[TAP] Fix intermixed VOTable documents in synchronous mode. (25a783a8) · Commits · Sonia Zorba / vollt

src/tap/formatter/FITSFormat.java

+37 −20

Original line number	Diff line number	Diff line
		@@ -16,7 +16,8 @@ package tap.formatter;
		* 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 2014-2015 - Astronomisches Rechen Institut (ARI)
		* Copyright 2014-2020 - UDS/Centre de Données astronomiques de Strasbourg (CDS)
		* Astronomisches Rechen Institut (ARI)
		*/

		import java.io.IOException;
		@@ -35,21 +36,24 @@ import uk.ac.starlink.table.StoragePolicy;
		/**
		* Format any given query (table) result into FITS.
		*
		* @author Grégory Mantelet (ARI)
		* @version 2.1 (11/2015)
		* @author Grégory Mantelet (CDS;ARI)
		* @version 2.4 (08/2020)
		* @since 2.0
		*/
		public class FITSFormat implements OutputFormat {

		/** The {@link ServiceConnection} to use (for the log and to have some information about the service (particularly: name, description). */
		/** The {@link ServiceConnection} to use (for the log and to have some
		* information about the service (particularly: name, description). */
		protected final ServiceConnection service;

		/**
		* Creates a FITS formatter.
		*
		* @param service The service to use (for the log and to have some information about the service (particularly: name, description).
		* @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>.
		* @throws NullPointerException If the given service connection is NULL.
		*/
		public FITSFormat(final ServiceConnection service) throws NullPointerException {
		if (service == null)
		@@ -87,7 +91,20 @@ public class FITSFormat implements OutputFormat {
		LimitedStarTable table = new LimitedStarTable(result, colInfos, execReport.parameters.getMaxRec(), thread);

		// Copy the table on disk (or in memory if the table is short):
		StarTable copyTable = StoragePolicy.PREFER_DISK.copyTable(table);
		StarTable copyTable;
		try {
		copyTable = StoragePolicy.PREFER_DISK.copyTable(table);
		} catch(IOException ioe) {
		/* In case of time out, LimitedStarTable makes copyTable to stop by
		* throwing an IOException. In such case, this IOException has to be
		* interpreted as a normal interruption: */
		if (thread.isInterrupted())
		throw new InterruptedException();
		/* Otherwise, the error has to be managed properly (so, wrap it
		* inside a TAPException): */
		else
		throw new TAPException("Unexpected error while formatting the result!", ioe);
		}

		if (thread.isInterrupted())
		throw new InterruptedException();

src/tap/formatter/VOTableFormat.java

+268 −155

Original line number	Diff line number	Diff line
		@@ -16,7 +16,7 @@ package tap.formatter;
		* 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 2012-2019 - UDS/Centre de Données astronomiques de Strasbourg (CDS)
		* Copyright 2012-2020 - UDS/Centre de Données astronomiques de Strasbourg (CDS)
		* Astronomisches Rechen Institut (ARI)
		*/

		@@ -54,49 +54,70 @@ import uk.ac.starlink.votable.VOStarTable;
		import uk.ac.starlink.votable.VOTableVersion;

		/**
		* <p>Format any given query (table) result into VOTable.</p>
		* Format any given query (table) result into VOTable.
		*
		* <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.
		* 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>
		* <p><i><b>Note:</b>
		* The MIME type is automatically set in function of the given VOTable
		* serialization:
		* </i></p>
		* <ul>
		* <li><b>none or unknown</b>: equivalent to BINARY</li>
		* <li><b>BINARY</b>: "application/x-votable+xml" = "votable"</li>
		* <li><b>BINARY2</b>: "application/x-votable+xml;serialization=BINARY2" = "votable/b2"</li>
		* <li><b>TABLEDATA</b>: "application/x-votable+xml;serialization=TABLEDATA" = "votable/td"</li>
		* <li><b>FITS</b>: "application/x-votable+xml;serialization=FITS" = "votable/fits"</li>
		* <li><b>BINARY</b>: "application/x-votable+xml"
		* = "votable"</li>
		* <li><b>BINARY2</b>: "application/x-votable+xml;serialization=BINARY2"
		* = "votable/b2"</li>
		* <li><b>TABLEDATA</b>: "application/x-votable+xml;serialization=TABLEDATA"
		* = "votable/td"</li>
		* <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>
		* 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>
		* <p>
		* In addition of the INFO elements for QUERY_STATUS="OK",
		* QUERY_STATUS="OVERFLOW" and QUERY_STATUS="ERROR", two additional INFO
		* elements are written:
		* </p>
		* <ul>
		* <li>PROVIDER = {@link ServiceConnection#getProviderName()} and {@link ServiceConnection#getProviderDescription()}</li>
		* <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>
		* 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 2.3 (03/2019)
		* @version 2.4 (08/2020)
		*/
		public class VOTableFormat implements OutputFormat {

		/** The {@link ServiceConnection} to use (for the log and to have some information about the service (particularly: name, description). */
		/** The {@link ServiceConnection} to use (for the log and to have some
		* information about the service (particularly: name, description). */
		protected final ServiceConnection service;

		/** Format of the VOTable data part in which data must be formatted. Possible values are: TABLEDATA, BINARY, BINARY2 or FITS. By default, it is set to BINARY. */
		/** Format of the VOTable data part in which data must be formatted.
		* Possible values are: TABLEDATA, BINARY, BINARY2 or FITS.
		* By default, it is set to BINARY. */
		protected final DataFormat votFormat;

		/** VOTable version in which table data must be formatted. By default, it is set to v13. */
		/** VOTable version in which table data must be formatted.
		* By default, it is set to v13. */
		protected final VOTableVersion votVersion;

		/** MIME type associated with this format. */
		@@ -106,61 +127,90 @@ public class VOTableFormat implements OutputFormat {
		protected String shortMimeType;

		/**
		* <p>Creates a VOTable formatter.</p>
		* Creates a VOTable formatter.
		*
		* <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)}.
		* <p><i><b>Note:</b>
		* 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).
		* @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>.
		* @throws NullPointerException If the given service connection is NULL.
		*/
		public VOTableFormat(final ServiceConnection service) throws NullPointerException {
		this(service, null, null);
		}

		/**
		* <p>Creates a VOTable formatter.</p>
		* Creates a VOTable formatter.
		*
		* <i>Note: The MIME type is automatically set in function of the given VOTable serialization:</i>
		* <p><i><b>Note:</b>
		* The MIME type is automatically set in function of the given VOTable
		* serialization:
		* </i></p>
		* <ul>
		* <li><i><b>none or unknown</b>: equivalent to BINARY</i></li>
		* <li><i><b>BINARY</b>: "application/x-votable+xml" = "votable"</i></li>
		* <li><i><b>BINARY2</b>: "application/x-votable+xml;serialization=BINARY2" = "votable/b2"</i></li>
		* <li><i><b>TABLEDATA</b>: "application/x-votable+xml;serialization=TABLEDATA" = "votable/td"</i></li>
		* <li><i><b>FITS</b>: "application/x-votable+xml;serialization=FITS" = "votable/fits"</i></li>
		* <li><i><b>BINARY</b>: "application/x-votable+xml"
		* = "votable"</i></li>
		* <li><i><b>BINARY2</b>: "application/x-votable+xml;serialization=BINARY2"
		* = "votable/b2"</i></li>
		* <li><i><b>TABLEDATA</b>: "application/x-votable+xml;serialization=TABLEDATA"
		* = "votable/td"</i></li>
		* <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>
		* <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 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>.
		* @throws NullPointerException If the given service connection is NULL.
		*/
		public VOTableFormat(final ServiceConnection service, final DataFormat votFormat) throws NullPointerException {
		this(service, votFormat, null);
		}

		/**
		* <p>Creates a VOTable formatter.</p>
		* Creates a VOTable formatter.
		*
		* <i>Note: The MIME type is automatically set in function of the given VOTable serialization:</i>
		* <p><i><b>Note:</b>
		* The MIME type is automatically set in function of the given VOTable
		* serialization:
		* </i></p>
		* <ul>
		* <li><i><b>none or unknown</b>: equivalent to BINARY</i></li>
		* <li><i><b>BINARY</b>: "application/x-votable+xml" = "votable"</i></li>
		* <li><i><b>BINARY2</b>: "application/x-votable+xml;serialization=BINARY2" = "votable/b2"</i></li>
		* <li><i><b>TABLEDATA</b>: "application/x-votable+xml;serialization=TABLEDATA" = "votable/td"</i></li>
		* <li><i><b>FITS</b>: "application/x-votable+xml;serialization=FITS" = "votable/fits"</i></li>
		* <li><i><b>BINARY</b>: "application/x-votable+xml"
		* = "votable"</i></li>
		* <li><i><b>BINARY2</b>: "application/x-votable+xml;serialization=BINARY2"
		* = "votable/b2"</i></li>
		* <li><i><b>TABLEDATA</b>: "application/x-votable+xml;serialization=TABLEDATA"
		* = "votable/td"</i></li>
		* <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>
		* <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 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>.
		* @throws NullPointerException If the given service connection is NULL.
		*/
		public VOTableFormat(final ServiceConnection service, final DataFormat votFormat, final VOTableVersion votVersion) throws NullPointerException {
		if (service == null)
		@@ -202,12 +252,16 @@ public class VOTableFormat implements OutputFormat {
		}

		/**
		* <p>Set the MIME type associated with this format.</p>
		* Set the MIME type associated with this format.
		*
		* <p><i>Note: NULL means no modification of the current value:</i></p>
		* <p><i><b>Note:</b>
		* 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>
		* @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>
		*/
		public final void setMimeType(final String mimeType, final String shortForm) {
		if (mimeType != null)
		@@ -245,12 +299,14 @@ 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.
		* Write the given error message as VOTable document.
		*
		* <p><i><b>Note:</b>
		* 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>
		@@ -267,7 +323,8 @@ public class VOTableFormat implements OutputFormat {
		* </pre>
		*
		* @param message Error message to display to the user.
		* @param otherInfo List of other additional information to display. <i>optional</i>
		* @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.
		@@ -341,29 +398,69 @@ public class VOTableFormat implements OutputFormat {
		/* 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)
		if (votFormat == DataFormat.FITS) {
		try {
		voser = VOSerializer.makeSerializer(votFormat, votVersion, StoragePolicy.PREFER_DISK.copyTable(table));
		} catch(IOException ioe) {
		/* As in the class FITSFormat, the caught IOException may be due
		* to an interruption from LimitedStarTable. In such case,
		* propagate the interruption: */
		if (thread.isInterrupted())
		throw new InterruptedException();
		/* Any other error should be properly wrapped: */
		else
		throw new TAPException("Unexpected error while formatting the result!", ioe);
		}
		}
		// otherwise, just use the default VOTable serializer:
		else
		voser = VOSerializer.makeSerializer(votFormat, votVersion, table);

		BufferedWriter out = new BufferedWriter(new OutputStreamWriter(output));

		/* Write header. */
		writeHeader(votVersion, execReport, out);

		if (thread.isInterrupted())
		throw new InterruptedException();

		/* Write table element. */
		if (!thread.isInterrupted()) {
		try {
		voser.writeInlineTableElement(out);
		execReport.nbRows = table.getNbReadRows();
		out.flush();
		} catch(Exception ex) {
		/* If synchronous, the partially written VOTable should be
		* properly closed and an error INFO should be appended: */
		if (execReport.synchronous) {
		if (votFormat != DataFormat.TABLEDATA) {
		out.write("</STREAM>\n</BINARY>\n</DATA>\n</TABLE>");
		out.newLine();
		}
		out.write("<INFO name=\"QUERY_STATUS\" value=\"ERROR\">Result truncated due to an unexpected grave error: " + VOSerializer.formatText(ex.getMessage()) + "</INFO>");
		out.newLine();
		}
		// If asynchronous, just propagate the error:
		else {
		if (ex instanceof TAPException \|\| ex instanceof IOException \|\| ex instanceof InterruptedException)
		throw ex;
		else
		throw new TAPException(ex);
		}
		}
		}

		if (thread.isInterrupted())
		/* If Timed Out... */
		if (thread.isInterrupted()) {
		// ...if synchronous, end properly the VOTable with an error INFO:
		if (execReport != null && execReport.synchronous) {
		out.write("<INFO name=\"QUERY_STATUS\" value=\"ERROR\">Time out! (Hint: Try running this query in asynchronous mode to get the complete result)</INFO>");
		out.newLine();
		}
		// ...if asynchronous, merely propagate the interruption:
		else
		throw new InterruptedException();

		/* Check for overflow and write INFO if required. */
		if (table.lastSequenceOverflowed()){
		}
		/* If Overflow, declare this in an INFO: */
		else if (table.lastSequenceOverflowed()) {
		out.write("<INFO name=\"QUERY_STATUS\" value=\"OVERFLOW\"/>");
		out.newLine();
		}
		@@ -378,14 +475,17 @@ 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>
		* Writes the first VOTable nodes/elements preceding the data: VOTABLE,
		* RESOURCE and 3 INFOS (QUERY_STATUS, PROVIDER, QUERY).
		*
		* @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).
		* @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).
		*/
		protected void writeHeader(final VOTableVersion votVersion, final TAPExecutionReport execReport, final BufferedWriter out) throws IOException, TAPException {
		// Set the root VOTABLE node:
		@@ -453,15 +553,19 @@ 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 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).
		* @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 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.
		* @throws InterruptedException If the given thread has been
		* interrupted.
		*/
		public static final ColumnInfo[] toColumnInfos(final TableIterator result, final TAPExecutionReport execReport, final Thread thread) throws IOException, TAPException, InterruptedException {
		// Get the metadata extracted/guesses from the ADQL query:
		@@ -495,7 +599,8 @@ 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.
		* 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.
		@@ -518,7 +623,8 @@ public class VOTableFormat implements OutputFormat {
		}

		/**
		* Convert the given {@link TAPColumn} object into a {@link ColumnInfo} object.
		* Convert the given {@link TAPColumn} object into a {@link ColumnInfo}
		* object.
		*
		* @param tapCol {@link TAPColumn} to convert into {@link ColumnInfo}.
		*
		@@ -554,7 +660,8 @@ public class VOTableFormat implements OutputFormat {
		}

		/**
		* Convert the VOTable datatype string into a corresponding {@link Class} object.
		* Convert the VOTable datatype string into a corresponding {@link Class}
		* object.
		*
		* @param datatype Value of the VOTable attribute "datatype".
		* @param arraysize Value of the VOTable attribute "arraysize".
		@@ -627,10 +734,9 @@ public class VOTableFormat implements OutputFormat {
		}

		/**
		* <p>
		* 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>
		* Special {@link StarTable} able to read a fixed maximum number of rows
		* {@link TableIterator}. However, if no limit is provided, all rows are
		* read.
		*
		* @author Grégory Mantelet (CDS;ARI)
		* @version 2.1 (11/2015)
		@@ -647,17 +753,21 @@ public class VOTableFormat implements OutputFormat {
		/** Iterator over the data to read using this special {@link StarTable} */
		private final TableIterator tableIt;

		/** Thread covering this execution. If it is interrupted, the writing must stop as soon as possible.
		/** Thread covering this execution. If it is interrupted, the writing
		* must stop as soon as possible.
		* @since 2.1 */
		private final Thread threadToWatch;

		/** Limit on the number of rows to read. Over this limit, an "overflow" event occurs and {@link #overflow} is set to TRUE. */
		/** Limit on the number of rows to read. Over this limit, an "overflow"
		* event occurs and {@link #overflow} is set to TRUE. */
		private final long maxrec;

		/** Indicates whether the maximum allowed number of rows has already been read or not. When true, no more row can be read. */
		/** Indicates whether the maximum allowed number of rows has already
		* been read or not. When true, no more row can be read. */
		private boolean overflow;

		/** Last read row. If NULL, no row has been read or no more row is available. */
		/** Last read row. If NULL, no row has been read or no more row is
		* available. */
		private Object[] row = null;

		/** Number of rows read until now. */
		@@ -666,10 +776,13 @@ public class VOTableFormat implements OutputFormat {
		/**
		* Build this special {@link StarTable}.
		*
		* @param tableIt Data on which to iterate using 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>
		* @param thread Parent thread. When an interruption is detected the writing must stop as soon as possible.
		* @param maxrec Limit on the number of rows to read.
		* <i>(if negative, there will be no limit)</i>
		* @param thread Parent thread. When an interruption is detected the
		* writing must stop as soon as possible.
		*/
		LimitedStarTable(final TableIterator tableIt, final ColumnInfo[] colInfos, final long maxrec, final Thread thread) {
		this.tableIt = tableIt;