creates flat VOTable response (removes Subsurvey) (08308c0f) · Commits · ViaLactea / vlkb-siav2

data-discovery/Makefile

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		@@ -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/webapi/DBConn.java→data-discovery/src/main/java/common/DBConn.java

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data-discovery/src/main/java/common/Subsurvey.java

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		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

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		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

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