[TAP] Add coordinate system information in TAP_SCHEMA and VOTable (cf COOSYS).

import tap.data.TableIterator;

import tap.log.TAPLog;

import tap.metadata.TAPColumn;

import tap.metadata.TAPCoosys;

import tap.metadata.TAPForeignKey;

import tap.metadata.TAPMetadata;

import tap.metadata.TAPMetadata.STDSchema;

				logger.logDB(LogLevel.INFO, this, "LOAD_TAP_SCHEMA", "Loading TAP_SCHEMA.tables.", null);

			List<TAPTable> lstTables = loadTables(tap_schema.getTable(STDTable.TABLES.label), metadata, stmt);

			// load all coordinate systems from TAP_SCHEMA.coosys: [non standard]

			Map<String, TAPCoosys> mapCoosys = null;

			if (isTableExisting(tap_schema.getDBName(), STDTable.COOSYS.label, stmt.getConnection().getMetaData())){

				if (logger != null)

					logger.logDB(LogLevel.INFO, this, "LOAD_TAP_SCHEMA", "Loading TAP_SCHEMA.coosys.", null);

				mapCoosys = loadCoosys(tap_schema.getTable(STDTable.COOSYS.label), metadata, stmt);

			}

			// load all columns from TAP_SCHEMA.columns:

			if (logger != null)

				logger.logDB(LogLevel.INFO, this, "LOAD_TAP_SCHEMA", "Loading TAP_SCHEMA.columns.", null);

			loadColumns(tap_schema.getTable(STDTable.COLUMNS.label), lstTables, stmt);

			loadColumns(tap_schema.getTable(STDTable.COLUMNS.label), lstTables, mapCoosys, stmt);

			// load all foreign keys from TAP_SCHEMA.keys and TAP_SCHEMA.key_columns:

			if (logger != null)

		}

	}

	/**

	 * Load all coordinate systems declared in the TAP_SCHEMA.

	 * 

	 * @param tableDef		Definition of the table TAP_SCHEMA.coosys.

	 * @param metadata		Metadata in which the found coordinate systems will be inserted (see {@link TAPMetadata#addCoosys(TAPCoosys)}).

	 * @param stmt			Statement to use in order to interact with the database.

	 * 

	 * @return	A map containing all declared coordinate systems (key=coosys ID, value={@link TAPCoosys}).

	 *        	<i>note: this map is required by {@link #loadColumns(TAPTable, List, Map, Statement)}.</i>

	 * 

	 * @throws DBException	If any error occurs while interacting with the database.

	 * 

	 * @since 2.1

	 */

	protected Map<String, TAPCoosys> loadCoosys(final TAPTable tableDef, final TAPMetadata metadata, final Statement stmt) throws DBException{

		ResultSet rs = null;

		try{

			// Build the SQL query:

			StringBuffer sqlBuf = new StringBuffer("SELECT ");

			sqlBuf.append(translator.getColumnName(tableDef.getColumn("id")));

			sqlBuf.append(", ").append(translator.getColumnName(tableDef.getColumn("system")));

			sqlBuf.append(", ").append(translator.getColumnName(tableDef.getColumn("equinox")));

			sqlBuf.append(", ").append(translator.getColumnName(tableDef.getColumn("epoch")));

			sqlBuf.append(" FROM ").append(translator.getTableName(tableDef, supportsSchema));

			sqlBuf.append(" ORDER BY 1,2,3,4");

			// Execute the query:

			rs = stmt.executeQuery(sqlBuf.toString());

			// Create all coosys:

			HashMap<String, TAPCoosys> mapCoosys = new HashMap<String, TAPCoosys>();

			while(rs.next()){

				String coosysId = rs.getString(1),

						system = rs.getString(2), equinox = rs.getString(3),

						epoch = rs.getString(4);

				// create the new coosys:

				TAPCoosys newCoosys = new TAPCoosys(coosysId, system, nullifyIfNeeded(equinox), nullifyIfNeeded(epoch));

				// create and add the new coosys:

				metadata.addCoosys(newCoosys);

				mapCoosys.put(coosysId, newCoosys);

			}

			return mapCoosys;

		}catch(SQLException se){

			if (!isCancelled() && logger != null)

				logger.logDB(LogLevel.ERROR, this, "LOAD_TAP_SCHEMA", "Impossible to load coordinate systems from TAP_SCHEMA.coosys!", se);

			throw new DBException("Impossible to load coordinate systems from TAP_SCHEMA.coosys!", se);

		}finally{

			close(rs);

		}

	}

	/**

	 * <p>Load into the corresponding tables all columns listed in TAP_SCHEMA.columns.</p>

	 * 

	 * @param stmt			Statement to use in order to interact with the database.

	 * 

	 * @throws DBException	If a table can not be found, or if any other error occurs while interacting with the database.

	 * 

	 * @deprecated	This method is now replaced by {@link #loadColumns(TAPTable, List, Map, Statement)} which has an additional parameter:

	 *            	the list of declared coordinate systems. 

	 */

	@Deprecated

	protected void loadColumns(final TAPTable tableDef, final List<TAPTable> lstTables, final Statement stmt) throws DBException{

		loadColumns(tableDef, lstTables, null, stmt);

	}

	/**

	 * <p>Load into the corresponding tables all columns listed in TAP_SCHEMA.columns.</p>

	 * 

	 * <p><i>Note:

	 * 	Tables are searched in the given list by their ADQL name and case sensitively.

	 * 	If they can not be found a {@link DBException} is thrown.

	 * </i></p>

	 * 

	 * <p><i>Note 2:

	 * 	If the column column_index exists, column entries are retrieved ordered by ascending table_name, then column_index, and finally column_name.

	 * 	If this column does not exist, column entries are retrieved ordered by ascending table_name and then column_name.

	 * </i></p>

	 * 

	 * @param tableDef		Definition of the table TAP_SCHEMA.columns.

	 * @param lstTables		List of all published tables (= all tables listed in TAP_SCHEMA.tables).

	 * @param mapCoosys		List of all published coordinate systems (= all coordinates systems listed in TAP_SCHEMA.coosys).

	 * @param stmt			Statement to use in order to interact with the database.

	 * 

	 * @throws DBException	If a table can not be found, or if any other error occurs while interacting with the database.

	 * 

	 * @since 2.1

	 */

	protected void loadColumns(final TAPTable tableDef, final List<TAPTable> lstTables, final Map<String, TAPCoosys> mapCoosys, final Statement stmt) throws DBException{

		ResultSet rs = null;

		try{

			// Determine whether the dbName column exists:

			// Determine whether the columnIndex column exists:

			boolean hasColumnIndex = isColumnExisting(tableDef.getDBSchemaName(), tableDef.getDBName(), "column_index", connection.getMetaData());

			// Determine whether the coosys_id column exists:

			boolean hasCoosys = (mapCoosys != null) && isColumnExisting(tableDef.getDBSchemaName(), tableDef.getDBName(), "coosys_id", connection.getMetaData());

			// Build the SQL query:

			StringBuffer sqlBuf = new StringBuffer("SELECT ");

			sqlBuf.append(translator.getColumnName(tableDef.getColumn("table_name")));

				sqlBuf.append(", ");

				translator.appendIdentifier(sqlBuf, DB_NAME_COLUMN, IdentifierField.COLUMN);

			}

			if (hasCoosys)

				sqlBuf.append(", ").append(translator.getColumnName(tableDef.getColumn("coosys_id")));

			sqlBuf.append(" FROM ").append(translator.getTableName(tableDef, supportsSchema));

			if (hasColumnIndex)

				sqlBuf.append(" ORDER BY 1,12,2");

				newColumn.setDBName(dbName);

				newColumn.setIndex(colIndex);

				// set the coordinate system if any is specified:

				if (hasCoosys){

					int indCoosys = 12; 

					if (hasColumnIndex)

						indCoosys++;

					if (hasDBName)

						indCoosys++;

					String coosysId = rs.getString(indCoosys);

					if (coosysId != null){

						newColumn.setCoosys(mapCoosys.get(coosysId));

						if (logger != null && newColumn.getCoosys() == null)

							logger.logDB(LogLevel.WARNING, this, "LOAD_TAP_SCHEMA", "No coordinate system for the column \""+columnName+"\"! Cause: unknown coordinate system: \""+coosysId+"\".", null);

					}

				}

				// add the new column inside its corresponding table:

				table.addColumn(newColumn);

			}

import java.io.OutputStream;

import java.io.OutputStreamWriter;

import java.io.PrintWriter;

import java.util.HashSet;

import java.util.Iterator;

import java.util.Map;

import tap.data.TableIterator;

import tap.error.DefaultTAPErrorWriter;

import tap.metadata.TAPColumn;

import tap.metadata.TAPCoosys;

import tap.metadata.VotType;

import tap.metadata.VotType.VotDatatype;

import uk.ac.starlink.table.AbstractStarTable;

import uk.ac.starlink.table.ColumnInfo;

import uk.ac.starlink.table.DefaultValueInfo;

import uk.ac.starlink.table.DescribedValue;

import uk.ac.starlink.table.RowSequence;

import uk.ac.starlink.table.StarTable;

import uk.ac.starlink.votable.DataFormat;

import uk.ac.starlink.votable.VOSerializer;

import uk.ac.starlink.votable.VOStarTable;

import uk.ac.starlink.votable.VOTableVersion;

import adql.db.DBColumn;

import adql.db.DBType;

			out.newLine();

		}

		/* TODO Add somewhere in the table header the different Coordinate Systems used in this result!

		 * 2 ways to do so:

		 * 	1/ COOSYS (deprecated from VOTable 1.2, but soon un-deprecated)

		 * 	2/ a GROUP item with the STC expression of the coordinate system. 

		 */

		// Insert the definition of all used coordinate systems:

		HashSet<String> insertedCoosys = new HashSet<String>(10);

		for(DBColumn col : execReport.resultingColumns){

			// ignore columns with no coossys:

			if (col instanceof TAPColumn && ((TAPColumn)col).getCoosys() != null){

				// get its coosys:

				TAPCoosys coosys = ((TAPColumn)col).getCoosys();

				// insert the coosys definition ONLY if not already done because of another column:

				if (!insertedCoosys.contains(coosys.getId())){

					// write the VOTable serialization of this coordinate system definition:

					out.write("<COOSYS"+VOSerializer.formatAttribute("ID", coosys.getId()));

					if (coosys.getSystem() != null)

						out.write(VOSerializer.formatAttribute("system", coosys.getSystem()));

					if (coosys.getEquinox() != null)

						out.write(VOSerializer.formatAttribute("equinox", coosys.getEquinox()));

					if (coosys.getEpoch() != null)

						out.write(VOSerializer.formatAttribute("epoch", coosys.getEpoch()));

					out.write(" />");

					out.newLine();

					// remember this coosys has already been written:

					insertedCoosys.add(coosys.getId());

				}

			}

		}

		out.flush();

	}

		// Set the XType (if any):

		if (votType.xtype != null)

			colInfo.setAuxDatum(new DescribedValue(new DefaultValueInfo("xtype", String.class, "VOTable xtype attribute"), votType.xtype));

			colInfo.setAuxDatum(new DescribedValue(VOStarTable.XTYPE_INFO, votType.xtype));

		// Set the additional information: unit, UCD and UType:

		colInfo.setUnitString(tapCol.getUnit());

		colInfo.setUCD(tapCol.getUcd());

		colInfo.setUtype(tapCol.getUtype());

		// Set the coosys ref (if any):

		if (tapCol.getCoosys() != null)

			colInfo.setAuxDatum(new DescribedValue(VOStarTable.REF_INFO, tapCol.getCoosys().getId()));

		return colInfo;

	}

 * You should have received a copy of the GNU Lesser General Public License

 * along with TAPLibrary.  If not, see <http://www.gnu.org/licenses/>.

 * 

 * Copyright 2012-2016 - UDS/Centre de Données astronomiques de Strasbourg (CDS),

 * Copyright 2012-2017 - UDS/Centre de Données astronomiques de Strasbourg (CDS),

 *                       Astronomisches Rechen Institut (ARI)

 */

 * </p>

 * 

 * @author Grégory Mantelet (CDS;ARI)

 * @version 2.1 (07/2016)

 * @version 2.1 (07/2017)

 */

public class TAPColumn implements DBColumn {

	 * @since 2.1 */

	private int index = -1;

	/** Coordinate system used by this column values.

	 * <i>Note: Of course, this attribute has to be set only on coordinate columns.</i>

	 * @since 2.1 */

	private TAPCoosys coosys = null;

	/** Let add some information in addition of the ones of the TAP protocol.

	 * <i>Note: This object can be anything: an {@link Integer}, a {@link String}, a {@link Map}, a {@link List}, ...

	 * Its content is totally free and never used or checked.</i> */

		this.index = columnIndex;

	}

	/**

	 * Get the used coordinate system.

	 * 

	 * @return	Its coordinate system.

	 * 

	 * @since 2.1

	 */

	public final TAPCoosys getCoosys(){

		return coosys;

	}

	/**

	 * Set the the coordinate system to use.

	 * 

	 * @param newCoosys	Its new coordinate system.

	 * 

	 * @since 2.1

	 */

	public final void setCoosys(final TAPCoosys newCoosys){

		this.coosys = newCoosys;

	}

	/**

	 * <p>Get the other (piece of) information associated with this column.</p>

	 * 

package tap.metadata;

/*

 * This file is part of TAPLibrary.

 * 

 * TAPLibrary is free software: you can redistribute it and/or modify

 * it under the terms of the GNU Lesser General Public License as published by

 * the Free Software Foundation, either version 3 of the License, or

 * (at your option) any later version.

 * 

 * TAPLibrary is distributed in the hope that it will be useful,

 * but WITHOUT ANY WARRANTY; without even the implied warranty of

 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 * GNU Lesser General Public License for more details.

 * 

 * You should have received a copy of the GNU Lesser General Public License

 * along with TAPLibrary.  If not, see <http://www.gnu.org/licenses/>.

 * 

 * Copyright 2017 - Astronomisches Rechen Institut (ARI)

 */

/**

 * Definition of a coordinate system.

 * 

 * <p>

 * 	This object just annotates a {@link TAPColumn} object (see {@link TAPColumn#getCoosys()}

 * 	and {@link TAPColumn#setCoosys(TAPCoosys)}). Its only purpose is to enrich the VOTable

 * 	metadata so that VO clients (like Aladin and TOPCAT) can use the coordinates the most

 * 	precisely as possible.

 * </p>

 * 

 * @author Grégory Mantelet (ARI)

 * @version 2.1 (07/2017)

 * @since 2.1

 */

public class TAPCoosys {

	/** ID of this coordinate system definition.

	 * <p>It is particularly used in the VOTable to associate columns with it.</p>

	 * <i>Note: This attribute can NOT be NULL.</i> */

	protected final String id;

	/** Name of the coordinate system.

	 * <p>

	 * 	It should be a value among:

	 * 	"ICRS", "eq FK5", "eq FK4", "ecl FK4", "ecl FK5",

	 * 	"galactic", "supergalactic", "barycentric", "geo app"

	 * 	and a user-defined "xy" value.

	 * </p> */

	protected final String system;

	/** Equinox of this coordinate system.

	 * <p>

	 * 	This parameter required to fix the equatorial or ecliptic systems

	 * 	(as e.g. "J2000" as the default "eq FK5" or "B1950" as the default "eq FK4").

	 * </p> */

	protected String equinox;

	/** Epoch at which the coordinates were measured. */

	protected String epoch;

	/**

	 * Create a minimum coordinate system definition.

	 * 

	 * @param id		ID of the definition to create. <i>(must NOT be NULL)</i>

	 * @param system	Coordinate system. <i>(must NOT be NULL)</i>

	 * 

	 * @throws NullPointerException	If any of the given parameters is NULL or an empty string.

	 */

	public TAPCoosys(final String id, final String system) throws NullPointerException {

		this(id, system, null, null);

	}

	/**

	 * Create a coordinate system definition.

	 * 

	 * <p>

	 * 	Only the ID and the system are required.

	 * 	The equinox and especially the epoch are optional.

	 * </p>

	 * 

	 * @param id		ID of the definition to create. <i>(must NOT be NULL)</i>

	 * @param system	Coordinate system. <i>(must NOT be NULL)</i>

	 * @param equinox	Equinox of this coordinate system.

	 * @param epoch		Epoch at which the coordinates were measured.

	 * 

	 * @throws NullPointerException	If the ID or the system is NULL or an empty string.

	 */

	public TAPCoosys(final String id, final String system, final String equinox, final String epoch) throws NullPointerException {

		if (id == null || id.trim().length() == 0)

			throw new NullPointerException("Missing Coosys ID!");

		this.id = id;

		if (system == null || system.trim().length() == 0)

			throw new NullPointerException("Missing coordinate system!");

		this.system = system;

		this.equinox = equinox;

		this.epoch = epoch;

	}

	/**

	 * Get the ID of this coordinate system definition.

	 * 

	 * @return	Its ID. <i>(can NOT be NULL)</i>

	 */

	public final String getId() {

		return id;

	}

	/**

	 * Get the coordinate system of this definition.

	 * 

	 * @return	Its system. <i>(can NOT be NULL)</i>

	 */

	public final String getSystem() {

		return system;

	}

	/**

	 * Get the equinox of this coordinate system.

	 * 

	 * @return	Its equinox. <i>(may be NULL)</i>

	 */

	public final String getEquinox() {

		return equinox;

	}

	/**

	 * Set the equinox of this coordinate system.

	 * 

	 * @param equinox	Its new equinox. <i>(may be NULL)</i>

	 */

	public void setEquinox(final String equinox) {

		this.equinox = equinox;

	}

	/**

	 * Get the epoch at which the coordinates were measured.

	 * 

	 * @return	Its equinox. <i>(may be NULL)</i>

	 */

	public final String getEpoch() {

		return epoch;

	}

	/**

	 * Set the epoch at which the coordinates were measured.

	 * 

	 * @param epoch	Its new epoch. <i>(may be NULL)</i>

	 */

	public void setEpoch(final String epoch) {

		this.epoch = epoch;

	}

	@Override

	public int hashCode() {

		return id.hashCode();

	}

	@Override

	public boolean equals(Object obj){

		if (!(obj instanceof TAPCoosys))

			return false;

		TAPCoosys coosys = (TAPCoosys)obj;

		return coosys.getId().equals(getId());

	}

	@Override

	public String toString(){

		return id;

	}

}

import java.io.IOException;

import java.io.PrintWriter;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.Iterator;

import java.util.LinkedHashMap;

import java.util.Map;

 * </p>

 * 

 * @author Grégory Mantelet (CDS;ARI)

 * @version 2.1 (03/2017)

 * @version 2.1 (07/2017)

 */

public class TAPMetadata implements Iterable<TAPSchema>, VOSIResource, TAPResource {

	/** List of all schemas available through the TAP service. */

	protected final Map<String,TAPSchema> schemas;

	/** List of all coordinate systems used by columns published in the TAP_SCHEMA.

	 * @since 2.1 */

	protected final Map<String, TAPCoosys> coordinateSystems;

	/** Part of the TAP URI which identify this TAP resource.

	 * By default, it is the resource name ; so here, the corresponding TAP URI would be: "/tables". */

	protected String accessURL = getName();

	 */

	public TAPMetadata(){

		schemas = new LinkedHashMap<String,TAPSchema>();

		coordinateSystems = new HashMap<String, TAPCoosys>();

	}

	/**

		return nbTables;

	}

	/**

	 * Get the coordinate system definition associated with the given ID.

	 * 

	 * @param coosysId	ID of the coordinate system to get. <i>(case sensitive)</i>

	 * 

	 * @return	The corresponding coordinate system definition,

	 *        	or NULL if no match for the given ID.

	 * 

	 * @since 2.1

	 */

	public TAPCoosys getCoosys(final String coosysId) {

		return (coosysId == null ? null : coordinateSystems.get(coosysId));

	}

	/**

	 * Add the given coordinate system definition.

	 * 

	 * <p><b>Important:</b>

	 * 	If a coordinate system with the same ID (case sensitive) is already declared in

	 * 	this {@link TAPMetadata}, it will be replaced by the given one. The replaced

	 * 	coordinate system is returned by this function.

	 * </p>

	 * 

	 * @param newCoosys	The coordinate system definition to add.

	 * 

	 * @return	The coordinate system definition previously declared with the same ID in this {@link TAPMetadata},

	 *        	or NULL if no coord. sys. was declared with this ID.  

	 * 

	 * @since 2.1

	 */

	public TAPCoosys addCoosys(final TAPCoosys newCoosys) {

		if (newCoosys == null)

			return null;

		else{

			TAPCoosys formerValue = coordinateSystems.get(newCoosys.getId());

			coordinateSystems.put(newCoosys.getId(), newCoosys);

			return formerValue;

		}

	}

	/**

	 * Remove the coordinate system declared with the given ID.

	 * 

	 * @param coosysId	The ID of the coordinate system definition to remove.

	 * 

	 * @return	The removed coordinate system definition,

	 *        	or NULL if none is declared with the given ID.

	 * 

	 * @since 2.1

	 */

	public TAPCoosys removeCoosys(final String coosysId){

		return (coosysId == null) ? null : coordinateSystems.remove(coosysId);

	}

	/**

	 * Let iterating over the list of all tables contained in a given {@link TAPMetadata} object.

	 * 

				tables.addColumn("utype", new DBType(DBDatatype.VARCHAR), "UTYPE if table corresponds to a data model", null, null, null, false, false, true);

				return tables;

			case COOSYS:

				TAPTable coosys = new TAPTable(STDSchema.TAPSCHEMA + "." + STDTable.COOSYS, TableType.table, "List of coordinate systems published used this TAP service.", null);

				coosys.addColumn("id", new DBType(DBDatatype.VARCHAR), "ID of the coordinate system definition.", null, null, null, true, true, false);

				coosys.addColumn("system", new DBType(DBDatatype.VARCHAR), "The coordinate system (among \"ICRS\", \"eq_FK5\", \"eq_FK4\", \"ecl_FK4\", \"ecl_FK5\", \"galactic\", \"supergalactic\").", null, null, null, false, false, false);

				coosys.addColumn("equinox", new DBType(DBDatatype.VARCHAR), "Required to fix the equatorial or ecliptic systems (as e.g. \"J2000\" as the default \"eq_FK5\" or \"B1950\" as the default \"eq_FK4\").", null, null, null, false, false, false);

				coosys.addColumn("epoch", new DBType(DBDatatype.VARCHAR), "Epoch of the positions (if necessary).", null, null, null, false, false, false);

				return coosys;

			case COLUMNS:

				TAPTable columns = new TAPTable(STDSchema.TAPSCHEMA + "." + STDTable.COLUMNS, TableType.table, "List of columns of all tables listed in TAP_SCHEMA.TABLES and published in this TAP service.", null);

				columns.addColumn("column_index", new DBType(DBDatatype.INTEGER), "this index is used to recommend column ordering for clients", null, null, null, false, false, true);

				columns.addColumn("indexed", new DBType(DBDatatype.INTEGER), "an indexed column; 1 means true, 0 means false", null, null, null, false, false, true);

				columns.addColumn("principal", new DBType(DBDatatype.INTEGER), "a principal column; 1 means true, 0 means false", null, null, null, false, false, true);

				columns.addColumn("std", new DBType(DBDatatype.INTEGER), "a standard column; 1 means true, 0 means false", null, null, null, false, false, true);

				columns.addColumn("coosys_id", new DBType(DBDatatype.VARCHAR), "ID of the used coordinate systems (if any).", null, null, null, false, false, false);

				return columns;

			case KEYS:

	 * Enumeration of all tables of TAP_SCHEMA.

	 * 

	 * @author Grégory Mantelet (ARI)

	 * @version 2.0 (07/2014)

	 * @version 2.1 (07/2017)

	 * @since 2.0

	 */

	public enum STDTable{

		SCHEMAS("schemas"), TABLES("tables"), COLUMNS("columns"), KEYS("keys"), KEY_COLUMNS("key_columns");

		SCHEMAS("schemas"),

		TABLES("tables"),

		COLUMNS("columns"),

		KEYS("keys"),

		KEY_COLUMNS("key_columns"),

		/** Non standard table but anyway expected by this library in order to associated coordinate columns with a coordinate system.

		 * @since 2.1 */

		COOSYS("coosys");

		/** Real name of the table. */

		public final String label;