removes classes Inputs and SearchDescription and moves their data into FormatResponseWrapper (783651e6) · Commits · ViaLactea / vlkb-siav2

data-discovery/src/main/java/vlkb/output/Dataset.java

+4 −3

Original line number	Diff line number	Diff line
		@@ -26,6 +26,7 @@ class Dataset
		}


		String queryString;// was in Inputs
		String subsurvey_id;
		int overlapCodeSky;
		int overlapCodeVel;
		@@ -59,7 +60,7 @@ class Dataset
		}


		public Dataset(List<Dataset> datasetList, Inputs inputs, String mergeUrlRoot)
		public Dataset(List<Dataset> datasetList, AuthPolicy auth, Coord coord, SubsurveyId subsurveyId, boolean countNullValues, String mergeUrlRoot)
		{
		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
		@@ -69,9 +70,9 @@ class Dataset
		this.access = new Access();
		this.access.accessFileUrl = null;
		this.access.accessCutoutUrl = null;
		this.access.accessMosaicUrl = mergeUrlRoot + "?pubdid=" + publisherDid + "&" +inputs.queryString;
		this.access.accessMosaicUrl = mergeUrlRoot + "?pubdid=" + publisherDid + "&" + /inputs./queryString;

		this.vertices_deg = mergeVertices(datasetList, inputs.coord);
		this.vertices_deg = mergeVertices(datasetList, /inputs./coord);
		}

data-discovery/src/main/java/vlkb/output/Inputs.java

deleted100644 → 0

+0 −52

Original line number	Diff line number	Diff line


		import java.lang.StringBuilder;


		class Inputs
		{
		Coord coord;
		SubsurveyId subsurveyId;
		boolean countNullValues;
		AuthPolicy auth;

		String queryString;

		public Inputs(AuthPolicy auth, Coord coord, SubsurveyId subsurveyId, boolean countNullValues)
		{
		this.coord = coord;
		this.subsurveyId = subsurveyId;
		this.countNullValues = countNullValues;
		this.auth = auth;

		queryString = buildVoQueryString(coord, subsurveyId, countNullValues);
		//queryString = buildQueryString(coord, subsurveyId, countNullValues);
		}


		private String buildQueryString(Coord coord, SubsurveyId subsurveyId, boolean countNullValues)
		{
		StringBuilder queryString = new StringBuilder();

		queryString.append(coord.toQueryString());
		if(subsurveyId.surveyName != null) queryString.append("&surveyname=" + subsurveyId.surveyName);
		if(subsurveyId.species != null) queryString.append("&species=" + subsurveyId.species);
		if(subsurveyId.transition != null) queryString.append("&transition=" + subsurveyId.transition);

		return queryString.toString();
		}

		private String buildVoQueryString(Coord coord, SubsurveyId subsurveyId, boolean countNullValues)
		{
		StringBuilder queryString = new StringBuilder();

		queryString.append(coord.toVoQueryString());
		if(subsurveyId.surveyName != null) queryString.append("&surveyname=" + subsurveyId.surveyName);
		if(subsurveyId.species != null) queryString.append("&species=" + subsurveyId.species);
		if(subsurveyId.transition != null) queryString.append("&transition=" + subsurveyId.transition);

		return queryString.toString();
		}

		}

data-discovery/src/main/java/vlkb/output/SearchOutputData.java

+13 −7

Original line number	Diff line number	Diff line
		@@ -7,26 +7,32 @@ class SearchOutputData
		private static final Logger LOGGER = Logger.getLogger("SearchOutputData");

		String description;
		Inputs inputs;
		AuthPolicy auth;
		Coord coord;
		SubsurveyId subsurveyId;
		boolean countNullValues;
		int datacubeCount;
		String versionString;
		Subsurvey[] subsurveyArr;


		public static SearchOutputData marshall(Dataset[] datasetArr, Inputs inputs, String mergeUrlRoot, Subsurvey[] dbSubsurveys)
		public static SearchOutputData marshall(Dataset[] datasetArr, AuthPolicy auth, Coord coord, SubsurveyId subsurveyId, boolean countNullValues, String mergeUrlRoot, Subsurvey[] dbSubsurveys)
		{
		SearchOutputData sod = new SearchOutputData();

		sod.description = "Via Lactea Knowledge Base response (Search by pgSphere)";
		sod.inputs = inputs;
		sod.auth = auth;
		sod.coord = coord;
		sod.subsurveyId = subsurveyId;
		sod.countNullValues = countNullValues;
		sod.versionString = "Search (pgSphere) version " + Version.asString;
		sod.datacubeCount = datasetArr.length;

		sod.subsurveyArr = groupBySubsurveys(datasetArr, inputs, dbSubsurveys, mergeUrlRoot);
		sod.subsurveyArr = groupBySubsurveys(datasetArr, auth, coord, subsurveyId, countNullValues, dbSubsurveys, mergeUrlRoot);
		return sod;
		}

		private static Subsurvey[] groupBySubsurveys(Dataset[] datasetArr, Inputs inputs, Subsurvey[] dbSubsurveys, String mergeUrlRoot)
		private static Subsurvey[] groupBySubsurveys(Dataset[] datasetArr, AuthPolicy auth, Coord coord, SubsurveyId subsurveyId, boolean countNullValues, Subsurvey[] dbSubsurveys, String mergeUrlRoot)
		{
		List<Subsurvey> subsurveyList = new ArrayList<Subsurvey>();

		@@ -42,7 +48,7 @@ class SearchOutputData
		{
		if( Dataset.areDatasetsMergeable(datasetList) )
		{
		Dataset mergedDataset = new Dataset(datasetList, inputs, mergeUrlRoot);
		Dataset mergedDataset = new Dataset(datasetList, auth, coord, subsurveyId, countNullValues, mergeUrlRoot);
		datasetList.add(mergedDataset);
		}

		@@ -62,7 +68,7 @@ class SearchOutputData
		if( false )
		//if( Dataset.areDatasetsMergeable(datasetList) )
		{
		Dataset mergedDataset = new Dataset(datasetList, inputs, mergeUrlRoot);
		Dataset mergedDataset = new Dataset(datasetList, auth, coord, subsurveyId, countNullValues, mergeUrlRoot);
		datasetList.add(mergedDataset);
		}

data-discovery/src/main/java/vlkb/output/XmlSerializer.java

+8 −11

Original line number	Diff line number	Diff line
		@@ -177,7 +177,14 @@ public final class XmlSerializer
		writer.println("<?xml version=\"1.0\" encoding=\"" + charEncoding + "\" standalone=\"yes\"?>");
		writer.println("<results>");
		writer.println("<description> " + searchOutputData.description + " </description>");
		serialize(writer, searchOutputData.inputs);

		writer.println("<inputs>");
		if(searchOutputData.subsurveyId != null) writer.println(serialize(searchOutputData.subsurveyId));
		if(searchOutputData.coord != null) writer.println(serialize(searchOutputData.coord));
		if(searchOutputData.countNullValues) writer.println("<nullvals> set </nullvals>");
		if(searchOutputData.auth != null) writer.println(serialize(searchOutputData.auth));
		writer.println("</inputs>");

		writer.println("<msg> " + searchOutputData.versionString + " </msg>");
		writer.println("<DatacubeCount> " + searchOutputData.datacubeCount + " </DatacubeCount>");
		for(Subsurvey subsurvey : searchOutputData.subsurveyArr)
		@@ -234,16 +241,6 @@ public final class XmlSerializer
		}


		public static void serialize(PrintWriter writer, Inputs inputs)
		{
		writer.println("<input>");
		if(inputs.subsurveyId != null) writer.println(serialize(inputs.subsurveyId));
		if(inputs.coord != null) writer.println(serialize(inputs.coord));
		if(inputs.countNullValues) writer.println("<nullvals> set </nullvals>");
		if(inputs.auth != null) writer.println(serialize(inputs.auth));
		writer.println("</input>");
		}

		public static void serialize(PrintWriter writer, Subsurvey subsurvey)
		{
		writer.println("<survey>");

data-discovery/src/main/java/vlkb/webapi/FormatResponseFilter.java

+24 −19

Original line number	Diff line number	Diff line
		@@ -16,25 +16,31 @@ import java.nio.charset.Charset;

		class FormatResponseWrapper extends HttpServletResponseWrapper
		{
		private SearchDescription search;
		AuthPolicy auth;

		String[] pubdidArr;
		Coord coord;
		SubsurveyId subsurveyId;
		boolean countNullValues;
		String queryString;



		public FormatResponseWrapper(HttpServletResponse response)
		{
		super(response);
		search = null;
		}

		public void set(SearchDescription search) { this.search = search;}
		public SearchDescription get() { return this.search;}

		public void setPubdidArr(String[] pubdidArr) { this.search.pubdidArr = pubdidArr; }
		public String[] getPubdidArr() { return this.search.pubdidArr; }
		auth = null;
		countNullValues = false;
		}

		public void setPubdidArr(String[] pubdidArr) { this.pubdidArr = pubdidArr; }
		public String[] getPubdidArr() { return this.pubdidArr; }

		public void setAuth(AuthPolicy auth)
		{
		assert (this.search.inputs.auth != null);
		this.search.inputs.auth = auth;
		// assert (this.search.inputs.auth != null);
		this.auth = auth;
		}
		}

		@@ -83,18 +89,16 @@ public class FormatResponseFilter implements Filter
		//if (pubdidWrapper.getContentType().contains("text/plain"))
		{

		SearchDescription search = pubdidWrapper.get();

		Dataset[] datasetArr = getOutputData(
		search.pubdidArr,
		search.inputs.coord,
		search.inputs.subsurveyId,
		search.inputs.queryString,
		pubdidWrapper.getPubdidArr(),
		pubdidWrapper.coord,
		pubdidWrapper.subsurveyId,
		pubdidWrapper.queryString,
		settings.serviceUrls.cutoutUrl());

		SearchOutputData searchOutputData = SearchOutputData.marshall(
		datasetArr,
		search.inputs,
		pubdidWrapper.auth, pubdidWrapper.coord, pubdidWrapper.subsurveyId, pubdidWrapper.countNullValues,
		settings.serviceUrls.mergeUrl(),
		dbSubsurveyArr);

		@@ -210,6 +214,7 @@ public class FormatResponseFilter implements Filter

		dataset.obsDataset = obsDataset;

		dataset.queryString = queryString;
		dataset.subsurvey_id = obsDataset.obs_collection;
		dataset.overlapCodeSky = convertToOverlapCodeSky(obsDataset.inputInsideDb, obsDataset.dbInsideInput);
		dataset.overlapCodeVel = convertToOverlapCodeVel(coord, obsDataset.em_valid, obsDataset.em_min, obsDataset.em_max);