diff --git a/src/tap/formatter/VOTableFormat.java b/src/tap/formatter/VOTableFormat.java
index ccee023a839175f51337f6b4ab23856b0af9c106..cf3f7248774223213beabf2e250f5255c8f2fb74 100644
--- a/src/tap/formatter/VOTableFormat.java
+++ b/src/tap/formatter/VOTableFormat.java
@@ -2,21 +2,21 @@ package tap.formatter;
/*
* 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 2012-2017 - UDS/Centre de Données astronomiques de Strasbourg (CDS)
+ *
+ * Copyright 2012-2019 - UDS/Centre de Données astronomiques de Strasbourg (CDS)
* Astronomisches Rechen Institut (ARI)
*/
@@ -29,6 +29,9 @@ import java.util.HashSet;
import java.util.Iterator;
import java.util.Map;
+import adql.db.DBColumn;
+import adql.db.DBType;
+import adql.db.DBType.DBDatatype;
import tap.ServiceConnection;
import tap.TAPException;
import tap.TAPExecutionReport;
@@ -44,24 +47,22 @@ import uk.ac.starlink.table.ColumnInfo;
import uk.ac.starlink.table.DescribedValue;
import uk.ac.starlink.table.RowSequence;
import uk.ac.starlink.table.StarTable;
+import uk.ac.starlink.table.StoragePolicy;
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;
-import adql.db.DBType.DBDatatype;
/**
* <p>Format any given query (table) result into VOTable.</p>
- *
+ *
* <p>
* Format and version of the resulting VOTable can be provided in parameters at the construction time.
* This formatter is using STIL. So all formats and versions managed by STIL are also here.
* Basically, you have the following formats: TABLEDATA, BINARY, BINARY2 (only when using VOTable v1.3) and FITS.
* The versions are: 1.0, 1.1, 1.2 and 1.3.
* </p>
- *
+ *
* <p>Note: The MIME type is automatically set in function of the given VOTable serialization:</p>
* <ul>
* <li><b>none or unknown</b>: equivalent to BINARY</li>
@@ -71,21 +72,21 @@ import adql.db.DBType.DBDatatype;
* <li><b>FITS</b>: "application/x-votable+xml;serialization=FITS" = "votable/fits"</li>
* </ul>
* <p>It is however possible to change these default values thanks to {@link #setMimeType(String, String)}.</p>
- *
+ *
* <p>In addition of the INFO elements for QUERY_STATUS="OK" and QUERY_STATUS="OVERFLOW", two additional INFO elements are written:</p>
* <ul>
* <li>PROVIDER = {@link ServiceConnection#getProviderName()} and {@link ServiceConnection#getProviderDescription()}</li>
* <li>QUERY = the ADQL query at the origin of this result.</li>
* </ul>
- *
+ *
* <p>
* Furthermore, this formatter provides a function to format an error in VOTable: {@link #writeError(String, Map, PrintWriter)}.
* This is useful for TAP which requires to return in VOTable any error that occurs while any operation.
* <i>See {@link DefaultTAPErrorWriter} for more details.</i>
* </p>
- *
+ *
* @author Grégory Mantelet (CDS;ARI)
- * @version 2.1 (07/2017)
+ * @version 2.2 (03/2019)
*/
public class VOTableFormat implements OutputFormat {
@@ -106,14 +107,14 @@ public class VOTableFormat implements OutputFormat {
/**
* <p>Creates a VOTable formatter.</p>
- *
+ *
* <p><i>Note:
* The MIME type is automatically set to "application/x-votable+xml" = "votable".
* It is however possible to change this default value thanks to {@link #setMimeType(String, String)}.
* </i></p>
- *
+ *
* @param service The service to use (for the log and to have some information about the service (particularly: name, description).
- *
+ *
* @throws NullPointerException If the given service connection is <code>null</code>.
*/
public VOTableFormat(final ServiceConnection service) throws NullPointerException{
@@ -122,7 +123,7 @@ public class VOTableFormat implements OutputFormat {
/**
* <p>Creates a VOTable formatter.</p>
- *
+ *
* <i>Note: The MIME type is automatically set in function of the given VOTable serialization:</i>
* <ul>
* <li><i><b>none or unknown</b>: equivalent to BINARY</i></li>
@@ -132,10 +133,10 @@ public class VOTableFormat implements OutputFormat {
* <li><i><b>FITS</b>: "application/x-votable+xml;serialization=FITS" = "votable/fits"</i></li>
* </ul>
* <p><i>It is however possible to change these default values thanks to {@link #setMimeType(String, String)}.</i></p>
- *
+ *
* @param service The service to use (for the log and to have some information about the service (particularly: name, description).
* @param votFormat Serialization of the VOTable data part. (TABLEDATA, BINARY, BINARY2 or FITS).
- *
+ *
* @throws NullPointerException If the given service connection is <code>null</code>.
*/
public VOTableFormat(final ServiceConnection service, final DataFormat votFormat) throws NullPointerException{
@@ -144,7 +145,7 @@ public class VOTableFormat implements OutputFormat {
/**
* <p>Creates a VOTable formatter.</p>
- *
+ *
* <i>Note: The MIME type is automatically set in function of the given VOTable serialization:</i>
* <ul>
* <li><i><b>none or unknown</b>: equivalent to BINARY</i></li>
@@ -154,11 +155,11 @@ public class VOTableFormat implements OutputFormat {
* <li><i><b>FITS</b>: "application/x-votable+xml;serialization=FITS" = "votable/fits"</i></li>
* </ul>
* <p><i>It is however possible to change these default values thanks to {@link #setMimeType(String, String)}.</i></p>
- *
+ *
* @param service The service to use (for the log and to have some information about the service (particularly: name, description).
* @param votFormat Serialization of the VOTable data part. (TABLEDATA, BINARY, BINARY2 or FITS).
* @param votVersion Version of the resulting VOTable.
- *
+ *
* @throws NullPointerException If the given service connection is <code>null</code>.
*/
public VOTableFormat(final ServiceConnection service, final DataFormat votFormat, final VOTableVersion votVersion) throws NullPointerException{
@@ -202,9 +203,9 @@ public class VOTableFormat implements OutputFormat {
/**
* <p>Set the MIME type associated with this format.</p>
- *
+ *
* <p><i>Note: NULL means no modification of the current value:</i></p>
- *
+ *
* @param mimeType Full MIME type of this VOTable format. <i>note: if NULL, the MIME type is not modified.</i>
* @param shortForm Short form of this MIME type. <i>note: if NULL, the short MIME type is not modified.</i>
*/
@@ -217,7 +218,7 @@ public class VOTableFormat implements OutputFormat {
/**
* Get the set VOTable data serialization/format (e.g. BINARY, TABLEDATA).
- *
+ *
* @return The data format.
*/
public final DataFormat getVotSerialization(){
@@ -226,7 +227,7 @@ public class VOTableFormat implements OutputFormat {
/**
* Get the set VOTable version.
- *
+ *
* @return The VOTable version.
*/
public final VOTableVersion getVotVersion(){
@@ -245,13 +246,13 @@ public class VOTableFormat implements OutputFormat {
/**
* <p>Write the given error message as VOTable document.</p>
- *
+ *
* <p><i>Note:
* In the TAP protocol, all errors must be returned as VOTable. The class {@link DefaultTAPErrorWriter} is in charge of the management
* and reporting of all errors. It is calling this function while the error message to display to the user is ready and
* must be written in the HTTP response.
* </i></p>
- *
+ *
* <p>Here is the XML format of this VOTable error:</p>
* <pre>
* <VOTABLE version="..." xmlns="..." >
@@ -264,16 +265,16 @@ public class VOTableFormat implements OutputFormat {
* </RESOURCE>
* </VOTABLE>
* </pre>
- *
+ *
* @param message Error message to display to the user.
* @param otherInfo List of other additional information to display. <i>optional</i>
* @param writer Stream in which the VOTable error must be written.
- *
+ *
* @throws IOException If any error occurs while writing in the given output.
- *
+ *
* @since 2.0
*/
- public void writeError(final String message, final Map<String,String> otherInfo, final PrintWriter writer) throws IOException{
+ public void writeError(final String message, final Map<String, String> otherInfo, final PrintWriter writer) throws IOException{
BufferedWriter out = new BufferedWriter(writer);
// Set the root VOTABLE node:
@@ -298,9 +299,9 @@ public class VOTableFormat implements OutputFormat {
// Append the ADQL query at the origin of this result: [OPTIONAL]
if (otherInfo != null){
- Iterator<Map.Entry<String,String>> it = otherInfo.entrySet().iterator();
+ Iterator<Map.Entry<String, String>> it = otherInfo.entrySet().iterator();
while(it.hasNext()){
- Map.Entry<String,String> entry = it.next();
+ Map.Entry<String, String> entry = it.next();
if (entry.getValue() != null){
if (entry.getValue().startsWith("\n")){
int sep = entry.getValue().substring(1).indexOf('\n');
@@ -333,10 +334,18 @@ public class VOTableFormat implements OutputFormat {
/* Turns the result set into a table. */
LimitedStarTable table = new LimitedStarTable(queryResult, colInfos, execReport.parameters.getMaxRec(), thread);
- table.setName("result_"+execReport.jobID);
+ table.setName("result_" + execReport.jobID);
/* Prepares the object that will do the serialization work. */
- VOSerializer voser = VOSerializer.makeSerializer(votFormat, votVersion, table);
+ VOSerializer voser = null;
+ /* if FITS, copy the table on disk (or in memory if the table is short):
+ * (note: this is needed because STIL needs at least 2 passes on this
+ * table to format it correctly in FITS format) */
+ if (votFormat == DataFormat.FITS)
+ voser = VOSerializer.makeSerializer(votFormat, votVersion, StoragePolicy.PREFER_DISK.copyTable(table));
+ // otherwise, just use the default VOTable serializer:
+ else
+ voser = VOSerializer.makeSerializer(votFormat, votVersion, table);
BufferedWriter out = new BufferedWriter(new OutputStreamWriter(output));
/* Write header. */
@@ -370,11 +379,11 @@ public class VOTableFormat implements OutputFormat {
/**
* <p>Writes the first VOTable nodes/elements preceding the data: VOTABLE, RESOURCE and 3 INFOS (QUERY_STATUS, PROVIDER, QUERY).</p>
- *
+ *
* @param votVersion Target VOTable version.
* @param execReport The report of the query execution.
* @param out Writer in which the root node must be written.
- *
+ *
* @throws IOException If there is an error while writing the root node in the given Writer.
* @throws TAPException If there is any other error (by default: never happen).
*/
@@ -405,7 +414,7 @@ public class VOTableFormat implements OutputFormat {
out.write("<INFO name=\"QUERY\"" + VOSerializer.formatAttribute("value", adqlQuery) + "/>");
out.newLine();
}
-
+
// Insert the definition of all used coordinate systems:
HashSet<String> insertedCoosys = new HashSet<String>(10);
for(DBColumn col : execReport.resultingColumns){
@@ -416,7 +425,7 @@ public class VOTableFormat implements OutputFormat {
// 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()));
+ out.write("<COOSYS" + VOSerializer.formatAttribute("ID", coosys.getId()));
if (coosys.getSystem() != null)
out.write(VOSerializer.formatAttribute("system", coosys.getSystem()));
if (coosys.getEquinox() != null)
@@ -436,13 +445,13 @@ public class VOTableFormat implements OutputFormat {
/**
* Writes fields' metadata of the given query result.
- *
+ *
* @param result The query result from whose fields' metadata must be written.
* @param execReport The report of the query execution.
* @param thread The thread which asked for the result writing.
- *
+ *
* @return Extracted field's metadata, or NULL if no metadata have been found (theoretically, it never happens).
- *
+ *
* @throws IOException If there is an error while writing the metadata.
* @throws TAPException If there is any other error.
* @throws InterruptedException If the given thread has been interrupted.
@@ -480,10 +489,10 @@ public class VOTableFormat implements OutputFormat {
/**
* Try to get or otherwise to build appropriate metadata using those extracted from the ADQL query and those extracted from the result.
- *
+ *
* @param typeFromQuery Metadata extracted/guessed from the ADQL query.
* @param typeFromResult Metadata extracted/guessed from the result.
- *
+ *
* @return The most appropriate metadata.
*/
protected static final TAPColumn getValidColMeta(final DBColumn typeFromQuery, final TAPColumn typeFromResult){
@@ -503,9 +512,9 @@ public class VOTableFormat implements OutputFormat {
/**
* Convert the given {@link TAPColumn} object into a {@link ColumnInfo} object.
- *
+ *
* @param tapCol {@link TAPColumn} to convert into {@link ColumnInfo}.
- *
+ *
* @return The corresponding {@link ColumnInfo}.
*/
protected static final ColumnInfo getColumnInfo(final TAPColumn tapCol){
@@ -529,7 +538,7 @@ public class VOTableFormat implements OutputFormat {
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()));
@@ -539,17 +548,17 @@ public class VOTableFormat implements OutputFormat {
/**
* Convert the VOTable datatype string into a corresponding {@link Class} object.
- *
- * @param datatype Value of the VOTable attribute "datatype".
+ *
+ * @param datatype Value of the VOTable attribute "datatype".
* @param arraysize Value of the VOTable attribute "arraysize".
- *
+ *
* @return The corresponding {@link Class} object.
*/
protected static final Class<?> getDatatypeClass(final VotDatatype datatype, final String arraysize){
// Determine whether this type is an array or not:
boolean isScalar = arraysize == null || (arraysize.length() == 1 && arraysize.equals("1"));
- // Guess the corresponding Class object (see section "7.1.4 Data Types" of the STIL documentation):
+ // Guess the corresponding Class object (see section "7.1.4 Data Types" of the STIL documentation):
switch(datatype){
case BIT:
return boolean[].class;
@@ -580,9 +589,9 @@ public class VOTableFormat implements OutputFormat {
/**
* Convert the given VOTable arraysize into a {@link ColumnInfo} shape.
- *
+ *
* @param arraysize Value of the VOTable attribute "arraysize".
- *
+ *
* @return The corresponding {@link ColumnInfo} shape.
*/
protected static final int[] getShape(final String arraysize){
@@ -597,12 +606,12 @@ public class VOTableFormat implements OutputFormat {
// '*' or 'n*' => {-1}:
else if (arraysize.charAt(arraysize.length() - 1) == '*')
- return new int[]{-1};
+ return new int[]{ -1 };
// 'n' => {n}:
else{
try{
- return new int[]{Integer.parseInt(arraysize)};
+ return new int[]{ Integer.parseInt(arraysize) };
}catch(NumberFormatException nfe){
// if the given arraysize is incorrect (theoretically, never happens), it is like no arraysize has been provided:
return new int[0];
@@ -615,7 +624,7 @@ public class VOTableFormat implements OutputFormat {
* Special {@link StarTable} able to read a fixed maximum number of rows {@link TableIterator}.
* However, if no limit is provided, all rows are read.
* </p>
- *
+ *
* @author Grégory Mantelet (CDS;ARI)
* @version 2.1 (11/2015)
* @since 2.0
@@ -649,7 +658,7 @@ public class VOTableFormat implements OutputFormat {
/**
* Build this special {@link StarTable}.
- *
+ *
* @param tableIt Data on which to iterate using this special {@link StarTable}.
* @param colInfos Information about all columns.
* @param maxrec Limit on the number of rows to read. <i>(if negative, there will be no limit)</i>
@@ -703,7 +712,7 @@ public class VOTableFormat implements OutputFormat {
overflow = false;
row = new Object[nbCol];
- return new RowSequence(){
+ return new RowSequence() {
long irow = -1;
@Override
@@ -743,7 +752,8 @@ public class VOTableFormat implements OutputFormat {
}
@Override
- public void close() throws IOException{}
+ public void close() throws IOException{
+ }
};
}
}