+s.getValue().size()+" records");
}
}
}
/**
* return the local folder of the cache for HAPI data. This will end with
* a slash.
* @return the local folder of the cache for HAPI data.
*/
public static String getHapiCache() {
String hapiCache= System.getProperty("HAPI_DATA");
if ( hapiCache!=null ) {
String home=System.getProperty("user.home") ;
if ( hapiCache.contains("${HOME}") ) { // the filesystem settings used ${}, %{} seems more conventional.
hapiCache= hapiCache.replace("${HOME}", home );
} else if ( hapiCache.contains("%{HOME}") ) {
hapiCache= hapiCache.replace("%{HOME}", home );
}
}
if ( hapiCache!=null && hapiCache.contains("\\") ) { // Windows path sep
hapiCache= hapiCache.replaceAll("\\\\", "/" );
}
if ( hapiCache==null ) {
String s= AutoplotSettings.settings().resolveProperty(AutoplotSettings.PROP_FSCACHE);
if ( s.endsWith("/") ) s= s.substring(0,s.length()-1);
hapiCache= s + "/hapi/";
}
if ( !hapiCache.endsWith("/") ) hapiCache= hapiCache + "/";
if ( !hapiCache.endsWith("/") ) {
throw new IllegalArgumentException("hapiCache must end with /");
}
if ( HapiServer.useCache() ) {
if ( !new File(hapiCache).exists() ) {
if ( !new File(hapiCache).mkdirs() ) {
logger.log(Level.WARNING, "unable to mkdir directories {0}", hapiCache);
}
}
}
return hapiCache;
}
private static void writeToBinaryCachedData(String location, ParamDescription[] pp, Datum xx, ByteBuffer buf) throws IOException {
String hapiCache= getHapiCache();
TimeParser tp= TimeParser.create( "$Y/$m/$Y$m$d" );
String sxx= tp.format(xx);
String format= "binary";
String u= location;
Datum t0= lastRecordFound.get( u + "/" + sxx );
if ( t0==null ) {
String f= hapiCache + u + "/" + sxx + "." + pp[0].name + "." + format;
File ff= new File(f);
if ( ff.exists() ) {
try ( BufferedReader read= new BufferedReader(
new InputStreamReader( new FileInputStream(ff), HapiServer.UTF8 ) ) ) {
String line= read.readLine();
String lastLine= null;
while ( line!=null ) {
lastLine= line;
line= read.readLine();
}
if ( lastLine!=null ) {
try {
t0= Units.us2000.parse(lastLine);
lastRecordFound.put( u + "/" + sxx,t0);
} catch (ParseException ex) {
t0= null;
}
} else {
t0= null;
}
}
}
}
if ( t0!=null && t0.ge(xx) ) {
logger.log(Level.FINE, "clear all cached files for {0}", sxx);
for (ParamDescription pp1 : pp) {
String f = hapiCache + u + "/" + sxx + "." + pp1.name + "." +format;
File ff= new File(f);
if ( ff.exists() ) {
if ( !ff.delete() ) logger.log(Level.INFO, "unable to delete file: {0}", ff);
}
}
}
for (ParamDescription pp1 : pp) {
String f = u + "/" + sxx + "." + pp1.name + "." + format + "." + Thread.currentThread().getId();
logger.log(Level.FINER, "cache.get({0})", f);
ArrayList<ByteBuffer> sparam= binaryCache.get(f);
if ( sparam==null ) {
sparam= new ArrayList<>();
binaryCache.put(f,sparam);
logger.log(Level.FINE, "cache.put({0},ArrayList({1}))", new Object[]{f, sparam.size()});
}
ByteBuffer buf2= ByteBuffer.allocate( buf.capacity() );
buf2.put(buf);
sparam.add( buf2 );
}
lastRecordFound.put( u + "/" + sxx,xx);
}
private static void writeToCsvCachedData( String location, ParamDescription[] pp, Datum xx, String[] ss, boolean allParam) throws IOException {
String hapiCache= getHapiCache();
TimeParser tp= TimeParser.create( "$Y/$m/$Y$m$d" );
String sxx= tp.format(xx);
String u= location;
Datum t0= lastRecordFound.get( u + "/" + sxx );
if ( t0==null ) {
String f= hapiCache + u + "/" + sxx + "." + pp[0].name + ".csv";
File ff= new File(f);
if ( ff.exists() ) {
try ( BufferedReader read= new BufferedReader(
new InputStreamReader( new FileInputStream(ff), HapiServer.UTF8 ) ) ) {
String line= read.readLine();
String lastLine= null;
while ( line!=null ) {
lastLine= line;
line= read.readLine();
}
if ( lastLine!=null ) {
try {
t0= Units.us2000.parse(lastLine);
lastRecordFound.put( u + "/" + sxx,t0);
} catch (ParseException ex) {
t0= null;
}
} else {
t0= null;
}
}
}
}
if ( t0!=null && t0.ge(xx) ) {
logger.log(Level.FINE, "clear all cached files for {0}", sxx);
for (ParamDescription pp1 : pp) {
String f = hapiCache + u + "/" + sxx + "." + pp1.name + ".csv";
File ff= new File(f);
if ( ff.exists() ) {
if ( !ff.delete() ) logger.log(Level.INFO, "unable to delete file: {0}", ff);
}
}
}
int ifield=0;
for (ParamDescription pp1 : pp) {
String f = u + "/" + sxx + "." + pp1.name + ".csv" + "." + Thread.currentThread().getId();
logger.log(Level.FINER, "cache.get({0})", f);
ArrayList<String> sparam= csvCache.get(f);
if ( sparam==null ) {
sparam= new ArrayList<>();
csvCache.put(f,sparam);
logger.log(Level.FINE, "cache.put({0},ArrayList({1}))", new Object[]{f, sparam.size()});
}
StringBuilder build= new StringBuilder();
int length = pp1.nFields;
for ( int k=0; k<length; k++ ) {
if ( k>0 ) build.append(",");
build.append( ss[ifield++] );
}
sparam.add(build.toString());
}
lastRecordFound.put( u + "/" + sxx,xx);
}
/**
* See https://sourceforge.net/p/autoplot/bugs/2043/
* @param url url used to locate position in cache.
* @param pp parameters
* @param xx time used to id the file.
*/
private static void writeToBinaryCachedDataFinish(String location, ParamDescription[] pp, Datum xx, boolean allParam) throws IOException {
logger.log(Level.FINE, "writeToBinaryCachedDataFinish: {0}", xx);
String hapiCache= getHapiCache();
String format= "binary";
long currentTimeMillis= pp[0].modifiedDateMillis;
TimeParser tp= TimeParser.create( "$Y/$m/$Y$m$d" );
String sxx= tp.format(xx);
String u= location;
int ipos=0;
for (ParamDescription pp1 : pp) {
String f = u + "/" + sxx + "." + pp1.name + "." + format + "."+ Thread.currentThread().getId();
logger.log(Level.FINE, "remove from cache: {0}", f);
File ff= new File( hapiCache + u + "/" + sxx + "." + pp1.name + "." + format +"");
if ( !ff.getParentFile().exists() ) {
if ( !ff.getParentFile().mkdirs() ) {
throw new IOException("unable to mkdirs "+ff.getParent() );
}
}
File ffTemp= new File( hapiCache + u + "/" + sxx + "." + pp1.name + "."+ format + "."+Thread.currentThread().getId() );
ArrayList<ByteBuffer> data= binaryCache.get(f); //TODO: use "remove" after debugging.
int ilen= BufferDataSet.byteCount(pp1.type) * DataSetUtil.product(pp1.size);
try ( FileChannel ffTempChannel= new FileOutputStream(ffTemp).getChannel() ) {
for ( ByteBuffer buf: data ) {
buf.position(ipos);
buf.limit(ipos+ilen);
ffTempChannel.write(buf);
}
}
ipos+= pp1.length;
}
synchronized ( HapiDataSource.class ) {
for (ParamDescription pp1 : pp) {
File ffTemp= new File( hapiCache + u + "/" + sxx + "." + pp1.name + "."+ format + "."+Thread.currentThread().getId() );
File ff= new File( hapiCache + u + "/" + sxx + "." + pp1.name + "." + format +"");
if ( !ffTemp.renameTo(ff) ) {
logger.log(Level.WARNING, "rename to {0} failed", ff);
}
if ( currentTimeMillis>0 ) {
if ( !ff.setLastModified(currentTimeMillis) ) {
logger.log(Level.WARNING, "setLastModified for {0} failed", ff);
}
}
}
}
}
/**
* See https://sourceforge.net/p/autoplot/bugs/2043/
* @param url url used to locate position in cache.
* @param pp parameters
* @param xx time used to id the file.
*/
private static void writeToCsvCachedDataFinish(String location, ParamDescription[] pp, Datum xx) throws IOException {
logger.log(Level.FINE, "writeToCachedDataFinish: {0}", xx);
String hapiCache= getHapiCache();
String format= "csv";
long currentTimeMillis= pp[0].modifiedDateMillis;
TimeParser tp= TimeParser.create( "$Y/$m/$Y$m$d" );
String sxx= tp.format(xx);
String u= location;
for (ParamDescription pp1 : pp) {
String f = u + "/" + sxx + "." + pp1.name + "." + format + "."+ Thread.currentThread().getId();
logger.log(Level.FINE, "remove from cache: {0}", f);
ArrayList<String> sparam= csvCache.remove(f);
File ff= new File( hapiCache + u + "/" + sxx + "." + pp1.name + "." + format +".gz");
if ( !ff.getParentFile().exists() ) {
if ( !ff.getParentFile().mkdirs() ) {
throw new IOException("unable to mkdirs "+ff.getParent() );
}
}
File ffTemp= new File( hapiCache + u + "/" + sxx + "." + pp1.name + "."+ format + ".gz."+Thread.currentThread().getId() );
//int line=0;
try (final BufferedWriter w = new BufferedWriter( new OutputStreamWriter( new GZIPOutputStream( new FileOutputStream(ffTemp) ) ) ) ) {
if ( sparam!=null ) {
for ( String s123: sparam ) {
//line++;
w.write(s123);
w.newLine();
}
}
}
}
synchronized ( HapiDataSource.class ) {
for (ParamDescription pp1 : pp) {
File ff= new File( hapiCache + u + "/" + sxx + "." + pp1.name + "." + format +".gz");
File ffTemp= new File( hapiCache + u + "/" + sxx + "." + pp1.name + "."+ format + ".gz."+Thread.currentThread().getId() );
if ( !ffTemp.renameTo(ff) ) {
logger.log(Level.WARNING, "renameTo {0} failed", ff);
}
if ( currentTimeMillis>0 ) {
if ( !ff.setLastModified(currentTimeMillis) ) {
logger.log(Level.WARNING, "setLastModified for {0} failed", ff);
}
}
}
}
}
/**
* To assist in getting the CDAWeb HAPI server going, handle a few differences
* like:<ul>
* <li>parameters are returned within the JSON code.
* <li>Epoch is needed.
* </ul>
* @param monitor
* @return
* @throws Exception
*/
private QDataSet getDataSetCDAWeb( ProgressMonitor monitor) throws Exception {
URI server = this.resourceURI;
String id= getParam("id","" );
if ( id.equals("") ) throw new IllegalArgumentException("missing id");
id= URLDecoder.decode( id,"UTF-8" );
String pp= getParam("parameters","");
if ( !pp.equals("") && !pp.startsWith("Epoch,") ) {
pp= "Epoch,"+pp;
}
if ( id.equals("") ) throw new IllegalArgumentException("missing id");
id= URLDecoder.decode(id,"UTF-8");
DatumRange tr; // TSB = DatumRangeUtil.parseTimeRange(timeRange);
tr= tsb.getTimeRange();
URL url= HapiServer.getDataURL( server.toURL(), id, tr, pp );
url= new URL( url.toString()+"&include=header&format=json1" );
monitor.started();
monitor.setProgressMessage("server is preparing data");
long t0= System.currentTimeMillis() - 100; // -100 so it updates after receiving first record.
int lineNum=0;
StringBuilder builder= new StringBuilder();
logger.log(Level.FINE, "getDocument {0}", url.toString());
loggerUrl.log(Level.FINE, "GET {0}", new Object[] { url } );
HttpURLConnection httpConnect= ((HttpURLConnection)url.openConnection());
httpConnect.setConnectTimeout(FileSystem.settings().getConnectTimeoutMs());
httpConnect.setReadTimeout(FileSystem.settings().getReadTimeoutMs());
httpConnect= (HttpURLConnection) HttpUtil.checkRedirect( httpConnect );
try ( BufferedReader in= new BufferedReader(
new InputStreamReader( httpConnect.getInputStream(), HapiServer.UTF8 ) ) ) {
String line= in.readLine();
lineNum++;
while ( line!=null ) {
if ( System.currentTimeMillis()-t0 > 100 ) {
monitor.setProgressMessage("reading line "+lineNum);
t0= System.currentTimeMillis();
}
builder.append(line);
line= in.readLine();
}
} catch ( IOException ex ) {
ByteArrayOutputStream baos= new ByteArrayOutputStream();
FileSystemUtil.copyStream( httpConnect.getErrorStream(), baos, new NullProgressMonitor() );
String s= baos.toString("UTF-8");
if ( s.contains("No data available") ) {
logger.log(Level.FINE, "No data available, server responded with {0}: {1}", new Object[]{httpConnect.getResponseCode(), httpConnect.getResponseMessage()});
throw new NoDataInIntervalException("No data available");
} else {
if ( s.length()<256 ) {
throw new IOException( ex.getMessage() + ": "+s );
} else {
throw ex;
}
}
}
httpConnect.disconnect();
JSONObject o= new JSONObject(builder.toString());
JSONObject doc= o;
ParamDescription[] pds= getParameterDescriptions(doc);
monitor.setProgressMessage("parsing data");
int[] nfields= new int[pds.length];
for ( int i=0; i<pds.length; i++ ) {
if ( pds[i].size.length==0 || ( pds[i].size.length==1 && pds[i].size[0]==1 ) ) {
nfields[i]= 1;
} else {
nfields[i]= DataSetUtil.product(pds[i].size);
}
}
boolean[] timeVary= new boolean[pds.length];
//https://cdaweb.gsfc.nasa.gov/registry/hdp/hapi/data.xql?id=spase%3A%2F%2FVSPO%2FNumericalData%2FRBSP%2FB%2FEMFISIS%2FGEI%2FPT0.015625S&time.min=2012-10-09T00%3A00%3A00Z&time.max=2012-10-09T00%3A10%3A00Z¶meters=Magnitude
QDataSet result= null;
int ipd=0;
for ( ParamDescription pd: pds ) {
JSONArray param;
try {
param= doc.getJSONArray(pd.name);
} catch ( JSONException ex ) {
timeVary[ipd]= false;
continue; // DEPEND_1, etc...
}
timeVary[ipd]= true;
Units u= pd.units;
if ( nfields[ipd]>1 ) {
int nf= nfields[ipd];
DDataSet column= DDataSet.createRank2(param.length(),nfields[ipd]);
for ( int i=0; i<param.length(); i++ ) {
JSONObject jo= param.getJSONObject(i);
JSONArray joa= jo.getJSONArray("elements");
for ( int j=0; j<nf; j++ ) {
column.putValue( i, j, u.parse( joa.getString(j) ).doubleValue(u) );
}
}
if ( pd.hasFill ) column.putProperty( QDataSet.FILL_VALUE, pd.fillValue );
column.putProperty( QDataSet.TITLE, pd.description );
column.putProperty( QDataSet.UNITS, pd.units );
for ( int j=0; j<nf; j++ ) {
result= Ops.bundle( result, Ops.slice1(column,j) );
}
} else {
DDataSet column= DDataSet.createRank1(param.length());
for ( int i=0; i<param.length(); i++ ) {
column.putValue( i, u.parse(param.getString(i) ).doubleValue(u) );
}
if ( pd.hasFill ) column.putProperty( QDataSet.FILL_VALUE, pd.fillValue );
column.putProperty( QDataSet.TITLE, pd.description );
column.putProperty( QDataSet.UNITS, pd.units );
result= Ops.bundle( result, column );
}
ipd++;
}
monitor.finished();
int ntimeVary= 0;
for ( boolean b: timeVary ){
if ( b ) ntimeVary++;
}
ParamDescription[] newPds= new ParamDescription[ntimeVary];
int k=0;
for ( int j=0; j<pds.length; j++ ) {
if ( timeVary[j] ) newPds[k++]= pds[j];
}
// the data are sometimes delivered backwards
int[] sort= null;
// if ( UnitsUtil.isTimeLocation( newPds[ntimeVary-1].units ) ) {
// sort= new int[result.length()];
// for ( int j=0; j<ntimeVary; j++ ) {
// sort[j]= ntimeVary-1-j;
// }
// }
result = repackage(result,newPds,sort);
return result;
}
/**
* return the index of the parameter name.
* @param pds
* @param name
* @return
*/
private static int indexOfParameter( ParamDescription[] pds, String name ) {
for ( int i=0; i<pds.length; i++ ) {
if ( pds[i].name.equals(name) ) {
return i;
}
}
return -1;
}
/**
* replace this with String.join after Java8 upgrade.
* @param delim
* @param pieces
* @return
*/
private String join( String delim, List<String> pieces ) {
if ( pieces.isEmpty() ) return "";
StringBuilder b= new StringBuilder(pieces.get(0));
for ( int i=1; i<pieces.size(); i++ ) {
b.append(delim);
b.append(pieces.get(i));
}
return b.toString();
}
Map<Datum,Color> lookupColorCache= new HashMap<>();
private Color lookupColor( Map<Pattern,Color> lookup, Datum d ) {
Color c= lookupColorCache.get(d);
if ( c!=null ) return c;
for ( Entry<Pattern,Color> e: lookup.entrySet() ) {
Pattern p= e.getKey();
if ( p.matcher(d.toString()).matches() ) {
lookupColorCache.put( d, e.getValue() );
break;
}
}
return Color.GRAY;
}
@Override
public synchronized QDataSet getDataSet(ProgressMonitor monitor) throws Exception {
URI server = this.resourceURI;
String format= getParam("format","csv");
{ // This kludge was to support an early HAPI server which did not give a conformant data response.
String serverStr= server.toString();
if ( format.equals("json1") ||
( serverStr.startsWith("http://cdaweb") && serverStr.endsWith( "gsfc.nasa.gov/registry/hdp/hapi") ) ) {
return getDataSetCDAWeb(monitor);
}
}
monitor.setTaskSize(100);
monitor.started();
monitor.setProgressMessage("reading info");
String id= getParam("id","" ); // the name of the set of identifiers.
if ( id.equals("") ) throw new IllegalArgumentException("missing id");
id= URLDecoder.decode( id,"UTF-8" );
String pp= getParam("parameters","");
if ( pp.contains("%2C") ) { // commas are escaped
pp= URLDecoder.decode(pp,"UTF-8");
}
JSONObject info;
info= getInfo(id);
info= HapiUtil.resolveRefs(info);
String vers= info.getString("HAPI");
monitor.setProgressMessage("got info");
monitor.setTaskProgress(20);
ParamDescription[] pds= getParameterDescriptions(info);
DatumRange tr; // TSB = DatumRangeUtil.parseTimeRange(timeRange);
tr= tsb.getTimeRange();
if ( tr==null ) {
throw new IllegalArgumentException("timerange is missing");
}
Datum cadence= null;
if ( info.has("cadence") ) { // add one cadence length to beginning and end.
try {
int[] ii= DatumRangeUtil.parseISO8601Duration(info.getString("cadence"));
Datum t= TimeUtil.toDatumDuration(ii);
cadence= t;
tr= new DatumRange( tr.min().subtract(cadence), tr.max().add(cadence) );
} catch ( ParseException ex ) {
logger.log(Level.WARNING, "unable to parse cadence as ISO8601 duration: {0}", info.getString("cadence"));
}
}
String timeStampLocation= "CENTER";
if ( info.has("timeStampLocation" ) ) {
timeStampLocation= info.getString("timeStampLocation");
}
JSONArray parametersArray= info.getJSONArray("parameters");
int nparam= parametersArray.length(); // this is the actual number sent.
if ( pp.length()>0 ) {
String[] pps= pp.split(",");
for ( int i=0; i<pps.length; i++ ) {
pps[i]= pps[i].replace("+"," ");
pps[i]= pps[i].replaceAll("\\%2B","+");
}
Map<String,Integer> map= new HashMap();
for ( int i=0; i<nparam; i++ ) {
map.put( parametersArray.getJSONObject(i).getString("name"), i ); // really--should name/id are two names for the same thing...
}
if ( !pps[0].equals(parametersArray.getJSONObject(0).getString("name")) ) { // add Time if it wasn't specified.
pp= parametersArray.getJSONObject(0).getString("name") + ","+ pp;
pps= pp.split(",");
}
ArrayList namesNotFound= new ArrayList();
ParamDescription[] subsetPds= new ParamDescription[pps.length];
for ( int ip=0; ip<pps.length; ip++ ) {
Integer ii= map.get(pps[ip]);
if ( ii==null ) {
namesNotFound.add(pps[ip]);
} else {
int i= map.get(pps[ip]);
subsetPds[ip]= pds[i];
}
}
if ( namesNotFound.size()==1 ) {
throw new IllegalArgumentException("Parameter name not found: "+namesNotFound.get(0) );
} else if ( namesNotFound.size()>1 ) {
throw new IllegalArgumentException("Parameter names not found: "+join(",",namesNotFound) );
}
if ( subsetPds.length==2 && subsetPds[1].size.length>0 ) {
// Oooh, it's a spectrogram. Maybe it has time-varying DEPEND_1.
String dependName= null;
String[] dependNames= null;
if ( subsetPds[1].dependName!=null ) {
dependNames= new String[subsetPds[1].dependName.length];
for ( int i=0; i<subsetPds[1].dependName.length; i++ ) {
dependNames[i]= subsetPds[1].dependName[i];
}
} else {
logger.warning("depend name missing!");
}
if ( dependNames!=null ) {
List<ParamDescription> subsetPds1= new ArrayList<>();
for ( int i=0; i<subsetPds.length; i++ ) {
subsetPds1.add( subsetPds[i] );
}
for ( int i=0; i<dependNames.length; i++ ) {
if ( dependNames[i]!=null ) {
int k= indexOfParameter( pds, dependNames[i] );
if ( k==-1 ) {
logger.log(Level.WARNING, "unable to find parameter: {0}", dependName);
} else {
subsetPds1.add(pds[k]);
pp= pp+","+dependNames[i];
}
}
}
subsetPds= subsetPds1.toArray( new ParamDescription[subsetPds1.size()] );
}
}
pds= subsetPds;
nparam= pds.length;
}
// 2043: trim the request to startDate/stopDate. TODO: caching needs to consider this as well.
DatumRange startStopDate= null;
try {
startStopDate= DatumRangeUtil.parseTimeRange( info.getString("startDate") + "/"+info.getString("stopDate") );
if ( tr.intersects( startStopDate ) ) {
tr= DatumRangeUtil.sloppyIntersection( tr, startStopDate );
} else {
if ( tr.max().lt(startStopDate.min() ) ) {
throw new NoDataInIntervalException("info startDate ("+info.getString("startDate")+") is after requested time range ("+tr+")" );
} else {
throw new NoDataInIntervalException("info stopDate ("+info.getString("stopDate")+") is before requested time range ("+tr+")");
}
}
//TODO: caching when enabled may round out to day boundaries.
} catch ( ParseException ex ) {
logger.log(Level.INFO, "unable to parse startDate/stopDate: {0}", ex.getMessage());
} catch ( NullPointerException ex ) {
logger.info("startDate and stopDate was missing");
}
URL url= HapiServer.getDataURL( server.toURL(), id, tr, pp );
if ( !format.equals("csv") ) {
url= new URL( url+"&format="+format );
}
logger.log(Level.FINE, "getDataSet {0}", url.toString());
int[] nfields= new int[nparam];
for ( int i=0; i<nparam; i++ ) {
if ( pds[i].size.length==0 || ( pds[i].size.length==1 && pds[i].size[0]==1 ) ) {
nfields[i]= 1;
} else {
nfields[i]= DataSetUtil.product(pds[i].size);
}
}
int totalFields= DataSetUtil.sum(nfields);
QDataSet ds;
switch (format) {
case "binary":
ds= getDataSetViaBinary(totalFields, monitor, url, pds,
tr, nparam, nfields, getParam( "cache", "" ) );
break;
case "json":
ds= getDataSetViaJSON(totalFields, monitor, url, pds, tr, nparam, nfields);
break;
default:
boolean useCache= useCache(getParam( "cache", "" ));
if ( useCache ) { // round out to day boundaries, and load each day separately.
logger.finer("useCache, so make daily requests to form granules");
Datum minMidnight= TimeUtil.prevMidnight( tr.min() );
Datum maxMidnight= TimeUtil.nextMidnight( tr.max() );
tr= new DatumRange( minMidnight, maxMidnight );
tr= DatumRangeUtil.sloppyIntersection( tr, startStopDate );
Datum midnight= TimeUtil.prevMidnight( tr.min() );
DatumRange currentDay= new DatumRange( midnight, TimeUtil.next( TimeUtil.DAY, midnight) );
QDataSet dsall= null;
int nday= (int)Math.ceil( tr.width().doubleValue(Units.days) );
if ( nday>1 ) {
monitor.setTaskSize(nday*10);
monitor.started();
}
int iday=0;
while ( currentDay.min().le(tr.max()) ) {
logger.log(Level.FINER, "useCache, request {0}", currentDay);
ProgressMonitor mon1= nday==1 ? monitor : monitor.getSubtaskMonitor( 10*iday, 10*(iday+1), "read "+currentDay );
QDataSet ds1;
try {
DatumRange oneDaysRange= DatumRangeUtil.sloppyIntersection( currentDay, startStopDate );
if ( oneDaysRange.width().value()>0 ) {
URL url1= replaceTimeRangeURL(url,oneDaysRange,vers);
ds1 = getDataSetViaCsv(totalFields, mon1, url1, pds,
oneDaysRange, nparam, nfields, getParam( "cache", "" ) );
if ( ds1.length()>0 ) {
dsall= Ops.append( dsall, ds1 );
}
}
} catch ( NoDataInIntervalException ex ) {
if ( ! FileSystem.settings().isOffline() ) {
throw ex;
} else {
logger.log(Level.FINE, "no granule found for day, but we are offline: {0}", currentDay);
}
}
currentDay= currentDay.next();
iday++;
}
if ( dsall==null ) {
logger.info("no records found");
return null;
}
logger.finer("done useCache, so make daily requests to form granules");
ds= dsall;
ds= Ops.putProperty( ds, QDataSet.UNITS, null ); // kludge, otherwise time units are messed up. TODO: who puts unit here?
} else {
ds= getDataSetViaCsv(totalFields, monitor, url, pds, tr, nparam, nfields, getParam( "cache", "" ) );
}
break;
}
if ( ds.length()==0 ) {
monitor.finished();
throw new NoDataInIntervalException("no records found");
}
ds = repackage(ds,pds,null);
// look up colors for nominal data
if ( ds.rank()==1 && pds.length>1 && ( pds[1].units instanceof EnumerationUnits ) && cadence!=null ) {
JSONObject paramInfo= pds[1].parameter;
if ( paramInfo.has( HapiUtil.KEY_X_COLOR_LOOKUP ) ) {
JSONObject colorLookup= paramInfo.getJSONObject( HapiUtil.KEY_X_COLOR_LOOKUP );
QDataSet dep0= (QDataSet) ds.property(QDataSet.DEPEND_0);
QDataSet dep0Min= Ops.subtract( dep0, cadence.divide(2) );
QDataSet dep0Max= Ops.add( dep0, cadence.divide(2) );
IDataSet colors= IDataSet.createRank1(ds.length());
Iterator iter= colorLookup.keys();
Map<Pattern,Color> pelookUp= new HashMap<>();
while ( iter.hasNext() ) {
String k= (String)iter.next();
try {
Pattern p= Pattern.compile(k);
pelookUp.put( p, ColorUtil.decodeColor(colorLookup.getString(k)) );
} catch ( PatternSyntaxException e ) {
logger.log( Level.WARNING, e.getMessage(), e );
}
}
EnumerationUnits eu= (EnumerationUnits)pds[1].units;
for ( int i=0; i<ds.length(); i++ ) {
Datum d= eu.createDatum(ds.slice(i).svalue());
Color c= lookupColor( pelookUp, d );
colors.putValue( i, c.getRGB() );
}
ds= Ops.bundle( dep0Min, dep0Max, colors, ds );
}
}
Units u= (Units) ds.property(QDataSet.UNITS);
if ( u!=null && u.toString().trim().length()>0 ) {
String l= (String) ds.property(QDataSet.LABEL);
if ( l==null ) {
ds= Ops.putProperty( ds, QDataSet.LABEL, "%{UNITS}" );
} else {
ds= Ops.putProperty( ds, QDataSet.LABEL, l.trim() + " (%{UNITS})" );
}
}
// install a cacheTag. The following code assumes depend_0 is mutable.
QDataSet xds= (QDataSet) ds.property(QDataSet.DEPEND_0);
if ( xds==null && ( UnitsUtil.isTimeLocation( SemanticOps.getUnits(ds) ) ) ) {
xds= ds;
}
if ( timeStampLocation.equalsIgnoreCase("BEGIN") || timeStampLocation.equalsIgnoreCase("END" ) ) {
if ( cadence==null ) {
cadence= DataSetUtil.asDatum( DataSetUtil.guessCadenceNew( xds, null ) );
}
if ( cadence!=null ) {
if ( timeStampLocation.equalsIgnoreCase("BEGIN") ) {
xds= Ops.add( xds, cadence.divide(2) );
} else if ( timeStampLocation.equalsIgnoreCase("END") ) {
xds= Ops.subtract( xds, cadence.divide(2) );
}
} else {
logger.info("timetags are identified as BEGIN, but cadence was not available to center the data");
}
}
if ( xds!=null ) {
((MutablePropertyDataSet)xds).putProperty(QDataSet.CACHE_TAG, new CacheTag(tr,null) );
}
monitor.setTaskProgress(100);
monitor.finished();
return ds;
}
private static boolean useCache( String useCacheUriParam ) {
boolean useCache= HapiServer.useCache();
String cacheParam= useCacheUriParam;
if ( cacheParam.equals("F") ) {
useCache= false;
}
return useCache;
}
private static AbstractLineReader getCsvReader( AbstractLineReader cacheReader, URL url, HttpURLConnection httpConnect, boolean gzip ) throws IOException {
if ( cacheReader!=null ) {
return cacheReader;
} else {
InputStream ins1;
if ( httpConnect!=null ) {
ins1= httpConnect.getInputStream();
} else {
httpConnect= ((HttpURLConnection) url.openConnection());
if ( httpConnect.getResponseCode()==HttpURLConnection.HTTP_MOVED_PERM ||
httpConnect.getResponseCode()==HttpURLConnection.HTTP_MOVED_TEMP ) {
String newLocation = httpConnect.getHeaderField("Location");
if ( !newLocation.contains("?") ) {
String args= url.getQuery();
newLocation= newLocation + args;
}
url= new URL( newLocation );
httpConnect= ((HttpURLConnection) url.openConnection());
}
ins1= httpConnect.getInputStream();
}
if ( gzip ) {
ins1 = new GZIPInputStream( ins1 );
}
InputStreamReader isread= new InputStreamReader( ins1, HapiServer.UTF8 );
AbstractLineReader result= new SingleFileBufferedReader( new BufferedReader(isread) );
return result;
}
}
/**
* read the interval using CSV.
* @param totalFields
* @param monitor
* @param url
* @param pds
* @param tr
* @param nparam
* @param nfields
* @param useCacheUriParam
* @return
* @throws IllegalArgumentException
* @throws Exception
* @throws IOException
*/
public static QDataSet getDataSetViaCsv(int totalFields, ProgressMonitor monitor,
URL url, ParamDescription[] pds, DatumRange tr,
int nparam, int[] nfields, String useCacheUriParam ) throws IllegalArgumentException, Exception, IOException {
DataSetBuilder builder= new DataSetBuilder(2,100,totalFields);
monitor.setProgressMessage("reading data");
monitor.setTaskProgress(20);
long t0= System.currentTimeMillis() - 100; // -100 so it updates after receiving first record.
boolean cacheIsEnabled= useCache(useCacheUriParam);
AbstractLineReader cacheReader;
if ( cacheIsEnabled ) { // this branch posts the request, expecting that the server may respond with 304, indicating the cache should be used.
String[] parameters= new String[pds.length];
for ( int i=0; i<pds.length; i++ ) parameters[i]= pds[i].name;
cacheReader= getCsvCacheReader(url, parameters, tr, FileSystem.settings().isOffline(), 0L );
if ( cacheReader!=null ) {
logger.fine("reading from cache");
}
} else {
cacheReader= null;
}
HttpURLConnection httpConnect=null;
boolean gzip=false; // Let Java decompress the stream
if ( cacheReader==null ) {
if ( FileSystem.settings().isOffline() ) {
throw new NoDataInIntervalException("HAPI server is offline.");
//throw new FileSystem.FileSystemOfflineException("file system is offline");
} else {
loggerUrl.log(Level.FINE, "GET {0}", new Object[] { url } );
boolean doAllowGZip= false;
if ( doAllowGZip ) {
httpConnect= (HttpURLConnection)url.openConnection();
httpConnect.setConnectTimeout(FileSystem.settings().getConnectTimeoutMs());
httpConnect.setReadTimeout(FileSystem.settings().getReadTimeoutMs());
httpConnect.setRequestProperty( "Accept-Encoding", "gzip" );
httpConnect= (HttpURLConnection)HttpUtil.checkRedirect(httpConnect); // There's a problem, because it looks like the entire response is read here.
httpConnect.connect();
loggerUrl.log(Level.FINE, "--> {0} {1}", new Object[]{httpConnect.getResponseCode(), httpConnect.getResponseMessage()});
gzip=true;
}
}
} else {
httpConnect= null;
}
//Check to see what time ranges are from entire days, then only call writeToCachedData for these intervals.
Datum midnight= TimeUtil.prevMidnight( tr.min() );
DatumRange currentDay= new DatumRange( midnight, TimeUtil.next( TimeUtil.DAY, midnight) );
boolean completeDay= tr.contains(currentDay);
logger.log(Level.FINER, "parse {0}", cacheReader);
boolean writeDataToCache= cacheIsEnabled && cacheReader==null;
int linenumber=0;
Map<String,Integer> warnings= new LinkedHashMap<>();
String cacheLocation=null;
if ( writeDataToCache ) {
StringBuilder ub= new StringBuilder( url.getProtocol() + "/" + url.getHost() + url.getPath() );
if ( url.getQuery()!=null ) {
String[] querys= url.getQuery().split("\\&");
Pattern p= Pattern.compile("id=(.+)");
for ( String q : querys ) {
Matcher m= p.matcher(q);
if ( m.matches() ) {
ub.append("/").append(m.group(1));
break;
}
}
cacheLocation= ub.toString();
} else {
throw new IllegalArgumentException("query must be specified, implementation error");
}
}
try ( AbstractLineReader in = getCsvReader(cacheReader,url,httpConnect,gzip) ) {
String line= in.readLine();
if ( line!=null && line.startsWith("{") ) {
logger.log(Level.WARNING, "data response starts with \"{\", not data!");
StringBuilder sb= new StringBuilder();
while ( line!=null ) {
sb.append(line);
line= in.readLine(); // TODO: risk of reading entire data response.
}
String jsonResponse= sb.toString();
JSONObject jo= new JSONObject(jsonResponse);
if ( !jo.has("HAPI") ) throw new IllegalArgumentException("Expected HAPI version in JSON response");
String vers= jo.getString("HAPI");
if ( !( vers.startsWith("2") || vers.startsWith("1") ) ) {
String msg= "Only version 1 and 2 servers can have JSON response where CSV was expected";
if ( jsonResponse.length()<400 ) {
msg= msg + ": "+jsonResponse;
}
throw new IllegalArgumentException(msg);
}
if ( !jo.has("status") ) throw new IllegalArgumentException("Expected status in JSON response");
JSONObject status= jo.getJSONObject("status");
if ( status.getInt("code")==1201 ) {
throw new NoDataInIntervalException("server responds: "+status.getString("message") );
} else {
throw new IllegalArgumentException("unsupported server response "+status.getInt("code")+": "+status.getString("message"));
}
}
if ( line!=null && line.length()>0 && !Character.isDigit( line.charAt(0) ) ) {
logger.log(Level.WARNING, "expected first character to be a digit (first of ISO8601 time), but got \"{0}\"", line);
}
while ( line!=null ) {
linenumber++;
String[] ss= lineSplit(line);
if ( ss.length!=totalFields ) {
if ( line.trim().length()==0 ) {
logger.log(Level.WARNING, "expected {0} fields, got empty line at line {1}", new Object[]{totalFields,linenumber});
line= in.readLine();
continue;
} else {
logger.log(Level.WARNING, "expected {0} fields, got {1} at line {2}", new Object[]{totalFields, ss.length,linenumber});
if ( line.trim().startsWith("{") ) {
throw new IllegalArgumentException( String.format( "expected %d fields, got \"{\" at line %d", new Object[]{totalFields, linenumber} ) );
} else {
throw new IllegalArgumentException( String.format( "expected %d fields, got %d at line %d", new Object[]{totalFields, ss.length,linenumber} ) );
}
}
}
int ifield=0;
Datum xx;
try {
xx= pds[ifield].units.parse(ss[ifield]);
if ( System.currentTimeMillis()-t0 > 100 ) {
monitor.setProgressMessage("reading "+xx);
t0= System.currentTimeMillis();
double d= DatumRangeUtil.normalize( tr, xx );
monitor.setTaskProgress( 20 + (int)( 75 * d ) );
if ( monitor.isCancelled() )
throw new CancelledOperationException("cancel was pressed");
}
} catch ( ParseException ex ) {
if ( !warnings.containsKey( WARNING_TIME_MALFORMED ) ) {
logger.log(Level.INFO, "malformed time: {0}", ss[ifield]);
warnings.put( WARNING_TIME_MALFORMED, 1 );
} else {
warnings.put( WARNING_TIME_MALFORMED, warnings.get( WARNING_TIME_MALFORMED ) + 1 );
}
line= in.readLine();
continue;
}
// if a cache file is opened for the previous day, then close the file for the day, gzipping it.
if ( writeDataToCache ) {
if ( !currentDay.contains(xx) && tr.intersects(currentDay) && completeDay ) {
// https://sourceforge.net/p/autoplot/bugs/1968/ HAPI caching must not cache after "modificationDate" or partial days remain in cache
if ( pds[0].modifiedDateMillis==0 || currentDay.middle().doubleValue(Units.ms1970) - pds[0].modifiedDateMillis <= 0 ) {
writeToCsvCachedDataFinish(cacheLocation, pds, currentDay.middle() );
} else {
logger.fine("data after modification date is not cached.");
}
}
while ( !currentDay.contains(xx) && tr.intersects(currentDay ) ) { // find the new current day, writing empty files for any missing days.
currentDay= currentDay.next();
completeDay= tr.contains(currentDay);
if ( !currentDay.contains(xx) && tr.intersects(currentDay ) ) {
if ( pds[0].modifiedDateMillis==0 || currentDay.middle().doubleValue(Units.ms1970) - pds[0].modifiedDateMillis <= 0 ) {
// put empty file which is placeholder.
writeToCsvCachedDataFinish(cacheLocation, pds, currentDay.middle() );
}
}
}
if ( !currentDay.contains(xx) ) {
if ( !warnings.containsKey( WARNING_TIME_ORDER ) ) {
logger.log(Level.INFO, "something's gone wrong, perhaps out-of-order timetags: {0}", xx);
warnings.put( WARNING_TIME_ORDER, 1 );
} else {
warnings.put( WARNING_TIME_ORDER, warnings.get( WARNING_TIME_ORDER ) + 1 );
}
completeDay= false;
}
if ( completeDay ) {
if ( pds[0].modifiedDateMillis==0 || xx.doubleValue(Units.ms1970) - pds[0].modifiedDateMillis <= 0 ) {
writeToCsvCachedData(cacheLocation, pds, xx, ss, false );
}
}
}
builder.putValue( -1, ifield, xx );
ifield++;
for ( int i=1; i<nparam; i++ ) { // nparam is number of parameters, which may have multiple fields.
for ( int j=0; j<nfields[i]; j++ ) {
try {
String s= ss[ifield];
if ( pds[i].units instanceof EnumerationUnits ) {
builder.putValue( -1, ifield, ((EnumerationUnits)pds[i].units).createDatum(s) );
} else {
builder.putValue( -1, ifield, pds[i].units.parse(s) );
}
} catch ( ParseException ex ) {
builder.putValue( -1, ifield, pds[i].fillValue );
pds[i].hasFill= true;
}
ifield++;
}
}
builder.nextRecord();
line= in.readLine();
}
if ( writeDataToCache ) {
while ( completeDay && tr.intersects(currentDay) ) {
if ( pds[0].modifiedDateMillis==0 || currentDay.middle().doubleValue(Units.ms1970) - pds[0].modifiedDateMillis <= 0 ) {
// put empty file which is placeholder.
writeToCsvCachedDataFinish(cacheLocation, pds, currentDay.middle() );
}
currentDay= currentDay.next();
completeDay= tr.contains(currentDay);
}
}
} catch ( IOException e ) {
logger.log( Level.WARNING, e.getMessage(), e );
monitor.finished();
if ( httpConnect!=null ) {
logger.log(Level.WARNING, "IOException when trying to read {0}", httpConnect.getURL());
throw new IOException( httpConnect.getURL() + " results in\n"+String.valueOf(httpConnect.getResponseCode())+": "+httpConnect.getResponseMessage() );
} else {
throw e;
}
} catch ( Exception e ) {
logger.log( Level.WARNING, e.getMessage(), e );
monitor.finished();
throw e;
} finally {
if ( httpConnect!=null ) httpConnect.disconnect();
}
if ( !warnings.isEmpty() ) {
logger.warning("Warnings encountered:");
for ( Entry<String,Integer> e: warnings.entrySet() ) {
logger.log(Level.WARNING, " {0} ({1} times)", new Object[]{e.getKey(), e.getValue()});
}
}
logger.log(Level.FINER, "done parsing {0}", cacheReader);
if ( cacheReader!=null ) {
Map<String,String> cacheFiles= new HashMap<>();
cacheFiles.put( "cached", "true" );
builder.putProperty( QDataSet.USER_PROPERTIES, cacheFiles );
}
monitor.setTaskProgress(95);
QDataSet ds= builder.getDataSet();
return ds;
}
private static TransferType getTimeTransferType( ParamDescription pdsi ) {
final Units u= pdsi.units;
final int length= pdsi.length;
final byte[] bytes= new byte[length];
return new TransferType() {
@Override
public void write(double d, ByteBuffer buffer) {
}
@Override
public double read(ByteBuffer buffer) {
buffer.get(bytes);
//buf2.get(bytes);
String s= new String( bytes );
Datum d= ((EnumerationUnits)u).createDatum(s);
return d.doubleValue(u);
}
@Override
public int sizeBytes() {
return length;
}
@Override
public boolean isAscii() {
return false;
}
@Override
public String name() {
return "string"+length;
}
};
}
/**
* read the interval using binary.
* @param totalFields
* @param monitor
* @param url
* @param pds
* @param tr
* @param nparam
* @param nfields
* @param useCacheUriParam
* @return
* @throws IllegalArgumentException
* @throws Exception
* @throws IOException
*/
public static QDataSet getDataSetViaBinary(int totalFields, ProgressMonitor monitor, URL url,
ParamDescription[] pds, DatumRange tr,
int nparam, int[] nfields, String useCacheUriParam ) throws IllegalArgumentException, Exception, IOException {
DataSetBuilder builder = new DataSetBuilder(2, 100, totalFields);
int icol=0;
for ( int i=0; i<pds.length; i++ ) {
ParamDescription pds1= pds[i];
for ( int j=0; j<pds1.nFields; j++ ) {
builder.setUnits( icol, pds1.units );
icol++;
}
}
monitor.setProgressMessage("reading data");
monitor.setTaskProgress(20);
long t0 = System.currentTimeMillis() - 100; // -100 so it updates after receiving first record.
boolean cacheIsEnabled= useCache(useCacheUriParam);
AbstractBinaryRecordReader cacheReader;
if ( cacheIsEnabled ) { // this branch posts the request, expecting that the server may respond with 304, indicating the cache should be used.
String[] parameters= new String[pds.length];
for ( int i=0; i<pds.length; i++ ) parameters[i]= pds[i].name;
cacheReader= getBinaryCacheReader( url, parameters, tr, FileSystem.settings().isOffline(), 0L );
if ( cacheReader!=null ) {
logger.fine("reading from cache");
}
} else {
cacheReader= null;
}
HttpURLConnection httpConnect;
if ( cacheReader==null ) {
if ( FileSystem.settings().isOffline() ) {
throw new NoDataInIntervalException("HAPI server is offline.");
//throw new FileSystem.FileSystemOfflineException("file system is offline");
} else {
loggerUrl.log(Level.FINE, "GET {0}", new Object[] { url } );
httpConnect= (HttpURLConnection)url.openConnection();
httpConnect.setConnectTimeout(FileSystem.settings().getConnectTimeoutMs());
httpConnect.setReadTimeout(FileSystem.settings().getReadTimeoutMs());
httpConnect.setRequestProperty( "Accept-Encoding", "gzip" );
httpConnect= (HttpURLConnection)HttpUtil.checkRedirect(httpConnect);
httpConnect.connect();
loggerUrl.log(Level.FINE, "--> {0} {1}", new Object[]{httpConnect.getResponseCode(), httpConnect.getResponseMessage()});
}
} else {
httpConnect= null;
}
//Check to see what time ranges are from entire days, then only call writeToCachedData for these intervals.
Datum midnight= TimeUtil.prevMidnight( tr.min() );
DatumRange currentDay= new DatumRange( midnight, TimeUtil.next( TimeUtil.DAY, midnight) );
boolean completeDay= tr.contains(currentDay);
boolean gzip = cacheReader==null ? "gzip".equals( httpConnect.getContentEncoding() ) : false;
boolean writeDataToCache= cacheIsEnabled && cacheReader==null;
String cacheLocation=null;
if ( writeDataToCache ) {
StringBuilder ub= new StringBuilder( url.getProtocol() + "/" + url.getHost() + url.getPath() );
if ( url.getQuery()!=null ) {
String[] querys= url.getQuery().split("\\&");
Pattern p= Pattern.compile("id=(.+)");
for ( String q : querys ) {
Matcher m= p.matcher(q);
if ( m.matches() ) {
ub.append("/").append(m.group(1));
break;
}
}
cacheLocation= ub.toString();
} else {
throw new IllegalArgumentException("query must be specified, implementation error");
}
}
int recordLengthBytes = 0;
TransferType[] tts = new TransferType[pds.length];
for (int i = 0; i < pds.length; i++) {
if (pds[i].type.startsWith("time")) {
recordLengthBytes += Integer.parseInt(pds[i].type.substring(4));
tts[i] = TransferType.getForName(pds[i].type, Collections.singletonMap(QDataSet.UNITS, (Object)pds[i].units));
} else if (pds[i].type.startsWith("string")) {
recordLengthBytes += pds[i].length;
tts[i] = getTimeTransferType(pds[i]);
} else {
Object type= pds[i].type;
recordLengthBytes += BufferDataSet.byteCount(type) * DataSetUtil.product(pds[i].size);
tts[i] = TransferType.getForName( type.toString(), Collections.singletonMap(QDataSet.UNITS, (Object)pds[i].units) );
}
if ( tts[i]==null ) {
throw new IllegalArgumentException("unable to identify transfer type for \""+pds[i].type+"\"");
}
}
totalFields= DataSetUtil.sum(nfields);
double[] result = new double[totalFields];
int recordnumber=0;
Map<String,Integer> warnings= new LinkedHashMap<>();
try ( AbstractBinaryRecordReader in = ( cacheReader!=null ? cacheReader :
new InputStreamBinaryRecordReader( gzip ? new GZIPInputStream(httpConnect.getInputStream()) : httpConnect.getInputStream() ) ) ) {
ByteBuffer buf = TransferType.allocate( recordLengthBytes,ByteOrder.LITTLE_ENDIAN );
int bytesRead = in.readRecord(buf);
if ( bytesRead>0 ) {
if ( (char)buf.get(0)=='{' ) {
logger.log(Level.WARNING, "data response starts with \"{\", not data!");
StringBuilder sb= new StringBuilder();
while ( bytesRead>-1 ) {
if ( buf.position()<buf.limit() ) {
while ( bytesRead>-1 ) {
bytesRead = in.readRecord(buf);
}
}
buf.flip();
sb.append( new String( buf.array(), 0, buf.limit(), "UTF-8" ) );
}
String jsonResponse= sb.toString();
JSONObject jo= new JSONObject(jsonResponse);
if ( !jo.has("HAPI") ) throw new IllegalArgumentException("Expected HAPI version in JSON response");
String vers= jo.getString("HAPI");
if ( !( vers.startsWith("2") || vers.startsWith("1") ) ) {
String msg= "Only version 1 and 2 servers can have JSON response where CSV was expected";
if ( jsonResponse.length()<400 ) {
msg= msg + ": "+jsonResponse;
}
throw new IllegalArgumentException(msg);
}
if ( !jo.has("status") ) throw new IllegalArgumentException("Expected status in JSON response");
JSONObject status= jo.getJSONObject("status");
if ( status.getInt("code")==1201 ) {
throw new NoDataInIntervalException("server responds: "+status.getString("message") );
} else {
throw new IllegalArgumentException("unsupported server response "+status.getInt("code")+": "+status.getString("message"));
}
}
}
while (bytesRead != -1) {
recordnumber++;
logger.log(Level.FINER, "read record number {0}", recordnumber);
buf.flip();
int ifield = 0;
for (int i = 0; i < pds.length; i++) {
for (int j = 0; j < nfields[i]; j++) {
result[ifield] = tts[i].read(buf);
ifield++;
}
}
if (ifield != totalFields) {
logger.log(Level.WARNING, "expected {0} got {1}", new Object[]{totalFields, ifield});
}
// copy the data from double array into the builder.
ifield= 0;
Datum xx;
try {
xx = pds[0].units.createDatum(result[0]);
if (System.currentTimeMillis() - t0 > 100) {
monitor.setProgressMessage("reading " + xx);
t0 = System.currentTimeMillis();
double d = DatumRangeUtil.normalize(tr, xx);
monitor.setTaskProgress(20 + (int) (75 * d));
if ( monitor.isCancelled() )
throw new CancelledOperationException("cancel was pressed");
}
} catch ( RuntimeException ex ) {
if ( !warnings.containsKey( WARNING_TIME_MALFORMED ) ) {
logger.log(Level.INFO, "malformed time");
warnings.put( WARNING_TIME_MALFORMED, 1 );
} else {
warnings.put( WARNING_TIME_MALFORMED, warnings.get( WARNING_TIME_MALFORMED ) + 1 );
}
buf.flip();
bytesRead = in.readRecord(buf);
continue;
}
// if a cache file is opened for the previous day, then close the file for the day, gzipping it.
if ( writeDataToCache ) {
if ( !currentDay.contains(xx) && tr.intersects(currentDay) && completeDay ) {
// https://sourceforge.net/p/autoplot/bugs/1968/ HAPI caching must not cache after "modificationDate" or partial days remain in cache
if ( pds[0].modifiedDateMillis==0 || currentDay.middle().doubleValue(Units.ms1970) - pds[0].modifiedDateMillis <= 0 ) {
writeToBinaryCachedDataFinish( cacheLocation, pds, currentDay.middle(), false );
} else {
logger.fine("data after modification date is not cached.");
}
}
while ( !currentDay.contains(xx) && tr.intersects(currentDay ) ) { // find the new current day, writing empty files for any missing days.
currentDay= currentDay.next();
completeDay= tr.contains(currentDay);
if ( !currentDay.contains(xx) && tr.intersects(currentDay ) ) {
if ( pds[0].modifiedDateMillis==0 || currentDay.middle().doubleValue(Units.ms1970) - pds[0].modifiedDateMillis <= 0 ) {
// put empty file which is placeholder.
writeToBinaryCachedDataFinish( cacheLocation, pds, currentDay.middle(), false );
}
}
}
}
if ( !currentDay.contains(xx) ) {
if ( !warnings.containsKey( WARNING_TIME_ORDER ) ) {
logger.log(Level.INFO, "something's gone wrong, perhaps out-of-order timetags: {0}", xx);
warnings.put( WARNING_TIME_ORDER, 1 );
} else {
warnings.put( WARNING_TIME_ORDER, warnings.get( WARNING_TIME_ORDER ) + 1 );
}
completeDay= false;
}
if ( writeDataToCache ) {
if ( completeDay ) {
if ( pds[0].modifiedDateMillis==0 || xx.doubleValue(Units.ms1970) - pds[0].modifiedDateMillis <= 0 ) {
buf.flip();
writeToBinaryCachedData(cacheLocation, pds, xx, buf );
}
}
}
builder.putValue(-1, ifield, xx);
ifield++;
for (int i = 1; i < nparam; i++) { // nparam is number of parameters, which may have multiple fields.
for (int j = 0; j < nfields[i]; j++) {
builder.putValue(-1, ifield, result[ifield]);
//TODO: fill?
ifield++;
}
}
builder.nextRecord();
buf.flip();
bytesRead = in.readRecord(buf);
}
if ( writeDataToCache ) {
while ( completeDay && tr.intersects(currentDay) ) {
if ( pds[0].modifiedDateMillis==0 || currentDay.middle().doubleValue(Units.ms1970) - pds[0].modifiedDateMillis <= 0 ) {
// put empty file which is placeholder.
writeToBinaryCachedDataFinish(null, pds, currentDay.middle(), false );
}
currentDay= currentDay.next();
completeDay= tr.contains(currentDay);
}
}
} catch (IOException e) {
logger.log( Level.WARNING, e.getMessage(), e );
monitor.finished();
throw new IOException(String.valueOf(httpConnect.getResponseCode()) + ":" + httpConnect.getResponseMessage());
} catch (Exception e) {
logger.log( Level.WARNING, e.getMessage(), e );
monitor.finished();
throw e;
} finally {
if ( httpConnect!=null ) httpConnect.disconnect();
}
if ( cacheReader!=null ) {
Map<String,String> cacheFiles= new HashMap<>();
cacheFiles.put( "cached", "true" );
builder.putProperty( QDataSet.USER_PROPERTIES, cacheFiles );
}
monitor.setTaskProgress(95);
QDataSet ds = builder.getDataSet();
return ds;
}
/**
* read data embedded within a JSON response. This current reads in the entire JSON document,
* but the final version should use a streaming JSON library.
* @param monitor
* @return the dataset.
* @throws Exception
*/
private static QDataSet getDataSetViaJSON( int totalFields, ProgressMonitor monitor, URL url, ParamDescription[] pds, DatumRange tr, int nparam, int[] nfields) throws IllegalArgumentException, Exception, IOException {
monitor.started();
monitor.setProgressMessage("server is preparing data");
long t0= System.currentTimeMillis() - 100; // -100 so it updates after receiving first record.
int lineNum=0;
StringBuilder builder= new StringBuilder();
logger.log(Level.FINE, "getDocument {0}", url.toString());
loggerUrl.log(Level.FINE, "GET {0}", new Object[] { url } );
HttpURLConnection httpConnect= ((HttpURLConnection)url.openConnection());
httpConnect.setConnectTimeout(FileSystem.settings().getConnectTimeoutMs());
httpConnect.setReadTimeout(FileSystem.settings().getReadTimeoutMs());
httpConnect= (HttpURLConnection) HttpUtil.checkRedirect(httpConnect);
loggerUrl.log(Level.FINE, "--> {0} {1}", new Object[]{httpConnect.getResponseCode(), httpConnect.getResponseMessage()});
try ( BufferedReader in= new BufferedReader(
new InputStreamReader( httpConnect.getInputStream(), HapiServer.UTF8 ) ) ) {
String line= in.readLine();
lineNum++;
while ( line!=null ) {
if ( System.currentTimeMillis()-t0 > 100 ) {
monitor.setProgressMessage("reading line "+lineNum);
t0= System.currentTimeMillis();
}
//if ( line.startsWith("{ \"data\" :") ) { // TODO: kludge for Jon's server
// in.readLine();
// line= in.readLine();
//}
builder.append(line);
line= in.readLine();
}
} catch ( IOException ex ) {
ByteArrayOutputStream baos= new ByteArrayOutputStream();
FileSystemUtil.copyStream( httpConnect.getErrorStream(), baos, new NullProgressMonitor() );
String s= baos.toString("UTF-8");
if ( s.contains("No data available") ) {
logger.log(Level.FINE, "No data available, server responded with {0}: {1}", new Object[]{httpConnect.getResponseCode(), httpConnect.getResponseMessage()});
throw new NoDataInIntervalException("No data available");
} else {
if ( s.length()<256 ) {
throw new IOException( ex.getMessage() + ": "+s );
} else {
throw ex;
}
}
}
httpConnect.disconnect(); // See unix tcptrack which shows there are many connections to the server. jbf@gardenhousepi:~ $ sudo tcptrack -i eth0
monitor.setProgressMessage("parsing data");
JSONObject jo= new JSONObject(builder.toString());
JSONArray data= jo.getJSONArray("data");
DataSetBuilder build= new DataSetBuilder( 2, data.length(), totalFields );
for ( int i=0; i<data.length(); i++ ) {
int ipd=0;
int ifield=0;
JSONArray record= data.getJSONArray(i);
for ( ParamDescription pd: pds ) {
if ( nfields[ipd]>1 ) {
JSONArray fields= record.getJSONArray(ipd);
int nf= nfields[ipd];
int lastField= nf+ifield;
for ( ; ifield<lastField; ifield++ ) {
build.putValue( -1, ifield, pd.units.parse( fields.getString(ipd) ) );
}
} else {
build.putValue( -1, ifield, pd.units.parse( record.getString(ipd) ) );
}
ifield+= nfields[ipd];
ipd++;
}
build.nextRecord();
}
QDataSet result;
result= build.getDataSet();
return result;
}
/**
* TODO: commas within quotes. remove extra whitespace.
* @param line
* @return
*/
private static String[] lineSplit( String line ) {
String[] ss= line.split(",",-2);
for ( int i=0; i<ss.length; i++ ) {
String s= ss[i].trim();
if ( s.startsWith("\"") && s.endsWith("\"") ) {
s= s.substring(1,s.length()-1);
}
ss[i]= s;
}
return ss;
}
/**
* return the folder containing data for this id.
* @param url the hapi URL, such as http://jfaden.net/HapiServerDemo/hapi
* @param id the ID, such as "Iowa City Conditions"
* @return the folder containing the cache.
*/
public static File cacheFolder( URL url, String id ) {
String cache= getHapiCache();
String dsroot= cache + "/" + url.getProtocol() + "/" + url.getHost() + "/" + url.getPath() + "/" + id.replaceAll(" ","+");
return new File( dsroot );
}
/**
* return the files that would be used for these parameters and time interval.
* This is repeated code from getCacheReader.
* @param url HAPI data request URL
* @param id identifier for the dataset on the server.
* @param parameters
* @param timeRange
* @param format
* @see #getCsvCacheReader(java.net.URL, java.lang.String[], org.das2.datum.DatumRange, boolean, long)
* @return
*/
protected static LinkedHashMap<String,DatumRange> getCacheFiles( URL url, String id, String[] parameters, DatumRange timeRange, String format ) {
String s= getHapiCache();
if ( s.endsWith("/") ) s= s.substring(0,s.length()-1);
String u= url.getProtocol() + "/" + url.getHost() + url.getPath();
u= u + "/data/" + id.replaceAll(" ","+");
LinkedHashMap<String,DatumRange> result= new LinkedHashMap<>();
try {
for (String parameter : parameters) {
String theFile= s + "/"+ u ;
FileStorageModel fsm = FileStorageModel.create(FileSystem.create( "file:" +theFile ), "$Y/$m/$Y$m$d." + parameter + "."+format+".gz");
String[] ff= fsm.getNamesFor(null);
for (String ff1 : ff) {
DatumRange tr1= fsm.getRangeFor(ff1);
if ( timeRange==null || timeRange.intersects(tr1)) {
result.put(ff1,tr1);
}
}
}
} catch ( IOException | IllegalArgumentException ex) {
logger.log(Level.FINE, "exception in cache", ex );
return null;
}
return result;
}
private static AbstractLineReader calculateCsvCacheReader( File[][] files ) {
ConcatenateBufferedReader cacheReader= new ConcatenateBufferedReader();
for (File[] file1 : files) {
boolean haveAllForDay= true;
if (haveAllForDay) {
PasteBufferedReader r1= new PasteBufferedReader();
r1.setDelim(',');
for (File file : file1) {
try {
FileInputStream fin = new FileInputStream(file);
InputStreamReader read= new InputStreamReader(fin,HapiServer.UTF8);
BufferedReader buff= new BufferedReader(read);
r1.pasteBufferedReader(
new SingleFileBufferedReader(
buff ) );
}catch ( IOException ex ) {
logger.log( Level.SEVERE, ex.getMessage(), ex );
return null;
}
}
cacheReader.concatenateBufferedReader(r1);
}
}
return cacheReader;
}
private static AbstractBinaryRecordReader calculateBinaryCacheReader( File[][] files ) {
ConcatenateBinaryRecordReader cacheReader= new ConcatenateBinaryRecordReader();
for (File[] file : files) {
boolean haveAllForDay= true;
if (haveAllForDay) {
PasteBinaryRecordReader r1= new PasteBinaryRecordReader();
for (File oneDayOneParam : file) {
try {
r1.pasteBufferedReader( new SingleFileBinaryReader( oneDayOneParam ) );
} catch (FileNotFoundException ex) {
Logger.getLogger(HapiDataSource.class.getName()).log(Level.SEVERE, null, ex);
}
}
cacheReader.concatenateReader(r1);
}
}
return cacheReader;
}
/**
* make a connection to the server, expecting that the server might send back a
* 304 indicating the cache files should be used.
* @param url HAPI data request URL
* @param files corresponding files within cache.
* @param lastModified non-zero to indicate time stamp of the oldest file found locally.
* @return null or the cache reader.
* @throws IOException
*/
private static AbstractLineReader maybeGetCsvCacheReader( URL url, File[][] files, long lastModified) throws IOException {
HttpURLConnection httpConnect;
if ( FileSystem.settings().isOffline() ) {
return null;
//throw new FileSystem.FileSystemOfflineException("file system is offline");
} else {
loggerUrl.log(Level.FINE, "GET {0}", new Object[] { url } );
httpConnect= (HttpURLConnection)url.openConnection();
httpConnect.setConnectTimeout(FileSystem.settings().getConnectTimeoutMs());
httpConnect.setReadTimeout(FileSystem.settings().getReadTimeoutMs());
httpConnect.setRequestProperty( "Accept-Encoding", "gzip" );
String s= new SimpleDateFormat("EEE, d MMM yyyy HH:mm:ss z").format(new Date(lastModified));
httpConnect.setRequestProperty( "If-Modified-Since", s );
httpConnect= (HttpURLConnection)HttpUtil.checkRedirect(httpConnect);
httpConnect.connect();
loggerUrl.log(Level.FINE, "--> {0} {1}", new Object[]{httpConnect.getResponseCode(), httpConnect.getResponseMessage()});
}
if ( httpConnect.getResponseCode()==304 ) {
logger.fine("using cache files because server says nothing has changed (304)");
return calculateCsvCacheReader( files );
}
boolean gzip= "gzip".equals( httpConnect.getContentEncoding() );
return new SingleFileBufferedReader( new BufferedReader(
new InputStreamReader( gzip ?
new GZIPInputStream( httpConnect.getInputStream() )
: httpConnect.getInputStream(), HapiServer.UTF8 ) ) );
}
/**
* See if it's possible to create a Reader based on the contents of the HAPI
* cache. null is returned when cached files cannot be used.
* @param url URL data request URL, where the time range parameters are ignored.
* @param parameters the parameters to load, from ParameterDescription.name
* @param timeRange the span to cover. This should be from midnight-to-midnight.
* @param offline if true, we are offline and anything available should be used.
* @param lastModified
* @return null or the reader to use.
* @see HapiServer#cacheAgeLimitMillis()
* @see #getCacheFiles which has copied code. TODO: fix this.
*/
private static AbstractLineReader getCsvCacheReader( URL url, String[] parameters, DatumRange timeRange, boolean offline, long lastModified) {
String s= getHapiCache();
if ( s.endsWith("/") ) s= s.substring(0,s.length()-1);
StringBuilder ub= new StringBuilder( url.getProtocol() + "/" + url.getHost() + "/" + url.getPath() );
if ( url.getQuery()!=null ) {
String[] querys= url.getQuery().split("\\&");
Pattern p= Pattern.compile("id=(.+)");
for ( String q : querys ) {
Matcher m= p.matcher(q);
if ( m.matches() ) {
ub.append("/").append(m.group(1));
break;
}
}
} else {
throw new IllegalArgumentException("query must be specified, implementation error");
}
DatumRange aday= TimeUtil.dayContaining(timeRange.min());
List<DatumRange> trs= DatumRangeUtil.generateList( timeRange, aday );
// which granules are available for all parameters?
boolean[][] hits= new boolean[trs.size()][parameters.length];
File[][] files= new File[trs.size()][parameters.length];
boolean staleCacheFiles;
String u= ub.toString();
if ( ! new File( s + "/" + u ).exists() ) {
return null;
}
try {
FileSystem fs= FileSystem.create( "file:" + s + "/"+ u );
staleCacheFiles= getCacheFilesWithTime( trs, parameters, fs, "csv", hits, files, offline, lastModified );
} catch ( IOException | IllegalArgumentException ex) {
logger.log(Level.FINE, "exception in cache", ex );
return null;
}
if ( staleCacheFiles && !offline ) {
logger.fine("old cache files found, but new data is available and accessible");
return null;
}
boolean haveSomething= false;
boolean haveAll= true;
for ( int i=0; i<trs.size(); i++ ) {
for ( int j=0; j<parameters.length; j++ ) {
if ( hits[i][j]==false ) {
haveAll= false;
}
}
if ( haveAll ) {
haveSomething= true;
}
}
if ( !haveAll ) {
checkMissingRange(trs, hits, timeRange);
}
if ( !offline && !haveAll ) {
logger.fine("some cache files missing, but we are on-line and should retrieve all of them");
return null;
}
if ( !haveSomething ) {
logger.fine("no cached data found");
return null;
}
AbstractLineReader result;
long timeStamp= getEarliestTimeStamp(files);
try {
result= maybeGetCsvCacheReader( url, files, timeStamp );
if ( result!=null ) return result;
} catch ( IOException ex ) {
logger.log( Level.WARNING, null, ex );
}
AbstractLineReader cacheReader= calculateCsvCacheReader( files );
return cacheReader;
}
/**
* make a connection to the server, expecting that the server might send back a
* 304 indicating the cache files should be used.
* @param url HAPI data request URL
* @param files corresponding files within cache.
* @param lastModified non-zero to indicate time stamp of the oldest file found locally.
* @return null or the cache reader.
* @throws IOException
*/
private static AbstractBinaryRecordReader maybeGetBinaryCacheReader( URL url, File[][] files, long lastModified) throws IOException {
HttpURLConnection httpConnect;
if ( FileSystem.settings().isOffline() ) {
return null;
//throw new FileSystem.FileSystemOfflineException("file system is offline");
} else {
loggerUrl.log(Level.FINE, "GET {0}", new Object[] { url } );
httpConnect= (HttpURLConnection)url.openConnection();
httpConnect.setConnectTimeout(FileSystem.settings().getConnectTimeoutMs());
httpConnect.setReadTimeout(FileSystem.settings().getReadTimeoutMs());
httpConnect.setRequestProperty( "Accept-Encoding", "gzip" );
String s= new SimpleDateFormat("EEE, d MMM yyyy HH:mm:ss z").format(new Date(lastModified));
httpConnect.setRequestProperty( "If-Modified-Since", s );
httpConnect= (HttpURLConnection)HttpUtil.checkRedirect(httpConnect);
httpConnect.connect();
loggerUrl.log(Level.FINE, "--> {0} {1}", new Object[]{httpConnect.getResponseCode(), httpConnect.getResponseMessage()});
}
if ( httpConnect.getResponseCode()==304 ) {
logger.fine("using cache files because server says nothing has changed (304)");
return calculateBinaryCacheReader( files );
}
boolean gzip= "gzip".equals( httpConnect.getContentEncoding() );
return new InputStreamBinaryRecordReader( gzip ? new GZIPInputStream( httpConnect.getInputStream() ) : httpConnect.getInputStream() );
}
/**
* See if it's possible to create a Reader based on the contents of the HAPI
* cache. null is returned when cached files cannot be used.
* @param url URL data request URL, where the time range parameters are ignored.
* @param parameters the parameters to load, from ParameterDescription.name
* @param timeRange the span to cover. This should be from midnight-to-midnight.
* @param offline if true, we are offline and anything available should be used.
* @param lastModified
* @return null or the reader to use.
* @see HapiServer#cacheAgeLimitMillis()
* @see #getCacheFiles which has copied code. TODO: fix this.
*/
private static AbstractBinaryRecordReader getBinaryCacheReader( URL url, String[] parameters, DatumRange timeRange, boolean offline, long lastModified) {
String s= getHapiCache();
if ( s.endsWith("/") ) s= s.substring(0,s.length()-1);
StringBuilder ub= new StringBuilder( url.getProtocol() + "/" + url.getHost() + "/" + url.getPath() );
if ( url.getQuery()!=null ) {
String[] querys= url.getQuery().split("\\&");
Pattern p= Pattern.compile("id=(.+)");
for ( String q : querys ) {
Matcher m= p.matcher(q);
if ( m.matches() ) {
ub.append("/").append(m.group(1));
break;
}
}
} else {
throw new IllegalArgumentException("query must be specified, implementation error");
}
DatumRange aday= TimeUtil.dayContaining(timeRange.min());
List<DatumRange> trs= DatumRangeUtil.generateList( timeRange, aday );
// which granules are available for all parameters?
boolean[][] hits= new boolean[trs.size()][parameters.length];
File[][] files= new File[trs.size()][parameters.length];
boolean staleCacheFiles;
String u= ub.toString();
if ( ! new File( s + "/" + u ).exists() ) {
return null;
}
try {
FileSystem fs= FileSystem.create( "file:" + s + "/"+ u );
staleCacheFiles= getCacheFilesWithTime( trs, parameters, fs, "binary", hits, files, offline, lastModified );
} catch ( IOException | IllegalArgumentException ex) {
logger.log(Level.FINE, "exception in cache", ex );
return null;
}
if ( staleCacheFiles && !offline ) {
logger.fine("old cache files found, but new data is available and accessible");
return null;
}
boolean haveSomething= false;
boolean haveAll= true;
for ( int i=0; i<trs.size(); i++ ) {
for ( int j=0; j<parameters.length; j++ ) {
if ( hits[i][j]==false ) {
haveAll= false;
}
}
if ( haveAll ) {
haveSomething= true;
}
}
if ( !haveAll ) {
checkMissingRange(trs, hits, timeRange);
}
if ( !offline && !haveAll ) {
logger.fine("some cache files missing, but we are on-line and should retrieve all of them");
return null;
}
if ( !haveSomething ) {
logger.fine("no cached data found");
return null;
}
AbstractBinaryRecordReader result;
long timeStamp= getEarliestTimeStamp(files);
try {
result= maybeGetBinaryCacheReader( url, files, timeStamp );
if ( result!=null ) return result;
} catch ( IOException ex ) {
logger.log( Level.WARNING, null, ex );
}
AbstractBinaryRecordReader cacheReader= calculateBinaryCacheReader( files );
return cacheReader;
}
private static void checkMissingRange(List<DatumRange> trs, boolean[][] hits, DatumRange timeRange) throws IllegalArgumentException {
DatumRange missingRange=null;
for ( int i=0; i<trs.size(); i++ ) {
for ( int j=0; j<hits[i].length; j++ ) {
if ( hits[i][j]==false ) {
if ( missingRange==null ) {
missingRange= trs.get(i);
} else {
missingRange= DatumRangeUtil.union( missingRange, trs.get(i) );
}
}
}
}
logger.log(Level.FINE, "missingRange={0}", missingRange);
if ( missingRange!=null ) {
if ( missingRange.min().equals(timeRange.min()) || missingRange.max().equals(timeRange.max()) ) {
logger.log(Level.FINE, "candidate for new partial cache, only {0} needs to be loaded.", missingRange);
}
}
}
private static long getEarliestTimeStamp( File[][] files ) {
// digest all this into a single timestamp.
// For each day, what is the oldest any of the granules was created?
// For each interval, what was the oldest of any granule?
long timeStamp= Long.MAX_VALUE;
for (File[] files1 : files) {
for (File file1 : files1 ) {
timeStamp = Math.min(timeStamp, file1.lastModified());
}
}
return timeStamp;
}
private static boolean getCacheFilesWithTime(List<DatumRange> trs, String[] parameters, FileSystem fs, String format, boolean[][] hits, File[][] files, boolean offline, long lastModified) throws IOException, IllegalArgumentException {
boolean staleCacheFiles;
long timeNow= System.currentTimeMillis();
staleCacheFiles= false;
for ( int i=0; i<trs.size(); i++ ) {
DatumRange tr= trs.get(i);
for ( int j=0; j<parameters.length; j++ ) {
String parameter= parameters[j];
FileStorageModel fsm = FileStorageModel.create( fs, "$Y/$m/$Y$m$d." + parameter + "." + format );
File[] ff= fsm.getFilesFor(tr);
if ( ff.length==0 ) {
FileStorageModel fsmgz = FileStorageModel.create( fs, "$Y/$m/$Y$m$d." + parameter + "."+format+".gz");
ff= fsmgz.getFilesFor(tr);
}
if ( ff.length>1 ) {
throw new IllegalArgumentException("implementation error, should get just one file per day.");
} else if ( ff.length==0 ) {
hits[i][j]= false;
} else {
File f= ff[0];
long ageMillis= timeNow - f.lastModified();
boolean isStale= ( ageMillis > HapiServer.cacheAgeLimitMillis() );
if ( lastModified>0 ) {
isStale= f.lastModified() < lastModified; // Note FAT32 only has 4sec resolution, which could cause problems.
if ( !isStale ) {
logger.fine("server lastModified indicates the cache file can be used");
} else {
logger.fine("server lastModified indicates the cache file should be updated");
}
}
if ( offline || !isStale ) {
hits[i][j]= true;
files[i][j]= f;
} else {
logger.log(Level.FINE, "cached file is too old to use: {0}", f);
hits[i][j]= false;
staleCacheFiles= true;
}
}
}
}
return staleCacheFiles;
}
protected static Datum parseTime( String stopDate ) throws ParseException {
try {
return Units.ms1970.parse(stopDate);
} catch ( ParseException ex ) {
if ( stopDate.equals("lastday") ) {
stopDate= TimeUtil.prevMidnight( TimeUtil.now() ).toString();
logger.warning("\"lastday\" is not a valid time, and this should be fixed.");
} else if ( stopDate.equals("lasthour") ) {
stopDate= TimeUtil.prev( TimeUtil.HOUR, TimeUtil.now() ).toString();
logger.warning("\"lasthour\" is not a valid time, and this should be fixed.");
} else if ( stopDate.equals("now") ) {
stopDate= TimeUtil.now().toString();
logger.warning("\"now\" is not a valid time, and this should be fixed.");
} else {
throw ex;
}
return TimeUtil.create(stopDate);
}
}
public static ParamDescription[] getParameterDescriptions(JSONObject doc) throws IllegalArgumentException, ParseException, JSONException {
JSONArray parameters= doc.getJSONArray("parameters");
int nparameters= parameters.length();
long modificationDate= 0L;
if ( doc.has("modificationDate") ) {
String s= doc.getString("modificationDate");
Datum d= parseTime(s);
modificationDate= (long)( d.doubleValue(Units.ms1970) );
}
ParamDescription[] pds= new ParamDescription[nparameters];
for ( int i=0; i<nparameters; i++ ) {
final JSONObject jsonObjecti = parameters.getJSONObject(i);
String name= jsonObjecti.getString("name"); // the name of one of the parameters.
logger.log(Level.FINER, "unpacking {0}", name);
if ( name==null ) {
name="name"+i;
logger.log(Level.WARNING, "name not found for {0}th parameter", i );
}
pds[i]= new ParamDescription( name );
pds[i].modifiedDateMillis= modificationDate;
String type;
if ( jsonObjecti.has(HapiUtil.KEY_TYPE) ) {
type= jsonObjecti.getString(HapiUtil.KEY_TYPE);
if ( type==null ) type="";
} else {
type= "";
}
if ( type.equals("") ) {
logger.log(Level.FINE, "type is not defined: {0}", name);
}
pds[i].parameter= jsonObjecti;
if ( type.equalsIgnoreCase("isotime") ) {
if ( !type.equals("isotime") ) {
logger.log(Level.WARNING, "isotime should not be capitalized: {0}", type);
}
pds[i].units= Units.us2000;
if ( jsonObjecti.has("length") ) {
pds[i].type= "time"+jsonObjecti.getInt("length");
pds[i].length= jsonObjecti.getInt("length");
} else {
logger.log(Level.FINE, "server doesn''t report length for \"{0}\", assuming 24 characters, and that it doesn''t matter", name);
pds[i].type= "time24";
}
} else {
pds[i].type= type;
if ( jsonObjecti.has(HapiUtil.KEY_UNITS) ) {
Object ou= jsonObjecti.get(HapiUtil.KEY_UNITS);
if ( ou instanceof String ) {
String sunits= (String)ou;
pds[i].units= Units.lookupUnits(sunits);
}
} else {
pds[i].units= Units.dimensionless;
}
if ( type.equals("String") ) {
type="string";
logger.warning("String used for type instead of string (lower case)");
}
if ( type.equals("string") ) {
pds[i].units= EnumerationUnits.create(name);
}
if ( jsonObjecti.has(HapiUtil.KEY_FILL) ) {
String sfill= jsonObjecti.getString(HapiUtil.KEY_FILL);
if ( sfill!=null && !sfill.equals("null") ) {
if ( type.equals("string") ) {
pds[i].fillValue= ((EnumerationUnits)pds[i].units).createDatum( sfill ).doubleValue( pds[i].units );
pds[i].hasFill= true;
} else {
try {
pds[i].fillValue= pds[i].units.parse( sfill ).doubleValue( pds[i].units );
pds[i].hasFill= true;
} catch ( ParseException ex ) {
logger.log(Level.WARNING, "unable to use fill value: {0}", sfill);
}
}
}
} else {
pds[i].fillValue= FILL_VALUE; // when a value cannot be parsed, but it is not identified.
}
if ( jsonObjecti.has("description") ) {
pds[i].description= jsonObjecti.getString("description");
if ( pds[i].description==null ) pds[i].description= "";
} else {
pds[i].description= ""; // when a value cannot be parsed, but it is not identified.
}
if ( jsonObjecti.has( HapiUtil.KEY_LABEL ) ) { // The verifier code incorrectly marks "label" as not allowed, but I believe it is.
Object olabel= jsonObjecti.get( HapiUtil.KEY_LABEL );
if ( olabel instanceof String ) {
pds[i].label= (String)olabel;
pds[i].labels= null;
} else if ( olabel instanceof JSONArray ) {
JSONArray array= (JSONArray)olabel;
pds[i].labels= new String[array.length()];
for ( int j=0; j<array.length(); j++ ) {
pds[i].labels[j]= array.getString(j);
}
}
if ( pds[i].label==null ) pds[i].label= name;
} else {
pds[i].label= name;
}
if ( jsonObjecti.has( HapiUtil.KEY_LENGTH ) ) {
pds[i].length= jsonObjecti.getInt( HapiUtil.KEY_LENGTH );
}
if ( jsonObjecti.has( HapiUtil.KEY_SIZE ) ) {
Object o= jsonObjecti.get( HapiUtil.KEY_SIZE );
if ( !(o instanceof JSONArray) ) {
if ( o.getClass()==Integer.class ) {
pds[i].size= new int[] { ((Integer)o) };
pds[i].nFields= ((Integer)o);
logger.log( Level.WARNING, "size should be an int array, found int: {0}", name);
} else if ( o.getClass()==String.class ) {
pds[i].size= new int[] { Integer.parseInt( (String)o ) };
pds[i].nFields= (Integer.parseInt((String)o));
logger.log( Level.WARNING, "size should be an int array, found String: {0}", name);
} else {
throw new IllegalArgumentException( String.format( "size should be an int array: %s", name ) );
}
} else {
JSONArray a= (JSONArray)o;
pds[i].size= new int[a.length()];
int nFields=1;
for ( int j=0; j<a.length(); j++ ) {
pds[i].size[j]= a.getInt(j);
nFields*= pds[i].size[j];
}
pds[i].nFields= nFields;
}
if ( jsonObjecti.has( HapiUtil.KEY_BINS ) ) {
o= jsonObjecti.get( HapiUtil.KEY_BINS );
if ( o instanceof JSONArray ) {
JSONArray ja= (JSONArray)o;
pds[i].depend= new QDataSet[ja.length()];
pds[i].dependName= new String[ja.length()];
for ( int j=0; j<ja.length(); j++ ) {
JSONObject bins= ja.getJSONObject(j);
if ( bins.has( HapiUtil.KEY_CENTERS ) ) {
// rfe696: support time-varying DEPEND_1
Object o1= bins.get( HapiUtil.KEY_CENTERS );
if ( o1 instanceof String ) {
pds[i].dependName[j]= (String)o1;
} else {
QDataSet dep= getJSONBins(ja.getJSONObject(j));
pds[i].depend[j]= dep;
}
} else if ( bins.has( HapiUtil.KEY_RANGES ) ) {
// rfe696: support time-varying DEPEND_1
Object o1= bins.get( HapiUtil.KEY_RANGES );
if ( o1 instanceof String ) {
pds[i].dependName[j]= (String)o1;
} else {
QDataSet dep= getJSONBins(ja.getJSONObject(j));
pds[i].depend[j]= dep;
}
pds[i].renderType= QDataSet.VALUE_RENDER_TYPE_NNSPECTROGRAM;
} else if ( bins.has( HapiUtil.KEY_PARAMETER ) ) { // deprecated, see binsParameter below. TODO: revisit this.
logger.info("parameter found within bins, which is deprecated.");
int n= pds[i].nFields;
pds[i].depend[j]= Ops.findgen(n);
pds[i].dependName[j]= bins.getString( HapiUtil.KEY_PARAMETER );
} else {
int n= pds[i].size[j];
pds[i].depend[j]= Ops.findgen(n);
}
}
} else {
logger.warning("bins should be an array");
JSONObject bins= jsonObjecti.getJSONObject("bins");
if ( pds[i].depend==null ) pds[i].depend= new QDataSet[1];
if ( pds[i].dependName==null ) pds[i].dependName= new String[1];
if ( bins.has( HapiUtil.KEY_PARAMETER ) ) { // this will be implemented later.
int n= DataSetUtil.product(pds[i].size);
pds[i].depend[0]= Ops.findgen(n);
pds[i].dependName[0]= bins.getString( HapiUtil.KEY_PARAMETER );
} else if ( bins.has("values") ) {
QDataSet dep1= getJSONBins(bins);
pds[i].depend[0]= dep1;
} else {
int n= DataSetUtil.product(pds[i].size);
pds[i].depend[0]= Ops.findgen(n);
}
}
} else if ( jsonObjecti.has("binsParameter") ) {
o= jsonObjecti.get("binsParameter");
if ( o instanceof JSONArray ) {
JSONArray ja= (JSONArray)o;
pds[i].depend= new QDataSet[ja.length()];
pds[i].dependName= new String[ja.length()];
for ( int j=0; j<ja.length(); j++ ) {
String s= ja.getString(j);
int n= DataSetUtil.product(pds[i].size);
pds[i].depend[j]= Ops.findgen(n);
pds[i].dependName[j]= s;
}
}
}
}
}
}
return pds;
}
/**
* copy label and units from the ParamDescription to the QDataSet.
* @param mpds the dataset
* @param pds1 the parameter description
* @return the data, possibly a copy, with the metadata.
*/
private MutablePropertyDataSet copyProperties( QDataSet mpds, ParamDescription pds1 ) {
MutablePropertyDataSet ds= Ops.putProperty( mpds, QDataSet.NAME, Ops.safeName(pds1.name) );
ds= Ops.putProperty( ds, QDataSet.LABEL, pds1.label );
ds= Ops.putProperty( ds, QDataSet.TITLE, pds1.description );
ds= Ops.putProperty( ds, QDataSet.UNITS, pds1.units );
if ( pds1.hasFill ) {
ds= Ops.putProperty( ds, QDataSet.FILL_VALUE, pds1.fillValue );
}
if ( pds1.labels!=null ) {
ds= Ops.putProperty( ds, QDataSet.DEPEND_1, Ops.labelsDataset( pds1.labels ) );
}
return ds;
}
/**
* Reform bundle into typical QDataSet schemes. For example, a rank 2 bundle
* ds[;T,N] would be reformed into rank 1 N[T].
* @param ds the bundle dataset
* @param pds metadata for each column.
* @param sort if non-null, resort the data with these indices.
* @return
*/
private QDataSet repackage(QDataSet ds, ParamDescription[] pds, int[] sort ) {
int nparameters= ds.length(0);
boolean combineRank2Depend1= pds.length==3 && pds[1].dependName!=null;
if ( ds.rank()==2 ) {
QDataSet bds= (QDataSet)ds.property(QDataSet.BUNDLE_1);
if ( bds!=null && bds.length()>1 ) {
Units u1= (Units)bds.property(QDataSet.UNITS,0);
Units u2= (Units)bds.property(QDataSet.UNITS,1);
if ( u1!=null && u2!=null && UnitsUtil.isTimeLocation( u1 ) && UnitsUtil.isTimeLocation( u2 ) ) {
QDataSet start= Ops.slice1( ds,0 );
QDataSet stop= Ops.slice1( ds,1 );
// It's an events dataset, but we better check that all stops are greater than starts!
if ( Ops.reduceMax( Ops.lt( stop, start ),0 ).value()==0 ) {
return Ops.createEvents(ds);
}
}
}
}
QDataSet depend0= Ops.slice1( ds,0 ); //TODO: this will be unnecessary after debugging.
if ( ds.length(0)==2 ) {
ds= Ops.copy( Ops.slice1( ds, 1 ) );
ds= Ops.putProperty( ds, QDataSet.DEPEND_0, depend0 );
ds= copyProperties( ds, pds[1] );
} else if ( pds.length==2 ) {
ds= Ops.copy( Ops.trim1( ds, 1, ds.length(0) ) );
if ( pds[1].size.length>1 ) {
ds= Ops.reform( ds, ds.length(), pds[1].size );
}
ds= Ops.putProperty( ds, QDataSet.DEPEND_0, depend0 );
ds= copyProperties( ds, pds[1] );
if ( pds[1].depend!=null ) {
for ( int j=0; j<pds[1].size.length; j++ ) {
ds= Ops.putProperty( ds, "DEPEND_"+(j+1), pds[1].depend[j] );
}
}
if ( pds.length==2 && QDataSet.VALUE_RENDER_TYPE_NNSPECTROGRAM.equals( pds[1].renderType ) ) {
ds= Ops.putProperty( ds, QDataSet.RENDER_TYPE, pds[1].renderType );
}
} else if ( pds.length==1 ) {
ds= Ops.link( depend0, depend0 );
ds= Ops.putProperty( ds, QDataSet.RENDER_TYPE, QDataSet.VALUE_RENDER_TYPE_EVENTS_BAR );
return ds;
} else if ( combineRank2Depend1 ) {
MutablePropertyDataSet theScienceDs= Ops.maybeCopy( Ops.trim1( ds, 1, 1+pds[1].nFields ) );
if ( pds[1].size.length>1 ) {
theScienceDs= Ops.maybeCopy( Ops.reform( theScienceDs, theScienceDs.length(), pds[1].size ) );
}
// we need to remove Epoch to DEPEND_0.
SparseDataSetBuilder[] sdsbs= new SparseDataSetBuilder[pds.length];
int ifield=1;
int length1=ds.length(0); // this should be overwritten
for ( int i=1; i<pds.length; i++ ) {
int nfields1= pds[i].nFields;
SparseDataSetBuilder sdsb= new SparseDataSetBuilder(2);
sdsb.setLength(nfields1);
int startIndex= sort==null ? ifield-1 : sort[ifield]-1;
if ( nfields1>1 ) {
//bdsb.putProperty( QDataSet.ELEMENT_DIMENSIONS, ifield-1, pds[i].size ); // not supported yet.
sdsb.putProperty( QDataSet.ELEMENT_NAME, startIndex, Ops.safeName( pds[i].name ) );
sdsb.putProperty( QDataSet.ELEMENT_LABEL, startIndex, pds[i].name );
for ( int j=0; j<pds[i].size.length; j++ ) {
sdsb.putValue( startIndex, j, pds[i].size[j] );
}
if ( pds[i].depend!=null ) {
if ( pds[i].size.length!=pds[i].depend.length ) throw new IllegalArgumentException("pds[i].size.length!=pds[i].depend.length");
for ( int j=0; j<pds[i].size.length; j++ ) {
if ( pds[i].dependName[j]!=null ) {
// wait until code below
} else {
sdsb.putProperty( "DEPEND_"+(j+1), startIndex, pds[i].depend[j]);
if ( i==1 ) {
theScienceDs.putProperty( "DEPEND_"+(j+1), pds[i].depend[j]) ;
}
}
}
}
//sdsb.putValue( QDataSet.ELEMENT_DIMENSIONS, ifield-1, pds[i].size );
}
for ( int j=0; j<nfields1; j++ ) {
if ( nfields1>1 ) {
sdsb.putProperty( QDataSet.START_INDEX, startIndex + j, startIndex );
sdsb.putProperty( QDataSet.LABEL, startIndex + j, pds[i].name +" ch"+j );
sdsb.putProperty( QDataSet.NAME, startIndex + j, Ops.safeName(pds[i].name)+"_"+j );
} else {
sdsb.putProperty( QDataSet.LABEL, startIndex + j, pds[i].name );
sdsb.putProperty( QDataSet.NAME, startIndex + j, Ops.safeName(pds[i].name) );
}
sdsb.putProperty( QDataSet.TITLE, startIndex + j, pds[i].description );
sdsb.putProperty( QDataSet.UNITS, startIndex + j, pds[i].units );
if ( pds[i].hasFill ) {
sdsb.putProperty( QDataSet.FILL_VALUE, startIndex + j, pds[i].fillValue );
}
if ( nfields1>1 ) {
sdsb.putProperty( QDataSet.START_INDEX, startIndex + j, startIndex );
}
ifield++;
}
length1= nfields1;
sdsbs[i]= sdsb;
}
int start= 1;
start= start+length1;
theScienceDs.putProperty( QDataSet.DEPEND_0, depend0 );
//theScienceDs.putProperty( QDataSet.BUNDLE_1, sdsbs[1].getDataSet() );
theScienceDs= copyProperties( theScienceDs, pds[1] );
for ( int i=1; i<pds.length; i++ ) { // only works for rank2!!!
if ( pds[i].dependName!=null ) {
for ( int j=0; j<pds[i].dependName.length; j++ ) {
String dependName= pds[i].dependName[j];
if (dependName != null) {
int k;
for (k=1; k<pds.length; k++) {
if (pds[k].name.equals(dependName)) {
break;
}
}
if ( k<pds.length ) {
MutablePropertyDataSet depds= Ops.copy( Ops.trim1( ds, start, start+length1 ) );
depds.putProperty( QDataSet.DEPEND_0, depend0 );
depds.putProperty( QDataSet.BUNDLE_1, sdsbs[k].getDataSet() );
depds= copyProperties( depds, pds[k] );
start= start+length1;
if ( pds[k].size.length>1 ) {
theScienceDs.putProperty( "DEPEND_"+(j+1), Ops.reform( depds, depds.length(), pds[k].size ) );
} else {
theScienceDs.putProperty( "DEPEND_"+(j+1), depds );
}
}
}
}
}
}
ds= theScienceDs;
} else {
// we need to remove Epoch to DEPEND_0.
SparseDataSetBuilder sdsb= new SparseDataSetBuilder(2);
sdsb.setLength(nparameters-1);
int ifield=1;
for ( int i=1; i<pds.length; i++ ) {
int nfields1= DataSetUtil.product(pds[i].size);
int startIndex= sort==null ? ifield-1 : sort[ifield]-1;
if ( nfields1>1 ) {
//bdsb.putProperty( QDataSet.ELEMENT_DIMENSIONS, ifield-1, pds[i].size ); // not supported yet.
sdsb.putProperty( QDataSet.ELEMENT_NAME, startIndex, Ops.safeName( pds[i].name ) );
sdsb.putProperty( QDataSet.ELEMENT_LABEL, startIndex, pds[i].name );
for ( int j=0; j<pds[i].size.length; j++ ) {
sdsb.putValue( startIndex, j, pds[i].size[j] );
}
if ( pds[i].depend!=null ) {
if ( pds[i].size.length!=pds[i].depend.length ) throw new IllegalArgumentException("pds[i].size.length!=pds[i].depend.length");
for ( int j=0; j<pds[i].size.length; j++ ) {
sdsb.putProperty( "DEPEND_"+(j+1), startIndex, pds[i].depend[j]);
}
}
//sdsb.putValue( QDataSet.ELEMENT_DIMENSIONS, ifield-1, pds[i].size );
}
for ( int j=0; j<nfields1; j++ ) {
if ( nfields1>1 ) {
sdsb.putProperty( QDataSet.START_INDEX, startIndex + j, startIndex );
sdsb.putProperty( QDataSet.LABEL, startIndex + j, pds[i].name +" ch"+j );
sdsb.putProperty( QDataSet.NAME, startIndex + j, Ops.safeName(pds[i].name)+"_"+j );
} else {
sdsb.putProperty( QDataSet.LABEL, startIndex + j, pds[i].name );
sdsb.putProperty( QDataSet.NAME, startIndex + j, Ops.safeName(pds[i].name) );
}
sdsb.putProperty( QDataSet.TITLE, startIndex + j, pds[i].description );
sdsb.putProperty( QDataSet.UNITS, startIndex + j, pds[i].units );
if ( pds[i].hasFill ) {
sdsb.putProperty( QDataSet.FILL_VALUE, startIndex + j, pds[i].fillValue );
}
if ( nfields1>1 ) {
sdsb.putProperty( QDataSet.START_INDEX, startIndex + j, startIndex );
}
ifield++;
}
}
ds= Ops.copy( Ops.trim1( ds, 1, ds.length(0) ) );
ds= Ops.putProperty( ds, QDataSet.DEPEND_0, depend0 );
ds= Ops.putProperty( ds, QDataSet.BUNDLE_1, sdsb.getDataSet() );
}
return ds;
}
}