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Commit 08308c0f authored by Robert Butora's avatar Robert Butora
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creates flat VOTable response (removes Subsurvey)

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with 103 additions and 834 deletions
data-discovery/Makefile
+ 3
− 3
View file @ 08308c0f
......@@ -12,7 +12,7 @@ AUTH_DIR := ../auth
# all sources
#IA2CONVFILTER = $(AUTH_DIR)/src/main/java/IA2TokenConvFilter.java
AUTHFILTERS = $(wildcard $(AUTH_DIR)/src/main/java/*Filter.java) $(AUTH_DIR)/src/main/java/AuthPolicy.java
SRC_DIR = src/main/java/common:src/main/java/output:src/main/java/search:src/main/java/webapi:$(AUTH_DIR)/src/main/java
SRC_DIR = src/main/java/common:src/main/java/search:src/main/java/webapi:src/main/java/webapi/formatfilter:src/main/java/webapi/authzfilter:$(AUTH_DIR)/src/main/java
VOSI = src/main/java/vosi/VlkbServletFile.java
FILTERS = $(wildcard src/main/java/webapi/*Filter.java)
SERVLETS = $(wildcard src/main/java/webapi/*Servlet.java)
......@@ -23,12 +23,12 @@ CLASSPATH = $(LIB_DIR)/*
.PHONY: build
build:
echo "class Version { static String asString = \"$(VERSION)\";}" > src/main/java/output/Version.java
echo "class Version { static String asString = \"$(VERSION)\";}" > src/main/java/webapi/Version.java
javac $(JFLAGS) -cp :$(CLASSPATH) -sourcepath $(SRC_DIR) -d $(CLASS_DIR) $(SERVLETS) $(FILTERS) $(AUTHFILTERS) $(VOSI)
.PHONY: clean
clean :
rm -fr src/main/java/output/Version.java target
rm -fr src/main/java/webapi/Version.java target
.PHONY: install
......
data-discovery/src/main/java/common/Subsurvey.java deleted 100644 → 0
+ 0
− 117
View file @ 32fdca74
import java.util.logging.Logger;
/* for loadSubsurveys from csv */
import com.opencsv.*;
import com.opencsv.exceptions.*;
import java.io.FileReader;
import java.io.FileNotFoundException;
import java.util.Map;
import java.util.List;
import java.util.ArrayList;
import java.io.IOException;
/* NOTE originally was in search/output : designed for serializing search output xml */
class Subsurvey
{
private static final Logger LOGGER = Logger.getLogger("Subsurvey");
String description;
String surveyname;
String species;
String transition;
double rf; // rest frequency
String rf_unit;
String vel_unit;
Dataset[] datasetArr;
Subsurvey() { datasetArr = null; }
Subsurvey(Subsurvey ss)
{
this.description = ss.description;;
this.surveyname = ss.surveyname;
this.species = ss.species;
this.transition = ss.transition;
this.rf = ss.rf;
this.rf_unit = ss.rf_unit;
this.vel_unit = ss.vel_unit;
this.datasetArr = null;
}
String id() { return (this.surveyname + " " + this.species + " " + this.transition); }
boolean matches(String id) { return id.equals(this.id()); }
static public Subsurvey findSubsurvey(Subsurvey[] dbSubsurveys, String subsurvey_id)
{
for(Subsurvey curr : dbSubsurveys)
{
if(curr.matches(subsurvey_id))
{
return curr;
}
}
throw new AssertionError(subsurvey_id + " not found in surveys table");
}
public static Subsurvey[] loadSubsurveys(String csvFilename)
{
List<Subsurvey> subsurveyList = new ArrayList<>();
try
{
// FIXME parser not robust:
// * eats space-character also within the field: , hu ha , --> "huha" not "hu ha"
// * double quote used inside string not escaped: ,"blabla 25\" res",
// * last record (line) is missing if that line is not closed with EOL
// * UTF-8 or US-ASACII ?
// * else ? how to validate/verify correctness
CSVReaderHeaderAware csvReader = new CSVReaderHeaderAware(new FileReader(csvFilename));
Map<String, String> values;
while ((values = csvReader.readMap()) != null)
{
Subsurvey subsurvey = new Subsurvey();
subsurvey.description = values.get("description");
subsurvey.surveyname = values.get("name");
subsurvey.species = values.get("species");
subsurvey.transition = values.get("transition");
subsurvey.rf = Double.parseDouble(values.get("rest_frequency"));
subsurvey.rf_unit = values.get("restf_fits_unit");
subsurvey.vel_unit = values.get("velocity_fits_unit");
subsurveyList.add(subsurvey);
}
}
catch(IOException ex)
{
LOGGER.info("Error while loading [" + csvFilename + "]: " + ex.getMessage());
//return null;
//throw new IllegalStateException("Error while loading " + csvFilename + " file", ex);
}
catch(CsvValidationException ex)
{
LOGGER.info("Error while reading [" + csvFilename + "]: " + ex.getMessage());
//return null;
//throw new IllegalStateException("Error while reading " + csvFilename + " file", ex);
}
return subsurveyList.toArray(new Subsurvey[0]);
}
}
data-discovery/src/main/java/output/SearchOutputData.java deleted 100644 → 0
+ 0
− 83
View file @ 32fdca74
import java.util.logging.Logger;
import java.util.List;
import java.util.ArrayList;
class SearchOutputData
{
private static final Logger LOGGER = Logger.getLogger("SearchOutputData");
String description;
int datacubeCount;
String versionString;
Subsurvey[] subsurveyArr;
public static SearchOutputData marshall(Dataset[] datasetArr,
/*SubsurveyId subsurveyId,*/ Subsurvey[] dbSubsurveys,
String mergeUrlRoot, String mergeQueryString)
{
SearchOutputData sod = new SearchOutputData();
sod.description = "Via Lactea Knowledge Base response (Search by pgSphere)";
sod.versionString = "Search (pgSphere) version " + Version.asString;
sod.datacubeCount = datasetArr.length;
sod.subsurveyArr = groupBySubsurveys(datasetArr, /*subsurveyId,*/ dbSubsurveys, mergeUrlRoot, mergeQueryString);
return sod;
}
// assumes datasetArr is already ordered by subsurveys
private static Subsurvey[] groupBySubsurveys(Dataset[] datasetArr,
/*SubsurveyId subsurveyId,*/ Subsurvey[] dbSubsurveys,
String mergeUrlRoot, String mergeQueryString)
{
List<Subsurvey> subsurveyList = new ArrayList<Subsurvey>();
if(datasetArr.length > 0)
{
List<Dataset> datasetList = new ArrayList<Dataset>();
String prevSubsurveyId = datasetArr[0].subsurvey_id;
for(Dataset dataset : datasetArr)
{
if( ! prevSubsurveyId.equals(dataset.subsurvey_id) )
{
if( false )//Dataset.areDatasetsMergeable(datasetList) )
{
Dataset mergedDataset = new Dataset(datasetList, /*subsurveyId,*/ mergeUrlRoot, mergeQueryString);
datasetList.add(mergedDataset);
}
Subsurvey subsurvey = new Subsurvey(Subsurvey.findSubsurvey(dbSubsurveys, prevSubsurveyId));
subsurvey.datasetArr = datasetList.toArray(new Dataset[0]);
subsurveyList.add(subsurvey);
datasetList.clear();
}
datasetList.add( dataset );
prevSubsurveyId = dataset.subsurvey_id;
}
if( false )//Dataset.areDatasetsMergeable(datasetList) )
{
Dataset mergedDataset = new Dataset(datasetList, /*subsurveyId,*/ mergeUrlRoot, mergeQueryString);
datasetList.add(mergedDataset);
}
Subsurvey subsurvey = new Subsurvey(Subsurvey.findSubsurvey(dbSubsurveys, prevSubsurveyId));
subsurvey.datasetArr = datasetList.toArray(new Dataset[0]);
subsurveyList.add(subsurvey);
datasetList.clear();
}
return subsurveyList.toArray(new Subsurvey[0]);
}
}
data-discovery/src/main/java/output/XmlSerializer.java deleted 100644 → 0
+ 0
− 475
View file @ 32fdca74
import java.io.PrintWriter;
// VOTable
import uk.ac.starlink.table.*;// StarTable needed
import uk.ac.starlink.votable.*;// Writer needed
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.BufferedWriter;
import java.util.List;
import java.util.ArrayList;
import vo.parameter.*;
final class XmlSerializer
{
private XmlSerializer() {}
// VOTable
public static void serializeToVoTable(
PrintWriter writer, String charEncoding,
SearchOutputData searchOutputData,
String cutoutUrl, String mergeUrl,
boolean showDuration, long startTime_msec) throws IOException
{
StarTable dstable = makeSearchResultsTable( searchOutputData.subsurveyArr );
dstable.setParameter(new DescribedValue(
new DefaultValueInfo( "subsurveyCount", Integer.class, "Count of subsurveys with found datacube(s)" ),
searchOutputData.subsurveyArr.length ) );
dstable.setParameter(new DescribedValue(
new DefaultValueInfo( "datacubeCount", Integer.class, "Count of all datacubes from VLKB-search" ),
searchOutputData.datacubeCount ) );
BufferedWriter out = new BufferedWriter( writer );
out.write("<?xml-stylesheet type='text/xsl' href='VOTable2XHTML.xsl'?>");
out.write( "<VOTABLE version='1.1'>" );
out.write( "<RESOURCE type=\"results\">" );
out.write( "<DESCRIPTION> " + searchOutputData.versionString + " </DESCRIPTION>" );
VOSerializer.makeSerializer( DataFormat.TABLEDATA, dstable ).writeInlineTableElement( out );
out.write( "</RESOURCE>" );
out.write( "<RESOURCE type=\"meta\" utype=\"adhoc:service\" name=\"CutoutService\" >" );
out.write( "<DESCRIPTION> VLKB cutout service </DESCRIPTION>");
out.write( "<PARAM name=\"standardID\" datatype=\"char\" arraysize=\"*\" value=\"ivo://ivoa.net/std/SODA#sync-1.0\" />");
out.write( "<PARAM name=\"accessURL\" datatype=\"char\" arraysize=\"*\" value=\"" + cutoutUrl + "\" />");
out.write( "<GROUP name=\"inputParams\">");
out.write( "<PARAM name=\"ID\" datatype=\"char\" arraysize=\"*\" value=\"\" ref=\"primaryID\" />"); // FIXME results table obs_publisher_did FIELD must have attrib: ID="primaryID"
out.write( "</GROUP>");
out.write( "</RESOURCE>" );
out.write( "</VOTABLE>" );
out.flush();
}
private static StarTable makeSearchResultsTable(Subsurvey[] ssurv)
{
RowListStarTable astro = new RowListStarTable( ObscoreExt.OBSCORE_VLKB_SUBSURVEY_COLINFO );
for(Subsurvey subsurvey : ssurv)
{
for(Dataset dataset : subsurvey.datasetArr)
{
if(dataset.obsCore == null) continue; // FIXME skip mergeable datasets
astro.addRow( ObscoreExt.obscoreVlkbSubsurveyRow(dataset, subsurvey) );
}
}
return astro;
}
public static void serializeToVoTableBySubsurveys(
PrintWriter writer, String charEncoding,
SearchOutputData searchOutputData,
boolean showDuration, long startTime_msec) throws IOException
{
StarTable[] tables = makeSubsurveyTables( searchOutputData.subsurveyArr );
BufferedWriter out = new BufferedWriter( writer );
out.write( "<VOTABLE version='1.1'>" );
out.write( "<RESOURCE>" );
out.write( "<DESCRIPTION> " + searchOutputData.versionString + " </DESCRIPTION>" );
for ( int i = 0; i < tables.length; i++ )
{
VOSerializer.makeSerializer( DataFormat.TABLEDATA, tables[ i ] ).writeInlineTableElement( out );
}
out.write( "</RESOURCE>" );
out.write( "</VOTABLE>" );
out.flush();
}
private static StarTable[] makeSubsurveyTables(Subsurvey[] subsurveyArr)
{
StarTable[] ssurvTableArr = new StarTable[subsurveyArr.length];
int ix = 0;
for(Subsurvey subsurvey : subsurveyArr)
{
RowListStarTable table = new RowListStarTable( ObscoreExt.OBSCORE_VLKB_COLINFO );
table.setParameter(new DescribedValue(
new DefaultValueInfo( "subsurveyCount", Integer.class, "Count of subsurveys with found datacube(s)" ),
subsurveyArr.length ) );
table.setParameter(new DescribedValue(
new DefaultValueInfo( "datacubeCount", Integer.class, "Count of all datacubes from VLKB-search" ),
subsurvey.datasetArr.length ) );
table.setParameter(new DescribedValue(
new DefaultValueInfo( "description", String.class, "Reference description" ),
subsurvey.description ) );
table.setParameter(new DescribedValue(
new DefaultValueInfo( "survey", String.class, "Survey name" ),
subsurvey.surveyname ) );
table.setParameter(new DescribedValue(
new DefaultValueInfo( "species", String.class, "Species" ),
subsurvey.species ) );
table.setParameter(new DescribedValue(
new DefaultValueInfo( "transition", String.class, "Transition" ),
subsurvey.transition ) );
table.setParameter(new DescribedValue(
new DefaultValueInfo( "frequency", Double.class, "Frequency" ),
subsurvey.rf ) );
for(Dataset dataset : subsurvey.datasetArr)
{
if(dataset.obsCore == null) continue; // FIXME skip mergeable datasets
table.addRow( ObscoreExt.obscoreVlkbRow(dataset) );
}
ssurvTableArr[ix++] = table;
}
return ssurvTableArr;
}
public static void serializeToVoTableBySurveys(
PrintWriter writer, String charEncoding,
SearchOutputData searchOutputData,
boolean showDuration, long startTime_msec) throws IOException
{
BufferedWriter out = new BufferedWriter( writer );
out.write( "<VOTABLE version='1.1'>" );
out.write( "<DESCRIPTION> " + searchOutputData.versionString +
" subsurvey count: " + searchOutputData.subsurveyArr.length + " </DESCRIPTION>" );
if((searchOutputData.subsurveyArr != null) && (searchOutputData.subsurveyArr.length > 0))
{
Subsurvey[] subsurv = searchOutputData.subsurveyArr;
// assumes ORDERED subsurveyArray: by surveyname
List<StarTable> tableList = new ArrayList();
String prevSurveyname, prevDescription;// = subsurv[0].surveyname.trim();
int ix = 0;
do
{
prevSurveyname = subsurv[ix].surveyname.trim();
prevDescription = subsurv[ix].description.trim();
do
{
StarTable table = makeSubsurveyTable( subsurv[ix] );
tableList.add(table);
ix++;
}
while((ix < subsurv.length) && prevSurveyname.equals(subsurv[ix].surveyname.trim()));
StarTable[] tables = tableList.toArray(new StarTable[0]);
writeResourceSurvey(out, prevSurveyname, prevDescription, tables);
tableList.clear();
}
while(ix < subsurv.length);
}
out.write( "</VOTABLE>" );
out.flush();
}
private static void writeResourceSurvey(BufferedWriter out, String name, String description,
StarTable[] tables) throws IOException
{
out.write( "<RESOURCE name=\"" + name + "\">" );
out.write( "<DESCRIPTION> " + description.replaceAll("&", "&amp;") + " </DESCRIPTION>" );
/* PLACEHOLDER FOR RESOURCE PARAM
table.setParameter(new DescribedValue(
new DefaultValueInfo("subsurveyCount",Integer.class,
"Count of subsurveys with found datacube(s)" ),
subsurveyArr.length ) );
table.setParameter(new DescribedValue(
new DefaultValueInfo( "survey", String.class,
"Survey name" ),
subsurvey.surveyname ) );
*/
for ( int i = 0; i < tables.length; i++ )
{
VOSerializer.makeSerializer( DataFormat.TABLEDATA, tables[i] ).writeInlineTableElement( out );
}
out.write( "</RESOURCE>" );
}
private static StarTable makeSubsurveyTable(Subsurvey subsurvey)
{
RowListStarTable table = new RowListStarTable( ObscoreExt.OBSCORE_VLKB_COLINFO );
table.setParameter(new DescribedValue(
new DefaultValueInfo("datacubeCount", Integer.class, "Count of all datacubes from VLKB-search" ),
subsurvey.datasetArr.length ) );
/* table.setParameter(new DescribedValue(
new DefaultValueInfo( "velocity_unit", String.class, "Unit of velocity in FITS header" ),
subsurvey.vel_unit ) );
table.setParameter(new DescribedValue(
new DefaultValueInfo( "survey", String.class, "Survey name" ),
subsurvey.surveyname ) );
*/
table.setParameter(new DescribedValue(
new DefaultValueInfo( "species", String.class, "Species" ),
subsurvey.species ) );
table.setParameter(new DescribedValue(
new DefaultValueInfo( "transition", String.class, "Transition" ),
subsurvey.transition ) );
table.setParameter(new DescribedValue(
new DefaultValueInfo( "frequency", Double.class, "Frequency" ),
subsurvey.rf ) );
/* table.setParameter(new DescribedValue(
new DefaultValueInfo( "description", String.class, "Reference description" ),
subsurvey.description ) );
*/
for(Dataset dataset : subsurvey.datasetArr)
{
if(dataset.obsCore == null) continue; // FIXME skip mergeable datasets
table.addRow( ObscoreExt.obscoreVlkbRow(dataset) );
}
return table;
}
// legacy
public static void serializeToLegacyResults(
PrintWriter writer, String charEncoding,
AuthPolicy inputAuth, Pos pos, Band band, SubsurveyId inputSubsurveyId,
SearchOutputData searchOutputData,
boolean showDuration, long startTime_msec)
{
writer.println("<?xml version=\"1.0\" encoding=\"" + charEncoding + "\" standalone=\"yes\"?>");
writer.println("<results>");
writer.println("<description> " + searchOutputData.description + " </description>");
writer.println("<inputs>");
if(inputSubsurveyId != null) writer.println(serialize(inputSubsurveyId));
if(pos != null) writer.println(serialize(pos));
if(band != null) writer.println(serialize(band));
if(inputAuth != null) writer.println(serialize(inputAuth));
writer.println("</inputs>");
writer.println("<msg> " + searchOutputData.versionString + " </msg>");
writer.println("<DatacubeCount> " + searchOutputData.datacubeCount + " </DatacubeCount>");
for(Subsurvey subsurvey : searchOutputData.subsurveyArr)
{
serialize(writer, subsurvey);
}
if(showDuration)
writer.println("<duration unit=\"msec\">" + (System.currentTimeMillis() - startTime_msec) + "</duration>");
writer.println("</results>");
}
private static String serialize(Pos pos)
{
StringBuilder xml = new StringBuilder();
if(pos != null)
{
xml.append("<SkySystem>"+pos.system+"</SkySystem>");
switch(pos.shape)
{
case CIRCLE:
xml.append("<l>" + String.valueOf(pos.circle.lon) + "</l>");
xml.append("<b>" + String.valueOf(pos.circle.lat) + "</b>");
xml.append("<r>" + String.valueOf(pos.circle.radius)+"</r>");
break;
case RANGE:
xml.append("<l>" + String.valueOf((pos.range.lon1 + pos.range.lon2)/2.0) + "</l>");
xml.append("<b>" + String.valueOf((pos.range.lat1 + pos.range.lat2)/2.0) + "</b>");
xml.append("<dl>" + String.valueOf(pos.range.lon2 - pos.range.lon1) + "</dl>");
xml.append("<db>" + String.valueOf(pos.range.lat2 - pos.range.lat1) + "</db>");
break;
default: // POLYGON was not used in VLKB-legacy -> let it fail with error
xml.append("<shape> unknown shape: " + pos.shape + " </shape>");
}
}
return xml.toString();
}
private static String serialize(Band band)
{
StringBuilder xml = new StringBuilder();
if(band != null)
{
xml.append("<vl>" + String.valueOf(band.getMin()) +"</vl>");
xml.append("<vu>" + String.valueOf(band.getMax()) +"</vu>");
xml.append("<vtype>"+ band.system +"</vtype>");
}
return xml.toString();
}
private static String serialize(SubsurveyId subsurveyId)
{
StringBuilder xml = new StringBuilder();
if(subsurveyId.surveyName != null) xml.append("<SurveyName>"+subsurveyId.surveyName+"</SurveyName>");
if(subsurveyId.species != null) xml.append("<Species>"+subsurveyId.species+"</Species>");
if(subsurveyId.transition != null) xml.append("<Transition>"+subsurveyId.transition+"</Transition>");
return xml.toString();
}
private static String serialize(AuthPolicy auth)
{
StringBuilder xml = new StringBuilder();
xml.append("<AccessPolicy>" + auth.getAccessPolicy() + "</AccessPolicy>");
String ug = auth.getUserGroupsAsString(" ");
if(auth.getUserName() != null) xml.append("<UserName>" + auth.getUserName() + "</UserName>");
if(ug != null) xml.append("<GroupNames>" + ug + "</GroupNames>");
return xml.toString();
}
private static void serialize(PrintWriter writer, Subsurvey subsurvey)
{
writer.println("<survey>");
// replace with escape the XML-predefined entities:
// <, >, &, %
if(subsurvey.description != null)
{
subsurvey.description = subsurvey.description.replace("&","&amp;");
subsurvey.description = subsurvey.description.replace("<","&lt;");
subsurvey.description = subsurvey.description.replace(">","&gt;");
subsurvey.description = subsurvey.description.replace("%","&#37;");
}
writer.println("<Description>" + subsurvey.description + "</Description>");
writer.println("<Survey>" + subsurvey.surveyname + "</Survey>");
writer.println("<Species>" + subsurvey.species + "</Species>");
writer.println("<Transition>" + subsurvey.transition + "</Transition>");
writer.println("<RestFreq>");
writer.println("<value>" + subsurvey.rf + "</value>");
writer.println("<unit>" + "Hz" + "</unit>"); // FIXME why was this needed? checj survey_populate,csv
writer.println("</RestFreq>");
writer.println("<VelocityUnit>" + subsurvey.vel_unit + "</VelocityUnit>");
for(Dataset dataset : subsurvey.datasetArr)
{
writer.println(serialize(dataset));
}
writer.println("</survey>");
}
private static String serialize(Dataset.Access access)
{
StringBuilder xml = new StringBuilder();
xml.append("<Access>");
if(access.accessFileUrl != null)
xml.append("<URL type=\"file\">" + access.accessFileUrl + "</URL>");
if(access.accessCutoutUrl != null)
xml.append("<URL type=\"cutout\">" + access.accessCutoutUrl.replaceAll("&","&amp;") + "</URL>");
if(access.accessMosaicUrl != null)
xml.append("<URL type=\"mosaic\">" + access.accessMosaicUrl.replaceAll("&","&amp;") + "</URL>");
xml.append("</Access>");
return xml.toString();
}
private static String serialize(Dataset.Vertices vertices)
{
StringBuilder xml = new StringBuilder();
xml.append("<vertices>");
xml.append("<SkyCoordSystem>");
for(int ix = 0; ix < vertices.VERT_COUNT; ix++)
{
xml.append("<P" + (ix+1) + ">");
xml.append("<longitude>" + vertices.lon[ix] + "</longitude>");
xml.append("<latitude>" + vertices.lat[ix] + "</latitude>");
xml.append("</P" + (ix+1) + ">");
}
xml.append("</SkyCoordSystem>");
xml.append("</vertices>");
return xml.toString();
}
private static String serialize(Dataset dataset)
{
StringBuilder xml = new StringBuilder();
xml.append("<datacube>");
xml.append(serializeOverlapCode("overlap", dataset.overlapCode));
if(dataset.overlapCodeSky > 0)
{
xml.append(serializeOverlapCode("overlapSky", dataset.overlapCodeSky));
}
if(dataset.overlapCodeVel > 0)
{
xml.append(serializeOverlapCode("overlapVelocity", dataset.overlapCodeVel));
}
xml.append("<DataType>" + dataset.dataType + "</DataType>");
xml.append("<PublisherDID>" + dataset.publisherDid + "</PublisherDID>");
xml.append(serialize(dataset.access));
xml.append(serialize(dataset.vertices_deg));
xml.append("</datacube>");
return xml.toString();
}
private static String serializeOverlapCode(String tagName, int ovCode)
{
final String[] overString =
{
"The check could not be performed because the input Region could not be mapped into the coordinate system of the datacube Region.",
"There is no overlap between the two Regions.",
"The datacube Region is completely inside the input Region.",
"The input Region is completely inside the datacube Region.",
"There is partial overlap between the two Regions.",
"The Regions are identical to within their uncertainties.",
"The input Region is the exact negation of the datacube Region to within their uncertainties."
};
StringBuilder xml = new StringBuilder();
xml.append("<" + tagName + ">");
xml.append("<description>" + ( ((ovCode>=0) && (ovCode<=6)) ? overString[ovCode] : (" ovCode out-of-range: "+ Integer.toString(ovCode)) ) + "</description>");
xml.append("<code>" + ovCode + "</code>");
xml.append("</" + tagName + ">");
return xml.toString();
}
}
data-discovery/src/main/java/webapi/MonitorFilter.java deleted 100644 → 0
+ 0
− 50
View file @ 32fdca74
//import it.inaf.ia2.aa.data.User;
import java.io.IOException;
import java.util.*; // ArrayList<String>
import java.util.logging.Logger;
import javax.servlet.Filter;
import javax.servlet.FilterChain;
import javax.servlet.FilterConfig;
import javax.servlet.ServletException;
import javax.servlet.ServletRequest;
import javax.servlet.ServletResponse;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import javax.servlet.http.HttpServletRequestWrapper;
import java.security.Principal;
public class MonitorFilter implements Filter
{
private static final Logger LOGGER = Logger.getLogger(MonitorFilter.class.getName());
@Override
public void init(FilterConfig fc) throws ServletException {}
@Override
public void destroy() {}
@Override
public void doFilter(ServletRequest req, ServletResponse res, FilterChain chain)
throws IOException, ServletException
{
HttpServletRequest request = (HttpServletRequest) req;
HttpServletResponse response = (HttpServletResponse) res;
LOGGER.info("before doFilter");
chain.doFilter(request, response);
LOGGER.info("after doFilter");
}
}
data-discovery/src/main/java/webapi/SearchServlet.java
+ 0
− 3
View file @ 08308c0f
......@@ -64,11 +64,8 @@ public class SearchServlet extends javax.servlet.http.HttpServlet
{
Map<String, String[]> params = request.getParameterMap();
// VLKB-legacy init
//Coord coord = new Coord(params);
SubsurveyId subsurveyId = new SubsurveyId(params);
Coord coord = new Coord();
coord.pos = Pos.parsePos(params, DEFAULT_SKY_SYSTEM);
coord.band = Band.parseBand(params, DEFAULT_SPEC_SYSTEM);
......
data-discovery/src/main/java/output/Dataset.java → data-discovery/src/main/java/webapi/formatfilter/Dataset.java
+ 2
− 4
View file @ 08308c0f
......@@ -26,7 +26,6 @@ class Dataset
}
String subsurvey_id;
int overlapCodeSky;
int overlapCodeVel;
int overlapCode;
......@@ -59,10 +58,9 @@ class Dataset
}
public Dataset(List<Dataset> datasetList, /*SubsurveyId subsurveyId,*/ String mergeUrlRoot, String mergeQueryString)
public Dataset(List<Dataset> datasetList, String mergeUrlRoot, String mergeQueryString)
{
this.subsurvey_id = datasetList.get(0).subsurvey_id; // mergeabiity condition is more then 1 element in list
this.overlapCode = 5; // 5: exact match --> legacy used 0 here FIXME 5 will not be correct on edges of Subsurvey coverage
this.overlapCode = 5; // 5: exact match --> legacy used 0 here FIXME 5 will not be correct on edges of subsurvey-coverage
this.publisherDid = mergePublisherDids(datasetList);
this.dataType = datasetList.get(0).dataType;
......
data-discovery/src/main/java/webapi/FormatResponseFilter.java → data-discovery/src/main/java/webapi/formatfilter/FormatResponseFilter.java
+ 18
− 45
View file @ 08308c0f
......@@ -27,8 +27,6 @@ class FormatResponseWrapper extends HttpServletResponseWrapper
String[] pubdidArr;
public FormatResponseWrapper(HttpServletResponse response)
{
super(response);
......@@ -61,7 +59,6 @@ public class FormatResponseFilter implements Filter
final String DEFAULT_SPEC_SYSTEM = settings.defaults.specSystem;
final String DEFAULT_TIME_SYSTEM = "MJD_UTC"; // FIXME take from confif file
protected Subsurvey[] dbSubsurveyArr = null;
private String reqQueryString;
protected void doUsageError(String message, PrintWriter printWriter)
......@@ -76,9 +73,6 @@ public class FormatResponseFilter implements Filter
LOGGER.info("trace");
String surveysAbsPathname = settings.serviceUrls.surveysAbsPathname();
LOGGER.info("Loading metadata from: " + surveysAbsPathname);
dbSubsurveyArr = Subsurvey.loadSubsurveys(surveysAbsPathname);
LOGGER.info("Surveys: loaded metadata for " + dbSubsurveyArr.length + " known surveys");
LOGGER.info("Default charset: " + Charset.defaultCharset());
LOGGER.info("DB: " + settings.dbConn.toString());
}
......@@ -87,7 +81,7 @@ public class FormatResponseFilter implements Filter
@Override
public void doFilter(ServletRequest request, ServletResponse response, FilterChain chain) throws IOException, ServletException
{
LOGGER.info("trace");
LOGGER.fine("trace");
LOGGER.info("REQUEST START =============================================================================================");
long startTime_msec = System.currentTimeMillis();
......@@ -103,71 +97,48 @@ public class FormatResponseFilter implements Filter
// VLKB: reconstruct cutout/merge queryStrings and overlap code
Map<String, String[]> params = request.getParameterMap();
SubsurveyId subsurveyId = new SubsurveyId(params); // for legacy-only Input
Pos pos = Pos.parsePos(params, DEFAULT_SKY_SYSTEM);
Band band = Band.parseBand(params, DEFAULT_SPEC_SYSTEM);
String queryStringBase = toQueryString(pos, band);
ObsCore[] obsCoreArr = queryObsCore(pubdidArr,
pos); // VLKB: calc overlap-code for sky
// VLKB: calc overlap-code for sky
ObsCore[] obsCoreArr = queryObsCore(pubdidArr, pos);
Dataset[] datasetArr = convert(obsCoreArr,
band, // VLKB: calc overlap-code for velocity
// VLKB: calc overlap-code for velocity
// convert overlap-codes and adds access-urls for cutout, merge
Dataset[] datasetArr = convert(obsCoreArr, band,
settings.serviceUrls.cutoutUrl(),
queryStringBase);
SearchOutputData searchOutputData = SearchOutputData.marshall(datasetArr,
/*subsurveyId,*/
dbSubsurveyArr,
settings.serviceUrls.mergeUrl(),
queryStringBase);
String respFormat;
String respFormatReq[] = params.get("RESPONSEFORMAT");
if(respFormatReq != null && (respFormatReq.length > 0) && !respFormatReq[0].isEmpty())
{
respFormat = respFormatReq[0];
LOGGER.info("responseFormat(from request): " + respFormat);
LOGGER.finest("responseFormat(from request): " + respFormat);
}
else
{
respFormat = settings.serviceUrls.responseFormat();
LOGGER.info("responseFormat(from settings): " + respFormat);
LOGGER.finest("responseFormat(from settings): " + respFormat);
}
response.setCharacterEncoding(RESPONSE_ENCODING);
if(respFormat.equals("application/x-vlkb+xml"))
{
response.setContentType("application/xml");
boolean showDuration = true;
XmlSerializer.serializeToLegacyResults(responseWriter, RESPONSE_ENCODING,
responseWrapper.auth, pos, band, subsurveyId, // <inputs/>
searchOutputData,
showDuration,startTime_msec);
}
else if(respFormat.startsWith("application/x-votable+xml"))
if(respFormat.startsWith("application/x-votable+xml"))
{
response.setContentType("application/xml");
boolean showDuration = false;
if(respFormat.contains("mode=bysubsurveys"))
XmlSerializer.serializeToVoTableBySubsurveys(responseWriter, RESPONSE_ENCODING,
searchOutputData,showDuration,startTime_msec);
else if(respFormat.contains("mode=bysurveys"))
XmlSerializer.serializeToVoTableBySurveys(responseWriter, RESPONSE_ENCODING,
searchOutputData,showDuration,startTime_msec);
else
XmlSerializer.serializeToVoTable(responseWriter, RESPONSE_ENCODING,
searchOutputData,
settings.serviceUrls.cutoutUrl(),settings.serviceUrls.mergeUrl(),
showDuration,startTime_msec);
XmlSerializer.serializeToVoTable(responseWriter, RESPONSE_ENCODING,
datasetArr,
settings.serviceUrls.cutoutUrl(),settings.serviceUrls.mergeUrl(),
showDuration,startTime_msec);
}
else
{
final String errMsg = "Illegal response format request: " + respFormat;
LOGGER.info(errMsg);
LOGGER.warning(errMsg);
response.setContentType("text/plain");
doUsageError(errMsg, responseWriter);
// FIXME set http err code
......@@ -177,7 +148,7 @@ public class FormatResponseFilter implements Filter
}
else
{
LOGGER.info("SearchServlet returned no ID's.");
LOGGER.fine("SearchServlet returned no ID's.");
}
LOGGER.info("REQUEST END =============================================================================================");
......@@ -202,8 +173,11 @@ public class FormatResponseFilter implements Filter
String dataproduct_type;
Integer calib_level;
String obs_collection;
String obs_title;
String obs_id;
String obs_publisher_did;
String bib_reference;
String data_rights;
String access_url;
String access_format;
......@@ -271,7 +245,6 @@ public class FormatResponseFilter implements Filter
dataset.obsCore = obsCore;
dataset.subsurvey_id = obsCore.obs_collection;
dataset.overlapCodeSky = convertToOverlapCodeSky(obsCore.inputInsideDb, obsCore.dbInsideInput);
dataset.overlapCodeVel = convertToOverlapCodeVel(band,obsCore.em_valid,obsCore.em_min,obsCore.em_max);
dataset.overlapCode = convertToOverlapCode(dataset.overlapCodeSky, dataset.overlapCodeVel);
......
data-discovery/src/main/java/output/ObscoreExt.java → data-discovery/src/main/java/webapi/formatfilter/ObscoreExt.java
+ 6
− 54
View file @ 08308c0f
......@@ -9,8 +9,11 @@ class ObscoreExt
new ColumnInfo( "dataproduct_type", String.class, "Dataproduct Type (image|cube)" ),
new ColumnInfo( "calib_level", Integer.class, "Calibration level" ),
new ColumnInfo( "obs_collection", String.class, "Collection" ),
new ColumnInfo( "obs_title", String.class, "Title" ),
new ColumnInfo( "obs_id", String.class, "Observation Id" ),
new ColumnInfo( "obs_publisher_did", String.class, "Publisher Did" ),
new ColumnInfo( "bib_reference", String.class, "Bibbliographic refererence" ),
new ColumnInfo( "data_rights", String.class, "Data rights" ),
new ColumnInfo( "access_url", String.class, "Access URL" ),
new ColumnInfo( "access_format", String.class, "Format (MIME type)" ),
......@@ -53,8 +56,11 @@ class ObscoreExt
dataset.obsCore.dataproduct_type,//dataset.dataType,
Integer.valueOf( dataset.obsCore.calib_level ),
dataset.obsCore.obs_collection,
dataset.obsCore.obs_title,
dataset.obsCore.obs_id,
dataset.obsCore.obs_publisher_did,
dataset.obsCore.bib_reference,
dataset.obsCore.data_rights,
dataset.obsCore.access_url,//dataset.access.accessCutoutUrl,
dataset.obsCore.access_format,
......@@ -95,24 +101,10 @@ class ObscoreExt
new ColumnInfo( "overlapSky", Integer.class, "Overlap Code for Sky axes" ),
new ColumnInfo( "overlapSpec", Integer.class, "Overlap Code for Spectral axis" ),
/* new ColumnInfo( "P1lon", Double.class, "P1 longitude" ),
new ColumnInfo( "P1lat", Double.class, "P1 latitude" ),
new ColumnInfo( "P2lon", Double.class, "P2 longitude" ),
new ColumnInfo( "P2lat", Double.class, "P2 latitude" ),
new ColumnInfo( "P3lon", Double.class, "P3 longitude" ),
new ColumnInfo( "P3lat", Double.class, "P3 latitude" ),
new ColumnInfo( "P4lon", Double.class, "P4 longitude" ),
new ColumnInfo( "P4lat", Double.class, "P4 latitude" ),
*/
new ColumnInfo( "s_region_galactic", String.class, "Region [GALACTIC]" ),
new ColumnInfo( "vel_min", Double.class, "Velocity min" ),
new ColumnInfo( "vel_max", Double.class, "Velocity max" ),
new ColumnInfo( "file_url", String.class, "Access URL: all file" ),
new ColumnInfo( "cutout_url", String.class, "Access URL: cut file" ),
new ColumnInfo( "merge_url", String.class, "Access URL: demosaicing files" ),
};
public static Object[] vlkbRow( Dataset dataset )
......@@ -123,42 +115,11 @@ class ObscoreExt
Integer.valueOf( dataset.overlapCodeSky ),
Integer.valueOf( dataset.overlapCodeVel ),
/* Double.valueOf(dataset.vertices_deg.lon[0]), Double.valueOf(dataset.vertices_deg.lat[0]),
Double.valueOf(dataset.vertices_deg.lon[1]), Double.valueOf(dataset.vertices_deg.lat[1]),
Double.valueOf(dataset.vertices_deg.lon[2]), Double.valueOf(dataset.vertices_deg.lat[2]),
Double.valueOf(dataset.vertices_deg.lon[3]), Double.valueOf(dataset.vertices_deg.lat[3]),
*/
dataset.obsCore.s_region_galactic,
dataset.obsCore.vel_min == null ? null : Double.valueOf(dataset.obsCore.vel_min),
dataset.obsCore.vel_min == null ? null : Double.valueOf(dataset.obsCore.vel_max),
dataset.access.accessFileUrl,
dataset.access.accessCutoutUrl,
dataset.access.accessMosaicUrl,
};
}
public static final ColumnInfo[] SUBSURVEY_COLINFO =
{
new ColumnInfo( "frequency", Double.class, "Frequency" ),
new ColumnInfo( "survey", String.class, "Survey name" ),
new ColumnInfo( "species", String.class, "Species" ),
new ColumnInfo( "transition", String.class, "Transition" ),
new ColumnInfo( "description", String.class, "Descritpion" )
};
public static Object[] subsurveyRow( Subsurvey subsurvey )
{
return new Object[]
{
subsurvey.rf,
subsurvey.surveyname,
subsurvey.species,
subsurvey.transition,
subsurvey.description
};
}
......@@ -172,15 +133,6 @@ class ObscoreExt
}
public static final ColumnInfo[] OBSCORE_VLKB_SUBSURVEY_COLINFO = concat(concat(OBSCORE_COLINFO, VLKB_COLINFO), SUBSURVEY_COLINFO);
public static Object[] obscoreVlkbSubsurveyRow( Dataset dataset, Subsurvey subsurvey )
{
return concat(concat(obscoreRow(dataset),vlkbRow(dataset)), subsurveyRow(subsurvey));
}
private static ColumnInfo[] concat(ColumnInfo[] arr1, ColumnInfo[] arr2)
{
......
data-discovery/src/main/java/webapi/formatfilter/XmlSerializer.java 0 → 100644
+ 74
− 0
View file @ 08308c0f
import java.io.PrintWriter;
// VOTable
import uk.ac.starlink.table.*;// StarTable needed
import uk.ac.starlink.votable.*;// Writer needed
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.BufferedWriter;
import java.util.List;
import java.util.ArrayList;
import vo.parameter.*;
final class XmlSerializer
{
private XmlSerializer() {}
// VOTable
public static void serializeToVoTable(
PrintWriter writer, String charEncoding,
Dataset[] datasetArr,
String cutoutUrl, String mergeUrl,
boolean showDuration, long startTime_msec) throws IOException
{
StarTable dstable = makeSearchResultsTable( datasetArr );
dstable.setParameter(new DescribedValue(
new DefaultValueInfo("datacubeCount", Integer.class, "Count of all datacubes from VLKB-search" ),
datasetArr.length ) );
BufferedWriter out = new BufferedWriter( writer );
out.write("<?xml-stylesheet type='text/xsl' href='VOTable2XHTML.xsl'?>");
out.write( "<VOTABLE version='1.1'>" );
out.write( "<RESOURCE type=\"results\">" );
out.write( "<DESCRIPTION> " + Version.asString + " </DESCRIPTION>" );
VOSerializer.makeSerializer( DataFormat.TABLEDATA, dstable ).writeInlineTableElement( out );
out.write( "</RESOURCE>" );
out.write( "<RESOURCE type=\"meta\" utype=\"adhoc:service\" name=\"CutoutService\" >" );
out.write( "<DESCRIPTION> VLKB cutout service </DESCRIPTION>");
out.write( "<PARAM name=\"standardID\" datatype=\"char\" arraysize=\"*\" value=\"ivo://ivoa.net/std/SODA#sync-1.0\" />");
out.write( "<PARAM name=\"accessURL\" datatype=\"char\" arraysize=\"*\" value=\"" + cutoutUrl + "\" />");
out.write( "<GROUP name=\"inputParams\">");
out.write( "<PARAM name=\"ID\" datatype=\"char\" arraysize=\"*\" value=\"\" ref=\"primaryID\" />"); // FIXME results table obs_publisher_did FIELD must have attrib: ID="primaryID"
out.write( "</GROUP>");
out.write( "</RESOURCE>" );
out.write( "</VOTABLE>" );
out.flush();
}
private static StarTable makeSearchResultsTable(Dataset[] datasetArr)
{
RowListStarTable astro = new RowListStarTable( ObscoreExt.OBSCORE_VLKB_COLINFO );
for(Dataset dataset : datasetArr)
{
if(dataset.obsCore == null) continue; // FIXME skip mergeable datasets
astro.addRow( ObscoreExt.obscoreVlkbRow(dataset) );
}
return astro;
}
}
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