diff --git a/data-discovery/Makefile b/data-discovery/Makefile
index 5349b91183a1ce2b77e1d25938789317635d5946..b48fd27c96761a38709f42a3d9abe1e35393dd11 100644
--- a/data-discovery/Makefile
+++ b/data-discovery/Makefile
@@ -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
diff --git a/data-discovery/src/main/java/webapi/DBConn.java b/data-discovery/src/main/java/common/DBConn.java
similarity index 100%
rename from data-discovery/src/main/java/webapi/DBConn.java
rename to data-discovery/src/main/java/common/DBConn.java
diff --git a/data-discovery/src/main/java/common/Subsurvey.java b/data-discovery/src/main/java/common/Subsurvey.java
deleted file mode 100644
index b8550a1c64c8b08a473dfecf82f599bbe26fdd9a..0000000000000000000000000000000000000000
--- a/data-discovery/src/main/java/common/Subsurvey.java
+++ /dev/null
@@ -1,117 +0,0 @@
-
-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]);
- }
-
-
-
-
-
-}
-
-
diff --git a/data-discovery/src/main/java/output/SearchOutputData.java b/data-discovery/src/main/java/output/SearchOutputData.java
deleted file mode 100644
index 9d2ab54505564070c147403d344ac8dedaa7c193..0000000000000000000000000000000000000000
--- a/data-discovery/src/main/java/output/SearchOutputData.java
+++ /dev/null
@@ -1,83 +0,0 @@
-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]);
- }
-
-}
-
diff --git a/data-discovery/src/main/java/output/XmlSerializer.java b/data-discovery/src/main/java/output/XmlSerializer.java
deleted file mode 100644
index b0f692841037c48e9df6d3b7bf51f3d2bb388165..0000000000000000000000000000000000000000
--- a/data-discovery/src/main/java/output/XmlSerializer.java
+++ /dev/null
@@ -1,475 +0,0 @@
-
-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("&", "&") + " </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("&","&");
- subsurvey.description = subsurvey.description.replace("<","<");
- subsurvey.description = subsurvey.description.replace(">",">");
- subsurvey.description = subsurvey.description.replace("%","%");
- }
-
- 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("&","&") + "</URL>");
-
- if(access.accessMosaicUrl != null)
- xml.append("<URL type=\"mosaic\">" + access.accessMosaicUrl.replaceAll("&","&") + "</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();
- }
-
-
-}
diff --git a/data-discovery/src/main/java/webapi/MonitorFilter.java b/data-discovery/src/main/java/webapi/MonitorFilter.java
deleted file mode 100644
index 721e4de77a8f4cd3fab06e18c49044f763a6d571..0000000000000000000000000000000000000000
--- a/data-discovery/src/main/java/webapi/MonitorFilter.java
+++ /dev/null
@@ -1,50 +0,0 @@
-
-//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");
-
- }
-
-
-
-}
-
diff --git a/data-discovery/src/main/java/webapi/SearchServlet.java b/data-discovery/src/main/java/webapi/SearchServlet.java
index 58d49d42134de8169118b504e27f45ea8f7c2e8e..7f510fb3dded4be91052b05906c7c5f8151c72a1 100644
--- a/data-discovery/src/main/java/webapi/SearchServlet.java
+++ b/data-discovery/src/main/java/webapi/SearchServlet.java
@@ -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);
diff --git a/data-discovery/src/main/java/webapi/AuthorizationResponseFilter.java b/data-discovery/src/main/java/webapi/authzfilter/AuthorizationResponseFilter.java
similarity index 100%
rename from data-discovery/src/main/java/webapi/AuthorizationResponseFilter.java
rename to data-discovery/src/main/java/webapi/authzfilter/AuthorizationResponseFilter.java
diff --git a/data-discovery/src/main/java/webapi/AuthorizationResponseSettings.java b/data-discovery/src/main/java/webapi/authzfilter/AuthorizationResponseSettings.java
similarity index 100%
rename from data-discovery/src/main/java/webapi/AuthorizationResponseSettings.java
rename to data-discovery/src/main/java/webapi/authzfilter/AuthorizationResponseSettings.java
diff --git a/data-discovery/src/main/java/output/Dataset.java b/data-discovery/src/main/java/webapi/formatfilter/Dataset.java
similarity index 91%
rename from data-discovery/src/main/java/output/Dataset.java
rename to data-discovery/src/main/java/webapi/formatfilter/Dataset.java
index d3aec3953af9c1044770ad6d64bc44d9e197e2cc..da87a712b02e6dbf6ad96ebfe00e2f2fd3fb124c 100644
--- a/data-discovery/src/main/java/output/Dataset.java
+++ b/data-discovery/src/main/java/webapi/formatfilter/Dataset.java
@@ -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;
diff --git a/data-discovery/src/main/java/webapi/FormatResponseFilter.java b/data-discovery/src/main/java/webapi/formatfilter/FormatResponseFilter.java
similarity index 81%
rename from data-discovery/src/main/java/webapi/FormatResponseFilter.java
rename to data-discovery/src/main/java/webapi/formatfilter/FormatResponseFilter.java
index 7c01c846a31bea0139d17a1910ad4d15acd0d42c..dd9163012d5a835b6d9986075c5a2f62b4ea0043 100644
--- a/data-discovery/src/main/java/webapi/FormatResponseFilter.java
+++ b/data-discovery/src/main/java/webapi/formatfilter/FormatResponseFilter.java
@@ -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);
diff --git a/data-discovery/src/main/java/webapi/FormatResponseSettings.java b/data-discovery/src/main/java/webapi/formatfilter/FormatResponseSettings.java
similarity index 100%
rename from data-discovery/src/main/java/webapi/FormatResponseSettings.java
rename to data-discovery/src/main/java/webapi/formatfilter/FormatResponseSettings.java
diff --git a/data-discovery/src/main/java/output/ObscoreExt.java b/data-discovery/src/main/java/webapi/formatfilter/ObscoreExt.java
similarity index 71%
rename from data-discovery/src/main/java/output/ObscoreExt.java
rename to data-discovery/src/main/java/webapi/formatfilter/ObscoreExt.java
index 4027f4564f46dc63d9ed2b06b4cc597f2288fce4..f9be0fb4264e85401673060de5c99d1d0287aa3e 100644
--- a/data-discovery/src/main/java/output/ObscoreExt.java
+++ b/data-discovery/src/main/java/webapi/formatfilter/ObscoreExt.java
@@ -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)
{
diff --git a/data-discovery/src/main/java/webapi/formatfilter/XmlSerializer.java b/data-discovery/src/main/java/webapi/formatfilter/XmlSerializer.java
new file mode 100644
index 0000000000000000000000000000000000000000..6e36122cf89a555402f1d57daebc4bff261aae17
--- /dev/null
+++ b/data-discovery/src/main/java/webapi/formatfilter/XmlSerializer.java
@@ -0,0 +1,74 @@
+
+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;
+ }
+
+
+}