Adql2.1jakarta

ADQLLib/build.gradle

@@ -1,9 +1,11 @@
 plugins {
-    id "org.javacc.javacc" version "3.0.0"
+    id "org.javacc.javacc" version "3.0.2"
+    id 'maven-publish'
+    // FIXME really need to sign too
 }
 
 // Describe the library:
-version = "2.0-beta"
+version = "2.0-SNAPSHOT"
 description = "Java library to parse, analyze and transform ADQL queries."
 
 // Name of the JAR name (which will be then suffixed by the version number):
@@ -15,7 +17,7 @@ distributions {
 }
 
 dependencies {
-    implementation 'uk.ac.starlink:stil:4.2'
+    implementation 'uk.ac.starlink:stil:4.3.1'
     implementation 'postgresql:postgresql:9.1-901.jdbc4'
 }
 
@@ -62,3 +64,40 @@ compileJavacc.doLast {
 
 // Ensure the generated Java classes and examples are included in the classpath:
 sourceSets.main.java.srcDirs = ["src", "examples", project.buildDir.absolutePath+'/generated']
+
+
+publishing {
+    publications {
+        maven(MavenPublication) {
+            groupId = 'fr.unistra.cds' //FIXME - is this what is wanted?
+            artifactId = 'ADQLlib'
+            version = '2.0-SNAPSHOT'
+
+            from components.java
+            pom {
+                name = 'ADQLlib'
+                description = 'Java library to parse, analyze and transform ADQL queries.'
+                url = 'http://cdsportal.u-strasbg.fr/adqltuto/'
+
+                licenses {
+                    license {
+                        name = 'GNU Lesser General Public License version 3'
+                        url = 'https://opensource.org/license/lgpl-3-0'
+                    }
+                }
+                developers {
+                    developer {
+                        id = 'gmantele'
+                        name = 'Grégory Mantelet'
+                        email = 'gregory.mantelet@astro.u-strasbg.fr'
+                    }
+                }
+                scm {
+                    connection = 'scm:git:git://github.com/gmantele/vollt.git'
+                    developerConnection = 'scm:git:ssh://github.com/gmantele/vollt.git'
+                    url = 'http://example.com/my-library/'
+                }
+            }
+        }
+    }
+}

ADQLLib/test/adql/translator/TestPgSphereTranslator.java

@@ -288,7 +288,7 @@ public void testTranslateGeometryFromDB() {
 
 		// OTHER
 		try {
-			translator.translateGeometryFromDB(new Double(12.3));
+			translator.translateGeometryFromDB(12.3);
 			fail("The translation of a Double as a geometry is not supported!");
 		} catch(Throwable t) {
 			assertTrue(t instanceof ParseException);

TAPLib/build.gradle

@@ -1,3 +1,6 @@
+plugins {
+    id 'maven-publish'
+}
 
 // Describe the library:
 version = "2.4-beta"
@@ -11,7 +14,7 @@ dependencies {
     implementation project(':UWSLib')
 
     implementation fileTree(dir: '../lib', includes: ['stil_3.3-2.jar'])
-    implementation 'javax.servlet:javax.servlet-api:3.0.1'
+    implementation 'jakarta.servlet:jakarta.servlet-api:5.0.0'
     implementation 'org.slf4j:slf4j-api:1.7.25'
     implementation 'org.json:json:20231013'
 
@@ -24,6 +27,44 @@ dependencies {
     testRuntimeOnly 'org.xerial:sqlite-jdbc:3.44.1.0'
 
     /* Needed to run Gradle with Java 9+: */
-    // https://mvnrepository.com/artifact/javax.xml.bind/jaxb-api
-	implementation group: 'javax.xml.bind', name: 'jaxb-api', version: '2.3.1'
+    implementation 'jakarta.xml.bind:jakarta.xml.bind-api:4.0.2'
+
+    implementation ("uk.ac.starlink:stil:4.3.1")
+}
+
+publishing {
+    publications {
+        maven(MavenPublication) {
+            groupId = 'fr.unistra.cds' // Change this to the correct group
+            artifactId = 'TAPlib' // Change this for each library
+            version = '2.4-SNAPSHOT'
+
+            from components.java
+            pom {
+                name = 'TAPlib'
+                description = 'Java library to deploy a TAP service. This is a cloned version of the original to allow the updating of older java functionality'
+                url = 'http://cdsportal.u-strasbg.fr/taptuto/'
+
+                licenses {
+                    license {
+                        name = 'GNU Lesser General Public License version 3'
+                        url = 'https://opensource.org/license/lgpl-3-0'
+                    }
+                }
+                developers {
+                    developer {
+                        id = 'gmantele'
+                        name = 'Grégory Mantelet'
+                        email = 'gregory.mantelet@astro.u-strasbg.fr'
+                    }
+                }
+                scm {
+                    connection = 'scm:git:git://github.com/slloyd-src/vollt.git'
+                    developerConnection = 'scm:git:ssh://github.com/slloyd-src/vollt.git'
+                    url = 'http://example.com/my-library/'
+                }
+            }
+        }
+    }
+
 }

TAPLib/docker/Dockerfile

@@ -49,8 +49,8 @@ RUN wget -O /usr/local/tomcat/webapps/tap/WEB-INF/lib/commons-fileupload.jar \
             'https://repo1.maven.org/maven2/commons-fileupload/commons-fileupload/1.3.3/commons-fileupload-1.3.3.jar'
 RUN wget -O /usr/local/tomcat/webapps/tap/WEB-INF/lib/commons-io.jar \
             'https://repo1.maven.org/maven2/commons-io/commons-io/2.6/commons-io-2.6.jar'
-RUN wget -O /usr/local/tomcat/webapps/tap/WEB-INF/lib/javax-servlet-api.jar \
-            'https://repo1.maven.org/maven2/javax/servlet/javax.servlet-api/3.0.1/javax.servlet-api-3.0.1.jar'
+RUN wget -O /usr/local/tomcat/webapps/tap/WEB-INF/lib/jakarta-servlet-api.jar \
+            'https://repo1.maven.org/maven2/jakarta/servlet/jakarta.servlet-api/3.0.1/jakarta.servlet-api-3.0.1.jar'
 RUN wget -O /usr/local/tomcat/webapps/tap/WEB-INF/lib/json.jar \
             'https://repo1.maven.org/maven2/org/json/json/20180813/json-20180813.jar'
 RUN wget -O /usr/local/tomcat/webapps/tap/WEB-INF/lib/slf4j-api.jar \

TAPLib/docker/scripts/tap-starter.sh

@@ -46,7 +46,7 @@ CONTEXT_FILE=$WEBAPPS_DIR/tap/META-INF/context.xml
 # Start the Context and Resource definitions:
 echo -e '<Context>\n\t<Resource name="jdbc/tapdb" auth="Container"' > $CONTEXT_FILE
 # Set the Resource type (SQL's Datasource):
-echo -e '\t\ttype="javax.sql.DataSource"' >> $CONTEXT_FILE
+echo -e '\t\ttype="jakarta.sql.DataSource"' >> $CONTEXT_FILE
 # Set the JDBC driver:
 case "$DB_TYPE" in
     postgres|pgsphere)

TAPLib/docker/tomcat/tap-webapp/WEB-INF/web.xml

@@ -12,7 +12,7 @@
 
   <resource-ref>
 		<res-ref-name>jdbc/testdb</res-ref-name>
-		<res-type>javax.sql.DataSource</res-type>
+		<res-type>jakarta.sql.DataSource</res-type>
 		<res-auth>Container</res-auth>
 	</resource-ref>
 

TAPLib/src/tap/ADQLExecutor.java

@@ -23,7 +23,7 @@
 import java.io.IOException;
 import java.io.OutputStream;
 
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponse;
 
 import adql.parser.ADQLParser;
 import adql.parser.ADQLQueryFactory;

TAPLib/src/tap/AbstractTAPFactory.java

@@ -26,7 +26,7 @@
 import java.util.List;
 import java.util.Map;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 
 import adql.db.DBChecker;
 import adql.parser.ADQLParser;

TAPLib/src/tap/TAPFactory.java

@@ -23,7 +23,7 @@
 import java.util.List;
 import java.util.Map;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 
 import adql.parser.ADQLParser;
 import adql.parser.ADQLQueryFactory;
@@ -308,7 +308,7 @@ protected TAPFactory(final ServiceConnection service) throws NullPointerExceptio
 	 * 	with the given request, in order to ensure that the returned object is always a {@link TAPJob}.
 	 * </p>
 	 *
-	 * @see uws.service.AbstractUWSFactory#createJob(javax.servlet.http.HttpServletRequest, uws.job.user.JobOwner)
+	 * @see uws.service.AbstractUWSFactory#createJob(jakarta.servlet.http.HttpServletRequest, uws.job.user.JobOwner)
 	 * @see #createTAPJob(HttpServletRequest, JobOwner)
 	 */
 	@Override

TAPLib/src/tap/TAPRequestParser.java

@@ -23,7 +23,7 @@
 import java.util.HashMap;
 import java.util.Map;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 
 import uws.UWSException;
 import uws.UWSToolBox;

TAPLib/src/tap/TAPSyncJob.java

@@ -24,7 +24,7 @@
 import java.util.Date;
 import java.util.Iterator;
 
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponse;
 
 import tap.parameters.TAPExecutionDurationController;
 import tap.parameters.TAPParameters;

TAPLib/src/tap/config/ConfigurableServiceConnection.java

@@ -45,11 +45,15 @@
 import uws.service.log.UWSLog.LogLevel;
 
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
 import java.net.MalformedURLException;
 import java.net.URL;
+import java.nio.file.InvalidPathException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -178,7 +182,7 @@ public final class ConfigurableServiceConnection implements ServiceConnection {
 	 * @throws NullPointerException	If the given properties set is NULL.
 	 * @throws TAPException			If a property is wrong or missing.
 	 */
-	public ConfigurableServiceConnection(final Properties tapConfig) throws NullPointerException, TAPException {
+	public ConfigurableServiceConnection(final Properties tapConfig) throws FileNotFoundException, TAPException {
 		this(tapConfig, null);
 	}
 
@@ -196,9 +200,9 @@ public ConfigurableServiceConnection(final Properties tapConfig) throws NullPoin
 	 * @throws NullPointerException	If the given properties set is NULL.
 	 * @throws TAPException			If a property is wrong or missing.
 	 */
-	public ConfigurableServiceConnection(final Properties tapConfig, final String webAppRootDir) throws NullPointerException, TAPException {
+	public ConfigurableServiceConnection(final Properties tapConfig, final String webAppRootDir) throws FileNotFoundException, TAPException {
 		if (tapConfig == null)
-			throw new NullPointerException("Missing TAP properties! ");
+			throw new FileNotFoundException("Missing TAP properties! ");
 
 		// 1. INITIALIZE THE FILE MANAGER:
 		initFileManager(tapConfig, webAppRootDir);
@@ -335,17 +339,27 @@ private void initFileManager(final Properties tapConfig, final String webAppRoot
 	 *
 	 * @throws ParseException	If the given file path is a URI/URL.
 	 */
-	protected static final File getFile(final String filePath, final String webAppRootPath, final String propertyName) throws TAPException {
-		if (filePath == null)
+	static File getFile(final String filePath, final String webAppRootPath, final String propertyName) throws TAPException {
+		if (filePath == null) {
 			return null;
-		else if (filePath.matches(".*:.*"))
-			throw new TAPException("Incorrect file path for the property \"" + propertyName + "\": \"" + filePath + "\"! URI/URLs are not expected here.");
+		}
 
-		File f = new File(filePath);
-		if (f.isAbsolute())
-			return f;
-		else
-			return new File(webAppRootPath, filePath);
+		// Convert the file path into a Path object to avoid manual checks
+		Path path;
+		try {
+			path = Paths.get(filePath);
+		} catch (InvalidPathException e) {
+			throw new TAPException("Invalid file path for the property \"" + propertyName + "\": \"" + filePath + "\"! Please check the path format.", e);
+		}
+
+		// If the path is absolute, return it as a File directly
+		if (path.isAbsolute()) {
+			return path.toFile();
+		}
+
+		// Otherwise, assume it's a relative path and resolve it against the webAppRootPath
+		Path resolvedPath = Paths.get(webAppRootPath).resolve(path);
+		return resolvedPath.toFile();
 	}
 
 	/**

TAPLib/src/tap/config/ConfigurableTAPServlet.java

@@ -37,11 +37,11 @@
 import java.io.InputStream;
 import java.util.Properties;
 
-import javax.servlet.ServletConfig;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletConfig;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 
 import tap.ServiceConnection;
 import tap.TAPException;
@@ -113,7 +113,9 @@ public void init(final ServletConfig config) throws ServletException{
 		}finally{
 			try{
 				input.close();
-			}catch(IOException ioe2){}
+			}catch(IOException ioe2){
+				ioe2.printStackTrace();
+			}
 		}
 
 		/* 4. CREATE THE TAP SERVICE */
@@ -127,8 +129,11 @@ public void init(final ServletConfig config) throws ServletException{
 			tap = null;
 			if (ex instanceof TAPException)
 				throw new ServletException(ex.getMessage(), ex.getCause());
-			else
-				throw new ServletException("Impossible to initialize the TAP service!", ex);
+			else {
+				ex.printStackTrace();
+				System.out.println(ex.getMessage());
+				throw new ServletException("Impossible to initialize the TAP services!" + ex.getMessage());
+			}
 		}
 
 		/* 4Bis. SET THE HOME PAGE */

TAPLib/src/tap/config/TAPConfiguration.java

@@ -810,7 +810,7 @@ public final static Object[] parseLimit(String value, final String propertyName,
 
 		// If empty value, return an infinite limit:
 		if (value == null || value.length() == 0)
-			return (longValue ? new Object[]{ new Long(-1L), LimitUnit.rows } : new Object[]{ new Integer(-1), LimitUnit.rows });
+			return (longValue ? new Object[]{-1L, LimitUnit.rows } : new Object[]{-1, LimitUnit.rows });
 
 		// A. Parse the string from the end in order to extract the unit part.
 		//    The final step of the loop is the extraction of the numeric value, when the first digit is encountered.
@@ -878,9 +878,9 @@ else if (buf.length() > 2)
 		}
 
 		if (numValue < 0)
-			return (longValue ? new Object[]{ new Long(-1L), unit } : new Object[]{ new Integer(-1), unit });
+			return (longValue ? new Object[]{-1L, unit } : new Object[]{-1, unit });
 		else
-			return (longValue ? new Object[]{ new Long(numValue), unit } : new Object[]{ new Integer((int)numValue), unit });
+			return (longValue ? new Object[]{numValue, unit } : new Object[]{(int) numValue, unit });
 	}
 
 }

TAPLib/src/tap/data/ResultSetTableIterator.java

@@ -760,11 +760,11 @@ else if (colType.type == DBDatatype.SMALLINT)
 
 			// if the type is Integer but it is declared as a SMALLINT cast the value (absolutely required for the FITS format):
 			else if (colValue instanceof Integer && colType != null && colValue != null && colType.type == DBDatatype.SMALLINT)
-				colValue = new Short(((Integer)colValue).shortValue());
+				colValue = ((Integer) colValue).shortValue();
 
 			// if the column value is a Boolean object, format it as a SMALLINT:
 			else if (colValue instanceof Boolean)
-				colValue = ((Boolean)colValue) ? new Short((short)1) : new Short((short)0);
+				colValue = ((Boolean)colValue) ? Short.valueOf((short)1) : Short.valueOf((short)0);
 
 			// if the column should be only a character:
 			else if (colType != null && colValue != null && colType.type == DBDatatype.CHAR && (colType.length == 1 || colType.length <= 0) && colValue instanceof String)

TAPLib/src/tap/error/DefaultTAPErrorWriter.java

@@ -31,8 +31,8 @@
 import java.util.LinkedHashMap;
 import java.util.Map;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 
 import tap.ServiceConnection;
 import tap.TAPException;