Release 1.3.0. Updated to newest julielab parent pom and Java 11.

pom.xml

@@ -2,7 +2,7 @@
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <artifactId>costosys</artifactId>
-    <version>1.2.5-SNAPSHOT</version>
+    <version>1.3.0</version>
     <name>Corpus Storage System</name>
     <description>A utility for managing documents stored in a PostgreSQL database. The documents are imported into a
         PostgreSQL DB as full texts with the goal to be able to retrieve the documents by their PubMedID efficiently.
@@ -13,8 +13,6 @@
     <build>
         <plugins>
             <plugin>
-                <!-- NOTE: We don't need a groupId specification because the group is
-                    org.apache.maven.plugins ...which is assumed by default. -->
                 <artifactId>maven-assembly-plugin</artifactId>
                 <version>2.2</version>
                 <configuration>
@@ -26,14 +24,12 @@
                             <mainClass>de.julielab.xmlData.cli.CLI</mainClass>
                         </manifest>
                     </archive>
-                    <!-- 					<appendAssemblyId>false</appendAssemblyId> -->
-                    <!-- 					<finalName>medline-manager</finalName> -->
                 </configuration>
                 <executions>
                     <execution>
-                        <phase>package</phase> <!-- append to the packaging phase. -->
+                        <phase>package</phase>
                         <goals>
-                            <goal>single</goal> <!-- goals == mojos -->
+                            <goal>single</goal>
                         </goals>
                     </execution>
                 </executions>
@@ -182,7 +178,7 @@
     <parent>
         <groupId>de.julielab</groupId>
         <artifactId>julielab-parent</artifactId>
-        <version>2.2.0</version>
+        <version>2.4.0</version>
     </parent>
     <organization>
         <name>JULIE Lab, Germany</name>

src/main/java/de/julielab/xmlData/cli/CLI.java

@@ -66,7 +66,7 @@ private static void logMessage(String msg) {
         LOG.info(msg);
     }
 
-    public static void main(String[] args) throws SQLException, TableSchemaMismatchException, ConfigurationNotFoundException, ConfigurationException, IOException, MedlineUpdateException {
+    public static void main(String[] args) throws Exception {
         long time = System.currentTimeMillis();
         String dbUrl;
         String user;

src/main/java/de/julielab/xmlData/dataBase/DataBaseConnector.java

@@ -505,7 +505,7 @@ public FieldConfig getActiveTableFieldConfiguration() {
      * @param pid             - will be saved in the subset table
      * @return An ArrayList of pmids which have not yet been processed
      */
-    public List<Object[]> retrieveAndMark(String subsetTableName, String readerComponent, String hostName, String pid) throws TableSchemaMismatchException {
+    public List<Object[]> retrieveAndMark(String subsetTableName, String readerComponent, String hostName, String pid) throws TableSchemaMismatchException, TableNotFoundException {
         return retrieveAndMark(subsetTableName, readerComponent, hostName, pid, RETRIEVE_MARK_LIMIT, null);
     }
 
@@ -530,7 +530,7 @@ public List<Object[]> retrieveAndMark(String subsetTableName, String readerCompo
      * @see #retrieveAndMark(String, String, String, String, int, String)
      */
     public List<Object[]> retrieveAndMark(String subsetTableName, String readerComponent, String hostName, String pid,
-                                          int limit, String order) throws TableSchemaMismatchException {
+                                          int limit, String order) throws TableSchemaMismatchException, TableNotFoundException {
         return retrieveAndMark(subsetTableName, activeTableSchema, readerComponent, hostName, pid, limit, order);
     }
 
@@ -566,7 +566,7 @@ public List<Object[]> retrieveAndMark(String subsetTableName, String readerCompo
      * @return An ArrayList of primary keys which have not yet been processed.
      */
     public List<Object[]> retrieveAndMark(String subsetTableName, String schemaName, String readerComponent,
-                                          String hostName, String pid, int limit, String order) throws TableSchemaMismatchException {
+                                          String hostName, String pid, int limit, String order) throws TableSchemaMismatchException, TableNotFoundException {
         checkTableDefinition(subsetTableName, schemaName);
         List<Object[]> ids = new ArrayList<>(limit);
         String sql = null;
@@ -3392,7 +3392,7 @@ public FieldConfig getFieldConfiguration(String schemaName) {
      * @param tableName The table to check.
      * @see #checkTableDefinition(String, String)
      */
-    public void checkTableDefinition(String tableName) throws TableSchemaMismatchException {
+    public void checkTableDefinition(String tableName) throws TableSchemaMismatchException, TableNotFoundException {
         checkTableDefinition(tableName, activeTableSchema);
     }
 
@@ -3409,10 +3409,10 @@ public void checkTableDefinition(String tableName) throws TableSchemaMismatchExc
      *
      * @param tableName - table to check
      */
-    public void checkTableDefinition(String tableName, String schemaName) throws TableSchemaMismatchException {
+    public void checkTableDefinition(String tableName, String schemaName) throws TableSchemaMismatchException, TableNotFoundException {
         try (CoStoSysConnection connection = obtainOrReserveConnection()) {
             if (!tableExists(tableName))
-                throw new IllegalArgumentException("The table '" + tableName + "' does not exist.");
+                throw new TableNotFoundException("The table '" + tableName + "' does not exist.");
             FieldConfig fieldConfig = fieldConfigs.get(schemaName);
 
             List<String> actualColumns = new ArrayList<>();

src/test/java/de/julielab/xmlData/dataBase/DataBaseConnectorTest.java

@@ -8,31 +8,32 @@
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
-import java.io.IOException;
 import java.io.UnsupportedEncodingException;
-import java.sql.Connection;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.util.*;
 
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.assertj.core.api.Assertions.assertThatCode;
 import static org.testng.AssertJUnit.assertEquals;
-import static org.assertj.core.api.Assertions.*;
+
 public class DataBaseConnectorTest {
 
     public static PostgreSQLContainer postgres;
     private static DataBaseConnector dbc;
 
     @BeforeClass
-    public static void setup(){
-        postgres =  new PostgreSQLContainer();
+    public static void setup() {
+        postgres = new PostgreSQLContainer();
         postgres.start();
         dbc = new DataBaseConnector(postgres.getJdbcUrl(), postgres.getUsername(), postgres.getPassword());
         dbc.setActiveTableSchema("medline_2016");
     }
 
     @AfterClass
-    public static void shutdown(){
-        postgres.stop();dbc.close();
+    public static void shutdown() {
+        postgres.stop();
+        dbc.close();
     }
 
 
@@ -45,11 +46,12 @@ public void testQueryAndExecution() {
                 e.printStackTrace();
             }
         });
-       boolean exists = dbc.withConnectionQueryBoolean(dbc -> dbc.tableExists("mytable"));
+        boolean exists = dbc.withConnectionQueryBoolean(dbc -> dbc.tableExists("mytable"));
         assertThat(exists).isTrue();
     }
+
     @Test
-    public void testRetrieveAndMark() throws SQLException, TableSchemaMismatchException {
+    public void testRetrieveAndMark() throws Exception {
         dbc.reserveConnection();
         dbc.createTable(Constants.DEFAULT_DATA_TABLE_NAME, "Test data table");
         dbc.importFromXMLFile("src/test/resources/documents/documentSet.xml.gz", Constants.DEFAULT_DATA_TABLE_NAME);
@@ -83,7 +85,7 @@ public void testStatus() throws SQLException, TableSchemaMismatchException, Tabl
 
     @Test(dependsOnMethods = "testRetrieveAndMark")
     public void testRandomSubset() throws SQLException {
-        try(CoStoSysConnection conn = dbc.reserveConnection()) {
+        try (CoStoSysConnection conn = dbc.reserveConnection()) {
             dbc.createSubsetTable("randomsubset", Constants.DEFAULT_DATA_TABLE_NAME, "Random Test Subset");
             dbc.initRandomSubset(10, "randomsubset", Constants.DEFAULT_DATA_TABLE_NAME);
             ResultSet rs = conn.createStatement().executeQuery("SELECT * FROM randomsubset");
@@ -112,8 +114,8 @@ public void testQuerySubset() throws SQLException {
     }
 
     @Test
-    public void testXmlData() throws  UnsupportedEncodingException {
-        dbc.withConnectionExecute(c -> c.createTable("myxmltest", "xmi_text","XML Test Table"));
+    public void testXmlData() throws UnsupportedEncodingException {
+        dbc.withConnectionExecute(c -> c.createTable("myxmltest", "xmi_text", "XML Test Table"));
         Map<String, Object> row = new HashMap<>();
         row.put("docid", "doc1");
         row.put("xmi", "some nonsense");