[TAP] Add an optional feature to enable quick fix of input ADQL query on error: (c3e97e6e) · Commits · Sonia Zorba / vollt

src/tap/ADQLExecutor.java

+101 −78

Original line number	Original line	Diff line number	Diff line
	@@ -16,7 +16,7 @@ package tap;
	* You should have received a copy of the GNU Lesser General Public License		* You should have received a copy of the GNU Lesser General Public License
	* along with TAPLibrary. If not, see <http://www.gnu.org/licenses/>.		* 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)		* Astronomisches Rechen Institut (ARI)
	*/		*/

	@@ -105,7 +105,7 @@ import uws.service.log.UWSLog.LogLevel;
	* </p>		* </p>
	*		*
	* @author Grégory Mantelet (CDS;ARI)		* @author Grégory Mantelet (CDS;ARI)
	* @version 2.1 (04/2017)		* @version 2.3 (03/2019)
	*/		*/
	public class ADQLExecutor {		public class ADQLExecutor {

	@@ -551,7 +551,30 @@ public class ADQLExecutor {
	parser.setQueryChecker(service.getFactory().createQueryChecker(uploadSchema));		parser.setQueryChecker(service.getFactory().createQueryChecker(uploadSchema));

	// Parse the ADQL query:		// Parse the ADQL query:
	ADQLQuery query = parser.parseQuery(tapParams.getQuery());		ADQLQuery query = null;
			// if the fixOnFail option is enabled...
			if (service.fixOnFailEnabled()){
			try{
			// try parsing the query:
			query = parser.parseQuery(tapParams.getQuery());
			}catch(ParseException pe){
			// if it fails...
			// ...log the auto fix attempt:
			logger.logTAP(LogLevel.INFO, report, "PARSING", "Parse attempt of the original input query failed! Trying auto-fix...", null);
			// ...try fixing the query:
			String fixedQuery = parser.tryQuickFix(tapParams.getQuery());
			// ...log the auto fixed query, if successful:
			logger.logTAP(LogLevel.INFO, report, "PARSING", "Auto-fixed query: " + fixedQuery.replaceAll("(\t\|\r?\n)+", " "), null);
			// ...keep this fixed query in the exec report:
			report.fixedQuery = fixedQuery;
			// ...and finally try parsing it a last time:
			query = parser.parseQuery(fixedQuery);
			}
			}
			// if not enabled, parse immediately the query:
			else{
			query = parser.parseQuery(tapParams.getQuery());
			}

	// Set or check the row limit:		// Set or check the row limit:
	final int limit = query.getSelect().getLimit();		final int limit = query.getSelect().getLimit();

src/tap/ServiceConnection.java

+15 −2

Original line number	Original line	Diff line number	Diff line
	@@ -16,7 +16,7 @@ package tap;
	* You should have received a copy of the GNU Lesser General Public License		* You should have received a copy of the GNU Lesser General Public License
	* along with TAPLibrary. If not, see <http://www.gnu.org/licenses/>.		* along with TAPLibrary. If not, see <http://www.gnu.org/licenses/>.
	*		*
	* Copyright 2012-2018 - UDS/Centre de Données astronomiques de Strasbourg (CDS),		* Copyright 2012-2019 - UDS/Centre de Données astronomiques de Strasbourg (CDS),
	* Astronomisches Rechen Institut (ARI)		* Astronomisches Rechen Institut (ARI)
	*/		*/

	@@ -44,7 +44,7 @@ import uws.service.file.UWSFileManager;
	* </p>		* </p>
	*		*
	* @author Grégory Mantelet (CDS;ARI)		* @author Grégory Mantelet (CDS;ARI)
	* @version 2.3 (09/2018)		* @version 2.3 (03/2019)
	*/		*/
	public interface ServiceConnection {		public interface ServiceConnection {

	@@ -744,4 +744,17 @@ public interface ServiceConnection {
	*/		*/
	public int[] getFetchSize();		public int[] getFetchSize();

			/**
			* <i><b>[MANDATORY]</b></i>
			* <p>This function tells whether TAP-Lib should automatically try to fix a
			* query whose parsing failed because of a token error. After this fix
			* attempt the query is parsed again for a last time.</p>
			*
			* @return <i>true</i> to allow automatic fix attempt in case of error,
			* <i>false</i> to disable this option.
			*
			* @since 2.3
			*/
			public boolean fixOnFailEnabled();

	}		}

src/tap/TAPExecutionReport.java

+62 −33

Original line number	Original line	Diff line number	Diff line
	package tap;		package tap;

			import adql.db.DBColumn;

	/*		/*
	* This file is part of TAPLibrary.		* This file is part of TAPLibrary.
	*		*
	@@ -16,34 +18,49 @@ package tap;
	* You should have received a copy of the GNU Lesser General Public License		* You should have received a copy of the GNU Lesser General Public License
	* along with TAPLibrary. If not, see <http://www.gnu.org/licenses/>.		* along with TAPLibrary. If not, see <http://www.gnu.org/licenses/>.
	*		*
	* Copyright 2012-2015 - UDS/Centre de Données astronomiques de Strasbourg (CDS),		* Copyright 2012-2019 - UDS/Centre de Données astronomiques de Strasbourg (CDS),
	* Astronomisches Rechen Institut (ARI)		* Astronomisches Rechen Institut (ARI)
	*/		*/

	import tap.parameters.TAPParameters;		import tap.parameters.TAPParameters;
	import adql.db.DBColumn;

	/**		/**
	* <p>Report the execution (including the parsing and the output writing) of an ADQL query.		* Report the execution (including the parsing and the output writing) of an
	* It gives information on the job parameters, the job ID, whether it is a synchronous task or not, times of each execution step (uploading, parsing, executing and writing),		* ADQL query.
	* the resulting columns and the success or not of the execution.</p>
	*		*
	* <p>This report is completely filled by {@link ADQLExecutor}, and aims to be used/read only at the end of the job or when it is definitely finished.</p>		* <p>
			* It gives information on the job parameters, the job ID, whether it is a
			* synchronous task or not, times of each execution step (uploading, parsing,
			* executing and writing), the resulting columns and the success or not of the
			* execution.
			* </p>
			*
			* <p>
			* This report is completely filled by {@link ADQLExecutor}, and aims to be
			* used/read only at the end of the job or when it is definitely finished.
			* </p>
	*		*
	* @author Grégory Mantelet (CDS;ARI)		* @author Grégory Mantelet (CDS;ARI)
	* @version 2.0 (04/2015)		* @version 2.3 (03/2019)
	*/		*/
	public class TAPExecutionReport {		public class TAPExecutionReport {

	/** ID of the job whose the execution is reported here. */		/** ID of the job whose the execution is reported here. */
	public final String jobID;		public final String jobID;

	/** Indicate whether this execution is done in a synchronous or asynchronous job. */		/** Indicate whether this execution is done in a synchronous or asynchronous
			* job. */
	public final boolean synchronous;		public final boolean synchronous;

	/** List of all parameters provided in the user request. */		/** List of all parameters provided in the user request. */
	public final TAPParameters parameters;		public final TAPParameters parameters;

			/** Input ADQL query after an automatic fix by TAP-Lib.
			* <p>This field is set only if the option fix_on_fail is enabled in the TAP
			* configuration and that a query has been fixed.</p>
			* @since 2.3 */
			public String fixedQuery = null;

	/** List of all resulting columns. <i>Empty array, if not yet known.</i> */		/** List of all resulting columns. <i>Empty array, if not yet known.</i> */
	public DBColumn[] resultingColumns = new DBColumn[0];		public DBColumn[] resultingColumns = new DBColumn[0];

	@@ -51,21 +68,26 @@ public class TAPExecutionReport {
	* @since 2.0 */		* @since 2.0 */
	public long nbRows = -1;		public long nbRows = -1;

	/** Duration of all execution steps. <i>For the moment only 4 steps (in the order): uploading, parsing, executing and writing.</i> */		/** Duration of all execution steps. <i>For the moment only 4 steps (in the
			* order): uploading, parsing, executing and writing.</i> */
	protected final long[] durations = new long[]{ -1, -1, -1, -1 };		protected final long[] durations = new long[]{ -1, -1, -1, -1 };

	/** Total duration of the job execution. */		/** Total duration of the job execution. */
	protected long totalDuration = -1;		protected long totalDuration = -1;

	/** Indicate whether this job has ended successfully or not. <i>At the beginning or while executing, this field is always FALSE.</i> */		/** Indicate whether this job has ended successfully or not.
			* <i>At the beginning or while executing, this field is always FALSE.</i> */
	public boolean success = false;		public boolean success = false;

	/**		/**
	* Build an empty execution report.		* Build an empty execution report.
	*		*
	* @param jobID ID of the job whose the execution must be described here.		* @param jobID ID of the job whose the execution must be described
	* @param synchronous <i>true</i> if the job is synchronous, <i>false</i> otherwise.		* here.
	* @param params List of all parameters provided by the user for the execution.		* @param synchronous <i>true</i> if the job is synchronous,
			* <i>false</i> otherwise.
			* @param params List of all parameters provided by the user for the
			* execution.
	*/		*/
	public TAPExecutionReport(final String jobID, final boolean synchronous, final TAPParameters params){		public TAPExecutionReport(final String jobID, final boolean synchronous, final TAPParameters params){
	this.jobID = jobID;		this.jobID = jobID;
	@@ -74,14 +96,20 @@ public class TAPExecutionReport {
	}		}

	/**		/**
	* <p>Map the execution progression with an index inside the {@link #durations} array.</p>		* Map the execution progression with an index inside the {@link #durations}
			* array.
	*		*
	* <p><i><b>Warning:</b> for the moment, only {@link ExecutionProgression#UPLOADING}, {@link ExecutionProgression#PARSING},		* <p><i><b>Warning:</b>
	* {@link ExecutionProgression#EXECUTING_ADQL} and {@link ExecutionProgression#WRITING_RESULT} are managed.</i></p>		* for the moment, only {@link ExecutionProgression#UPLOADING},
			* {@link ExecutionProgression#PARSING},
			* {@link ExecutionProgression#EXECUTING_ADQL} and
			* {@link ExecutionProgression#WRITING_RESULT} are managed.
			* </i></p>
	*		*
	* @param tapProgression Execution progression.		* @param tapProgression Execution progression.
	*		*
	* @return Index in the array {@link #durations}, or -1 if the given execution progression is not managed.		* @return Index in the array {@link #durations},
			* or -1 if the given execution progression is not managed.
	*/		*/
	protected int getIndexDuration(final ExecutionProgression tapProgression){		protected int getIndexDuration(final ExecutionProgression tapProgression){
	switch(tapProgression){		switch(tapProgression){
	@@ -103,7 +131,8 @@ public class TAPExecutionReport {
	*		*
	* @param tapStep Job execution step.		* @param tapStep Job execution step.
	*		*
	* @return The corresponding duration (in ms), or -1 if this step has not been (yet) processed.		* @return The corresponding duration (in ms), or -1 if this step has not
			* been (yet) processed.
	*		*
	* @see #getIndexDuration(ExecutionProgression)		* @see #getIndexDuration(ExecutionProgression)
	*/		*/

src/tap/config/ConfigurableServiceConnection.java

+45 −17

Original line number	Original line	Diff line number	Diff line
	@@ -16,13 +16,14 @@ package tap.config;
	* You should have received a copy of the GNU Lesser General Public License		* You should have received a copy of the GNU Lesser General Public License
	* along with TAPLibrary. If not, see <http://www.gnu.org/licenses/>.		* along with TAPLibrary. If not, see <http://www.gnu.org/licenses/>.
	*		*
	* Copyright 2016-2018 - UDS/Centre de Données astronomiques de Strasbourg (CDS),		* Copyright 2016-2019 - UDS/Centre de Données astronomiques de Strasbourg (CDS),
	* Astronomisches Rechen Institut (ARI)		* Astronomisches Rechen Institut (ARI)
	*/		*/

	import static tap.config.TAPConfiguration.DEFAULT_ASYNC_FETCH_SIZE;		import static tap.config.TAPConfiguration.DEFAULT_ASYNC_FETCH_SIZE;
	import static tap.config.TAPConfiguration.DEFAULT_DIRECTORY_PER_USER;		import static tap.config.TAPConfiguration.DEFAULT_DIRECTORY_PER_USER;
	import static tap.config.TAPConfiguration.DEFAULT_EXECUTION_DURATION;		import static tap.config.TAPConfiguration.DEFAULT_EXECUTION_DURATION;
			import static tap.config.TAPConfiguration.DEFAULT_FIX_ON_FAIL;
	import static tap.config.TAPConfiguration.DEFAULT_GROUP_USER_DIRECTORIES;		import static tap.config.TAPConfiguration.DEFAULT_GROUP_USER_DIRECTORIES;
	import static tap.config.TAPConfiguration.DEFAULT_LOGGER;		import static tap.config.TAPConfiguration.DEFAULT_LOGGER;
	import static tap.config.TAPConfiguration.DEFAULT_MAX_ASYNC_JOBS;		import static tap.config.TAPConfiguration.DEFAULT_MAX_ASYNC_JOBS;
	@@ -39,6 +40,7 @@ import static tap.config.TAPConfiguration.KEY_DEFAULT_UPLOAD_LIMIT;
	import static tap.config.TAPConfiguration.KEY_DIRECTORY_PER_USER;		import static tap.config.TAPConfiguration.KEY_DIRECTORY_PER_USER;
	import static tap.config.TAPConfiguration.KEY_FILE_MANAGER;		import static tap.config.TAPConfiguration.KEY_FILE_MANAGER;
	import static tap.config.TAPConfiguration.KEY_FILE_ROOT_PATH;		import static tap.config.TAPConfiguration.KEY_FILE_ROOT_PATH;
			import static tap.config.TAPConfiguration.KEY_FIX_ON_FAIL;
	import static tap.config.TAPConfiguration.KEY_GEOMETRIES;		import static tap.config.TAPConfiguration.KEY_GEOMETRIES;
	import static tap.config.TAPConfiguration.KEY_GROUP_USER_DIRECTORIES;		import static tap.config.TAPConfiguration.KEY_GROUP_USER_DIRECTORIES;
	import static tap.config.TAPConfiguration.KEY_LOGGER;		import static tap.config.TAPConfiguration.KEY_LOGGER;
	@@ -126,15 +128,17 @@ import uws.service.file.UWSFileManager;
	import uws.service.log.UWSLog.LogLevel;		import uws.service.log.UWSLog.LogLevel;

	/**		/**
	* <p>Concrete implementation of {@link ServiceConnection}, fully parameterized with a TAP configuration file.</p>		* Concrete implementation of {@link ServiceConnection}, fully parameterized
			* with a TAP configuration file.
	*		*
	* <p>		* <p>
	* Every aspects of the TAP service are configured here. This instance is also creating the {@link TAPFactory} using the		* Every aspects of the TAP service are configured here. This instance is also
	* TAP configuration file thanks to the implementation {@link ConfigurableTAPFactory}.		* creating the {@link TAPFactory} using the TAP configuration file thanks to
			* the implementation {@link ConfigurableTAPFactory}.
	* </p>		* </p>
	*		*
	* @author Grégory Mantelet (CDS;ARI)		* @author Grégory Mantelet (CDS;ARI)
	* @version 2.3 (11/2018)		* @version 2.3 (03/2019)
	* @since 2.0		* @since 2.0
	*/		*/
	public final class ConfigurableServiceConnection implements ServiceConnection {		public final class ConfigurableServiceConnection implements ServiceConnection {
	@@ -142,10 +146,12 @@ public final class ConfigurableServiceConnection implements ServiceConnection {
	/** File manager to use in the TAP service. */		/** File manager to use in the TAP service. */
	private UWSFileManager fileManager;		private UWSFileManager fileManager;

	/** Object to use in the TAP service in order to log different types of messages (e.g. DEBUG, INFO, WARNING, ERROR, FATAL). */		/** Object to use in the TAP service in order to log different types of
			* messages (e.g. DEBUG, INFO, WARNING, ERROR, FATAL). */
	private TAPLog logger;		private TAPLog logger;

	/** Factory which can create different types of objects for the TAP service (e.g. database connection). */		/** Factory which can create different types of objects for the TAP service
			* (e.g. database connection). */
	private TAPFactory tapFactory;		private TAPFactory tapFactory;

	/** Object gathering all metadata of this TAP service. */		/** Object gathering all metadata of this TAP service. */
	@@ -175,9 +181,11 @@ public final class ConfigurableServiceConnection implements ServiceConnection {
	private final ArrayList<OutputFormat> outputFormats;		private final ArrayList<OutputFormat> outputFormats;

	/** Array of 2 integers: resp. default and maximum output limit.		/** Array of 2 integers: resp. default and maximum output limit.
	* <em>Each limit is expressed in a unit specified in the array {@link #outputLimitTypes}.</em> */		* <em>Each limit is expressed in a unit specified in the array
			* {@link #outputLimitTypes}.</em> */
	private int[] outputLimits = new int[]{ -1, -1 };		private int[] outputLimits = new int[]{ -1, -1 };
	/** Array of 2 limit units: resp. unit of the default output limit and unit of the maximum output limit. */		/** Array of 2 limit units: resp. unit of the default output limit and unit
			* of the maximum output limit. */
	private LimitUnit[] outputLimitTypes = new LimitUnit[2];		private LimitUnit[] outputLimitTypes = new LimitUnit[2];

	/** Indicate whether the UPLOAD feature is enabled or not. */		/** Indicate whether the UPLOAD feature is enabled or not. */
	@@ -201,20 +209,31 @@ public final class ConfigurableServiceConnection implements ServiceConnection {
	private UserIdentifier userIdentifier = null;		private UserIdentifier userIdentifier = null;

	/** List of all allowed coordinate systems.		/** List of all allowed coordinate systems.
	* <em>If NULL, all coord. sys. are allowed. If empty list, none is allowed.</em> */		* <em>
			* If NULL, all coord. sys. are allowed. If empty list, none is allowed.
			* </em> */
	private ArrayList<String> lstCoordSys = null;		private ArrayList<String> lstCoordSys = null;

	/** List of all allowed ADQL geometrical functions.		/** List of all allowed ADQL geometrical functions.
	* <em>If NULL, all geometries are allowed. If empty list, none is allowed.</em> */		* <em>
			* If NULL, all geometries are allowed. If empty list, none is allowed.
			* </em> */
	private ArrayList<String> geometries = null;		private ArrayList<String> geometries = null;
	private final String GEOMETRY_REGEXP = "(AREA\|BOX\|CENTROID\|CIRCLE\|CONTAINS\|DISTANCE\|COORD1\|COORD2\|COORDSYS\|INTERSECTS\|POINT\|POLYGON\|REGION)";		private final String GEOMETRY_REGEXP = "(AREA\|BOX\|CENTROID\|CIRCLE\|CONTAINS\|DISTANCE\|COORD1\|COORD2\|COORDSYS\|INTERSECTS\|POINT\|POLYGON\|REGION)";

	/** List of all known and allowed User Defined Functions.		/** List of all known and allowed User Defined Functions.
	* <em>If NULL, any unknown function is allowed. If empty list, none is allowed.</em> */		* <em>If NULL, any unknown function is allowed. If empty list, none is
			* allowed.</em> */
	private Collection<FunctionDef> udfs = new ArrayList<FunctionDef>(0);		private Collection<FunctionDef> udfs = new ArrayList<FunctionDef>(0);

			/** Indicate whether the input ADQL query should be automatically fixed
			* if its parsing fails because of an incorrect tokenization.
			* @since 2.3 */
			private boolean isFixOnFailEnabled = DEFAULT_FIX_ON_FAIL;

	/**		/**
	* Create a TAP service description thanks to the given TAP configuration file.		* Create a TAP service description thanks to the given TAP configuration
			* file.
	*		*
	* @param tapConfig The content of the TAP configuration file.		* @param tapConfig The content of the TAP configuration file.
	*		*
	@@ -226,12 +245,15 @@ public final class ConfigurableServiceConnection implements ServiceConnection {
	}		}

	/**		/**
	* Create a TAP service description thanks to the given TAP configuration file.		* Create a TAP service description thanks to the given TAP configuration
			* file.
	*		*
	* @param tapConfig The content of the TAP configuration file.		* @param tapConfig The content of the TAP configuration file.
	* @param webAppRootDir The directory of the Web Application running this TAP service.		* @param webAppRootDir The directory of the Web Application running this
	* <em>In this directory another directory may be created in order to store all TAP service files		* TAP service. <em>In this directory another directory
	* if none is specified in the given TAP configuration file.</em>		* may be created in order to store all TAP service
			* files if none is specified in the given TAP
			* configuration file.</em>
	*		*
	* @throws NullPointerException If the given properties set is NULL.		* @throws NullPointerException If the given properties set is NULL.
	* @throws TAPException If a property is wrong or missing.		* @throws TAPException If a property is wrong or missing.
	@@ -284,6 +306,7 @@ public final class ConfigurableServiceConnection implements ServiceConnection {
	initCoordSys(tapConfig);		initCoordSys(tapConfig);
	initADQLGeometries(tapConfig);		initADQLGeometries(tapConfig);
	initUDFs(tapConfig);		initUDFs(tapConfig);
			isFixOnFailEnabled = Boolean.parseBoolean(getProperty(tapConfig, KEY_FIX_ON_FAIL));
	}		}

	/**		/**
	@@ -1735,4 +1758,9 @@ public final class ConfigurableServiceConnection implements ServiceConnection {
	return fetchSize;		return fetchSize;
	}		}

			@Override
			public boolean fixOnFailEnabled(){
			return isFixOnFailEnabled;
			}

	}		}

src/tap/config/TAPConfiguration.java

+11 −2

Original line number	Original line	Diff line number	Diff line
	@@ -16,7 +16,7 @@ package tap.config;
	* You should have received a copy of the GNU Lesser General Public License		* You should have received a copy of the GNU Lesser General Public License
	* along with TAPLibrary. If not, see <http://www.gnu.org/licenses/>.		* along with TAPLibrary. If not, see <http://www.gnu.org/licenses/>.
	*		*
	* Copyright 2015-2018 - UDS/Centre de Données astronomiques de Strasbourg (CDS),		* Copyright 2015-2019 - UDS/Centre de Données astronomiques de Strasbourg (CDS),
	* Astronomisches Rechen Institut (ARI)		* Astronomisches Rechen Institut (ARI)
	*/		*/

	@@ -41,7 +41,7 @@ import tap.backup.DefaultTAPBackupManager;
	* </i></p>		* </i></p>
	*		*
	* @author Grégory Mantelet (CDS;ARI)		* @author Grégory Mantelet (CDS;ARI)
	* @version 2.3 (11/2018)		* @version 2.3 (03/2019)
	* @since 2.0		* @since 2.0
	*/		*/
	public final class TAPConfiguration {		public final class TAPConfiguration {
	@@ -172,6 +172,15 @@ public final class TAPConfiguration {
	public final static String KEY_ASYNC_FETCH_SIZE = "async_fetch_size";		public final static String KEY_ASYNC_FETCH_SIZE = "async_fetch_size";
	/** Default value of the property {@link #KEY_ASYNC_FETCH_SIZE}: {@value #DEFAULT_ASYNC_FETCH_SIZE}. */		/** Default value of the property {@link #KEY_ASYNC_FETCH_SIZE}: {@value #DEFAULT_ASYNC_FETCH_SIZE}. */
	public final static int DEFAULT_ASYNC_FETCH_SIZE = 10000;		public final static int DEFAULT_ASYNC_FETCH_SIZE = 10000;
			/** Name/Key of the property specifying whether the fixOnFail option is
			* enabled or not. This option lets automatically fix the input ADQL query
			* if its tokenization fails.
			* @since 2.3 */
			public final static String KEY_FIX_ON_FAIL = "fix_on_fail";
			/** Default value of the property {@link #KEY_FIX_ON_FAIL}:
			* {@value #DEFAULT_FIX_ON_FAIL}.
			* @since 2.3 */
			public final static boolean DEFAULT_FIX_ON_FAIL = false;
	/** Name/Key of the property specifying the name of the DataSource into the JDNI. */		/** Name/Key of the property specifying the name of the DataSource into the JDNI. */
	public final static String KEY_DATASOURCE_JNDI_NAME = "datasource_jndi_name";		public final static String KEY_DATASOURCE_JNDI_NAME = "datasource_jndi_name";
	/** Name/Key of the property specifying the full class name of the JDBC driver.		/** Name/Key of the property specifying the full class name of the JDBC driver.