[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	Diff line number	Diff line
		@@ -16,7 +16,7 @@ package tap;
		* 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)
		*/

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

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

		// 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:
		final int limit = query.getSelect().getLimit();

src/tap/ServiceConnection.java

+15 −2

Original line number	Diff line number	Diff line
		@@ -16,7 +16,7 @@ package tap;
		* 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 2012-2018 - UDS/Centre de Données astronomiques de Strasbourg (CDS),
		* Copyright 2012-2019 - UDS/Centre de Données astronomiques de Strasbourg (CDS),
		* Astronomisches Rechen Institut (ARI)
		*/

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

		@@ -744,4 +744,17 @@ public interface ServiceConnection {
		*/
		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	Diff line number	Diff line
		package tap;

		import adql.db.DBColumn;

		/*
		* 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
		* 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)
		*/

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

		/**
		* <p>Report the execution (including the parsing and the output writing) of an ADQL query.
		* 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>
		* Report the execution (including the parsing and the output writing) of an
		* ADQL query.
		*
		* <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)
		* @version 2.0 (04/2015)
		* @version 2.3 (03/2019)
		*/
		public class TAPExecutionReport {

		/** ID of the job whose the execution is reported here. */
		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;

		/** List of all parameters provided in the user request. */
		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> */
		public DBColumn[] resultingColumns = new DBColumn[0];

		@@ -51,21 +68,26 @@ public class TAPExecutionReport {
		* @since 2.0 */
		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 };

		/** Total duration of the job execution. */
		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;

		/**
		* Build an empty execution report.
		*
		* @param jobID ID of the job whose the execution must be described here.
		* @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.
		* @param jobID ID of the job whose the execution must be described
		* here.
		* @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){
		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},
		* {@link ExecutionProgression#EXECUTING_ADQL} and {@link ExecutionProgression#WRITING_RESULT} are managed.</i></p>
		* <p><i><b>Warning:</b>
		* 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.
		*
		* @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){
		switch(tapProgression){
		@@ -103,7 +131,8 @@ public class TAPExecutionReport {
		*
		* @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)
		*/

src/tap/config/ConfigurableServiceConnection.java

+45 −17

Original line number	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
		* 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)
		*/

		import static tap.config.TAPConfiguration.DEFAULT_ASYNC_FETCH_SIZE;
		import static tap.config.TAPConfiguration.DEFAULT_DIRECTORY_PER_USER;
		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_LOGGER;
		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_FILE_MANAGER;
		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_GROUP_USER_DIRECTORIES;
		import static tap.config.TAPConfiguration.KEY_LOGGER;
		@@ -126,15 +128,17 @@ import uws.service.file.UWSFileManager;
		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>
		* Every aspects of the TAP service are configured here. This instance is also creating the {@link TAPFactory} using the
		* TAP configuration file thanks to the implementation {@link ConfigurableTAPFactory}.
		* Every aspects of the TAP service are configured here. This instance is also
		* creating the {@link TAPFactory} using the TAP configuration file thanks to
		* the implementation {@link ConfigurableTAPFactory}.
		* </p>
		*
		* @author Grégory Mantelet (CDS;ARI)
		* @version 2.3 (11/2018)
		* @version 2.3 (03/2019)
		* @since 2.0
		*/
		public final class ConfigurableServiceConnection implements ServiceConnection {
		@@ -142,10 +146,12 @@ public final class ConfigurableServiceConnection implements ServiceConnection {
		/** File manager to use in the TAP service. */
		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;

		/** 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;

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

		/** 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 };
		/** 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];

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

		/** 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;

		/** 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 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.
		* <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);

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

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

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

		}

src/tap/config/TAPConfiguration.java

+11 −2

Original line number	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
		* 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)
		*/

		@@ -41,7 +41,7 @@ import tap.backup.DefaultTAPBackupManager;
		* </i></p>
		*
		* @author Grégory Mantelet (CDS;ARI)
		* @version 2.3 (11/2018)
		* @version 2.3 (03/2019)
		* @since 2.0
		*/
		public final class TAPConfiguration {
		@@ -172,6 +172,15 @@ public final class TAPConfiguration {
		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}. */
		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. */
		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.