changes the base docker-image to be the official Tomcat9-image (on Ubuntu22) (a0a40ac7) · Commits · ViaLactea / vlkb-siav2

README.md

+25 −5

Original line number	Diff line number	Diff line
		## vlkb-siav2

		is a web-application to discover astronomical data stored in FITS-files and described in a VO ObsCore table.
		It implements the SIA version 2, IVOA recommendation (https://ivoa.net/documents/SIA/20151223/) with optional VLKB-specific features:
		is a web-application to discover astronomical data (supports FITS-files) and described in a VO ObsTAP table
		(https://ivoa.net/documents/ObsCore).
		It implements the SIA version 2, IVOA recommendation (https://ivoa.net/documents/SIA) with optional VLKB-specific features:

		- provides overlap code
		- the filtering paramters (POS, BAND) can be given in GALACTIC and VELO-LSRK-km/s coordinates systems
		- handles addtional metadata about the surveys (name, species, transformation)
		- VOTable response includes composed URLs for file download, file-cutout and files-demosaic services

		The service consists of vlkb-siav2 web-application and associated vlkb-obscore command line tool to create the VO ObsCore table from FITS-files.
		The service consists of vlkb-siav2 web-application and associated vlkb-obscore command line tool to create the ObsTAP table from FITS-files headers.

		The vlkb-obscore cli is available from https://ict.inaf.it/gitlab/butora/vlkb-datasets .
		Dockerized version of the web-app is available from https://ict.inaf.it/gitlab/butora/vlkb-datasets-docker .

		## Docker image

		To configure the application choose a context-root where the SIAv2 can be accessed,
		provide database URI which points to the ObsTAP table and provide URL for data-access
		(typically a SODA service).
		Example compose.yaml entry for VLKB-SIAv2:

		```yaml
		vlkb-siav2:
		container_name: vlkb-siav2
		image: git.ia2.inaf.it:5050/vialactea/vlkb-siav2/siav2:1.6
		ports:
		- 8080:8080
		environment:
		- DISCOVERY_CONTEXT_ROOT=vlkb#datasets#siav2
		- DB_URI=jdbc:postgresql://vlkb-db:5432/vialactea
		- DB_USERNAME=vialactea
		- DB_PASSWORD=ia2vlkb
		- CUTOUT_SERVICE_URL=http://vlkb-devel.ia2.inaf.it:8004/vlkb/datasets/soda
		```

		## Installation

		There is a war-package for the search web-application and the package (deb or rpm) with linux

data-discovery/src/main/java/search/DbPSearch.java

+12 −12

Original line number	Diff line number	Diff line
		@@ -37,7 +37,7 @@ public class DbPSearch

		public String[] queryOverlapingPubdid(Coord coord)
		{
		LOGGER.info("trace");
		LOGGER.fine("trace");

		String inputRegion = toPgSphereSqlTypeString(coord.pos);
		String dbRegion = toRegionColumnName(coord.pos.system);
		@@ -90,11 +90,11 @@ public class DbPSearch

		//theQuery += " ORDER BY obs_collection";

		LOGGER.info(theQuery);
		LOGGER.fine(theQuery);

		List<String> pubdidList = new ArrayList<>();

		LOGGER.info("Connecting to: " + dbConn.uri()
		LOGGER.fine("Connecting to: " + dbConn.uri()
		+ " with optional user/pwd: " + dbConn.userName() +" / "+ dbConn.password() );

		try(
		@@ -116,7 +116,7 @@ public class DbPSearch

		String[] pubdidArr = pubdidList.toArray(new String[0]);

		LOGGER.info("pubdidArr[] length: " + pubdidArr.length);
		LOGGER.fine("pubdidArr[] length: " + pubdidArr.length);

		return pubdidArr;
		}
		@@ -153,7 +153,7 @@ public class DbPSearch

		public FormatResponseFilter.ObsCore[] queryOutputData(String[] pubdidArr, Pos pos)
		{
		LOGGER.info("");
		LOGGER.fine("trace");

		String commaSepPubdids = String.join("\',\'", pubdidArr);

		@@ -167,11 +167,11 @@ public class DbPSearch

		theQuery += " ORDER BY obs_collection";

		//LOGGER.info(theQuery);
		//LOGGER.fine(theQuery);

		List<FormatResponseFilter.ObsCore> obsCoreList = new ArrayList<>();

		LOGGER.info("Connecting to: " + dbConn.uri()
		LOGGER.fine("Connecting to: " + dbConn.uri()
		+ " with optional user/pwd: " + dbConn.userName() +" / "+ dbConn.password() );
		try(
		Connection conn = DriverManager.getConnection(dbConn.uri(), dbConn.userName(), dbConn.password());
		@@ -237,7 +237,7 @@ public class DbPSearch
		obsCoreList.add(obsCore);
		}

		LOGGER.info("From DB collected # of ObsCore : " + obsCoreList.size());
		LOGGER.fine("From DB collected # of ObsCore : " + obsCoreList.size());
		}
		catch (SQLException se)
		{
		@@ -336,12 +336,12 @@ public class DbPSearch

		private void logSqlExInfo(SQLException se)
		{
		LOGGER.info("SQLState : " + se.getSQLState());
		LOGGER.info("ErrorCode: " + se.getErrorCode());
		LOGGER.info("Message : " + se.getMessage());
		LOGGER.fine("SQLState : " + se.getSQLState());
		LOGGER.fine("ErrorCode: " + se.getErrorCode());
		LOGGER.fine("Message : " + se.getMessage());
		Throwable t = se.getCause();
		while(t != null) {
		LOGGER.info("Cause: " + t);
		LOGGER.fine("Cause: " + t);
		t = t.getCause();
		}
		}

data-discovery/src/main/java/webapi/SearchServlet.java

+10 −8

Original line number	Diff line number	Diff line
		@@ -35,7 +35,7 @@ public class SearchServlet extends javax.servlet.http.HttpServlet
		{
		super.init();

		LOGGER.info("DB : " + settings.dbConn.toString());
		LOGGER.config("DB: " + settings.dbConn.toString());
		}

		protected void doMultiValuedParamNotSupported(String message, PrintWriter printWriter)
		@@ -57,7 +57,7 @@ public class SearchServlet extends javax.servlet.http.HttpServlet
		protected void doGet(HttpServletRequest request, HttpServletResponse response)
		throws ServletException, IOException, UnsupportedEncodingException
		{
		LOGGER.info("trace");
		LOGGER.fine("trace");
		legacyLogEntry(request);

		try
		@@ -105,13 +105,15 @@ public class SearchServlet extends javax.servlet.http.HttpServlet
		}
		String[] pubdidArr = dbps.queryOverlapingPubdid(coord);

		LOGGER.info("Found " + pubdidArr.length + " records");

		final String RESPONSE_ENCODING = "UTF-8";

		/* if filters installed response will be wrapped */

		if(response instanceof FormatResponseWrapper)
		{
		LOGGER.info("response-type is FormatResponseWrapper");
		LOGGER.finest("response-type is FormatResponseWrapper");

		response.setContentType("text/plain");
		response.setCharacterEncoding(RESPONSE_ENCODING);
		@@ -123,7 +125,7 @@ public class SearchServlet extends javax.servlet.http.HttpServlet
		}
		else
		{
		LOGGER.info("response-type is HttpServletResponse");
		LOGGER.finest("response-type is HttpServletResponse");

		response.setContentType("text/plain");
		response.setCharacterEncoding(RESPONSE_ENCODING);
		@@ -138,7 +140,7 @@ public class SearchServlet extends javax.servlet.http.HttpServlet
		}
		catch(MultiValuedParamNotSupported ex)
		{
		LOGGER.info("MultiValuedParamNotSupported: " + ex.getMessage());
		LOGGER.warning("MultiValuedParamNotSupported: " + ex.getMessage());

		response.setStatus(HttpServletResponse.SC_BAD_REQUEST);
		response.setContentType("text/plain");
		@@ -149,7 +151,7 @@ public class SearchServlet extends javax.servlet.http.HttpServlet
		}
		catch(IllegalArgumentException ex)
		{
		LOGGER.info("IllegalArgumentException: " + ex.getMessage());
		LOGGER.warning("IllegalArgumentException: " + ex.getMessage());

		response.setStatus(HttpServletResponse.SC_BAD_REQUEST);
		response.setContentType("text/plain");
		@@ -160,7 +162,7 @@ public class SearchServlet extends javax.servlet.http.HttpServlet
		}
		catch(Exception ex)
		{
		LOGGER.info("Exception: " + ex.getMessage());
		LOGGER.warning("Exception: " + ex.getMessage());
		ex.printStackTrace();

		response.setStatus(HttpServletResponse.SC_INTERNAL_SERVER_ERROR);
		@@ -183,7 +185,7 @@ public class SearchServlet extends javax.servlet.http.HttpServlet
		requestURL.append("?").append(request.getQueryString());
		String completeURL = requestURL.toString();
		String className = this.getClass().getSimpleName();
		LOGGER.info(className + " vlkb req from: "
		LOGGER.finest(className + " vlkb req from: "
		+ request.getRemoteAddr()
		+ " doGet: " + URLDecoder.decode(completeURL, "UTF-8"));
		}

data-discovery/src/main/java/webapi/SearchSettings.java

+1 −1

Original line number	Diff line number	Diff line
		@@ -9,7 +9,7 @@ import java.io.PrintWriter;

		class SearchSettings
		{
		private static final Logger LOGGER = Logger.getLogger("SearchSettings");
		//private static final Logger LOGGER = Logger.getLogger("SearchSettings");

		public static class DefaultParamValues
		{

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

+9 −9

Original line number	Diff line number	Diff line
		@@ -70,11 +70,11 @@ public class FormatResponseFilter implements Filter
		@Override
		public void init(FilterConfig filterConfig) throws ServletException
		{
		LOGGER.info("trace");
		LOGGER.fine("trace");

		String surveysAbsPathname = settings.serviceUrls.surveysAbsPathname();
		LOGGER.info("Default charset: " + Charset.defaultCharset());
		LOGGER.info("DB: " + settings.dbConn.toString());
		LOGGER.config("Default charset: " + Charset.defaultCharset());
		LOGGER.config("DB: " + settings.dbConn.toString());
		}


		@@ -82,7 +82,7 @@ public class FormatResponseFilter implements Filter
		public void doFilter(ServletRequest request, ServletResponse response, FilterChain chain) throws IOException, ServletException
		{
		LOGGER.fine("trace");
		LOGGER.info("REQUEST START =============================================================================================");
		LOGGER.fine("REQUEST START =============================================================================================");
		long startTime_msec = System.currentTimeMillis();

		FormatResponseWrapper responseWrapper = new FormatResponseWrapper((HttpServletResponse) response);
		@@ -151,7 +151,7 @@ public class FormatResponseFilter implements Filter
		LOGGER.fine("SearchServlet returned no ID's.");
		}

		LOGGER.info("REQUEST END =============================================================================================");
		LOGGER.fine("REQUEST END =============================================================================================");
		}


		@@ -159,7 +159,7 @@ public class FormatResponseFilter implements Filter
		@Override
		public void destroy()
		{
		LOGGER.info("trace");
		LOGGER.fine("trace");
		}


		@@ -217,7 +217,7 @@ public class FormatResponseFilter implements Filter

		private FormatResponseFilter.ObsCore[] queryObsCore(String[] pubdidArr, Pos pos)//, String fitsRemotePath)
		{
		LOGGER.info("trace");
		LOGGER.fine("trace");

		DbPSearch dbps;
		synchronized(DbPSearch.class)
		@@ -337,7 +337,7 @@ public class FormatResponseFilter implements Filter
		// generate cutout/merge queryStrings
		private String toQueryString(Pos pos, Band band)
		{
		LOGGER.info("trace");
		LOGGER.fine("trace");

		StringBuilder sb = new StringBuilder();

		@@ -358,7 +358,7 @@ public class FormatResponseFilter implements Filter
		break;

		default:
		LOGGER.info("Coord::toQueryString: unknown shape: " + pos.shape.toString());
		LOGGER.warning("Coord::toQueryString: unknown shape: " + pos.shape.toString());
		}
		}
		sb.append("&POSSYS=" + pos.system.toString());