#286 Rename package csv to file and sql to database.

algorithm_integration/src/main/java/de/metanome/algorithm_integration/input/TableInputGenerator.java

@@ -17,7 +17,7 @@
 package de.metanome.algorithm_integration.input;
 
 /**
- * Generates new copies of a sql table based {@link de.metanome.algorithm_integration.input.RelationalInput}.
+ * Generates new copies of a database table based {@link de.metanome.algorithm_integration.input.RelationalInput}.
  *
  * @author Jakob Zwiener
  */

backend/src/main/java/de/metanome/backend/configuration/ConfigurationValueDatabaseConnectionGenerator.java

@@ -23,12 +23,12 @@
 import de.metanome.algorithm_integration.configuration.ConfigurationSettingDatabaseConnection;
 import de.metanome.algorithm_integration.configuration.ConfigurationValue;
 import de.metanome.algorithm_integration.input.DatabaseConnectionGenerator;
-import de.metanome.backend.input.sql.DefaultDatabaseConnectionGenerator;
+import de.metanome.backend.input.database.DefaultDatabaseConnectionGenerator;
 
 import java.util.Set;
 
 /**
- * Represents sql input configuration values for {@link Algorithm}s.
+ * Represents database input configuration values for {@link Algorithm}s.
  *
  * @author Jakob Zwiener
  */

backend/src/main/java/de/metanome/backend/configuration/ConfigurationValueFileInputGenerator.java

@@ -23,7 +23,7 @@
 import de.metanome.algorithm_integration.configuration.ConfigurationSettingFileInput;
 import de.metanome.algorithm_integration.configuration.ConfigurationValue;
 import de.metanome.algorithm_integration.input.FileInputGenerator;
-import de.metanome.backend.input.csv.DefaultFileInputGenerator;
+import de.metanome.backend.input.file.DefaultFileInputGenerator;
 
 import java.util.Set;
 

backend/src/main/java/de/metanome/backend/configuration/ConfigurationValueTableInputGenerator.java

@@ -23,7 +23,7 @@
 import de.metanome.algorithm_integration.configuration.ConfigurationSettingTableInput;
 import de.metanome.algorithm_integration.configuration.ConfigurationValue;
 import de.metanome.algorithm_integration.input.TableInputGenerator;
-import de.metanome.backend.input.sql.DefaultTableInputGenerator;
+import de.metanome.backend.input.database.DefaultTableInputGenerator;
 
 import java.util.Set;
 

backend/src/main/java/de/metanome/backend/input/DefaultRelationalInputGeneratorInitializer.java

@@ -25,8 +25,8 @@
 import de.metanome.algorithm_integration.input.RelationalInputGenerator;
 import de.metanome.algorithm_integration.input.RelationalInputGeneratorInitializer;
 import de.metanome.backend.configuration.ConfigurationValueRelationalInputGenerator;
-import de.metanome.backend.input.csv.DefaultFileInputGenerator;
-import de.metanome.backend.input.sql.DefaultTableInputGenerator;
+import de.metanome.backend.input.file.DefaultFileInputGenerator;
+import de.metanome.backend.input.database.DefaultTableInputGenerator;
 
 import java.util.ArrayList;
 import java.util.List;

backend/src/main/java/de/metanome/backend/input/sql/DefaultDatabaseConnectionGenerator.java → backend/src/main/java/de/metanome/backend/input/database/DefaultDatabaseConnectionGenerator.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package de.metanome.backend.input.sql;
+package de.metanome.backend.input.database;
 
 import de.metanome.algorithm_integration.AlgorithmConfigurationException;
 import de.metanome.algorithm_integration.configuration.ConfigurationSettingDatabaseConnection;
@@ -85,7 +85,7 @@ public RelationalInput generateRelationalInputFromSql(String queryString)
       resultSetIterator = new ResultSetIterator(resultSet);
     } catch (SQLException e) {
       throw new InputGenerationException(
-          ExceptionParser.parse(e, "Could not construct sql input"), e);
+          ExceptionParser.parse(e, "Could not construct database input"), e);
     }
 
     return resultSetIterator;
@@ -105,14 +105,14 @@ protected ResultSet executeQuery(String queryString) throws InputGenerationExcep
       statements.add(sqlStatement);
     } catch (SQLException e) {
       throw new InputGenerationException(
-          ExceptionParser.parse(e, "Could not create sql statement on connection"), e);
+          ExceptionParser.parse(e, "Could not create database statement on connection"), e);
     }
     ResultSet resultSet;
     try {
       resultSet = sqlStatement.executeQuery(queryString);
     } catch (SQLException e) {
       throw new InputGenerationException(
-          ExceptionParser.parse(e, "Could not execute sql statement"), e);
+          ExceptionParser.parse(e, "Could not execute database statement"), e);
     }
 
     return resultSet;

backend/src/main/java/de/metanome/backend/input/sql/DefaultTableInputGenerator.java → backend/src/main/java/de/metanome/backend/input/database/DefaultTableInputGenerator.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package de.metanome.backend.input.sql;
+package de.metanome.backend.input.database;
 
 import de.metanome.algorithm_integration.AlgorithmConfigurationException;
 import de.metanome.algorithm_integration.configuration.ConfigurationSettingTableInput;
@@ -63,7 +63,7 @@ public DefaultTableInputGenerator(ConfigurationSettingTableInput setting)
    * Generates a new {@link de.metanome.algorithm_integration.input.RelationalInput} to iterate over the data in the table.
    *
    * @return the {@link de.metanome.algorithm_integration.input.RelationalInput}
-   * @throws InputGenerationException if the sql statement could not be executed
+   * @throws InputGenerationException if the database statement could not be executed
    */
   @Override
   public RelationalInput generateNewCopy() throws InputGenerationException {

backend/src/main/java/de/metanome/backend/input/sql/ResultSetIterator.java → backend/src/main/java/de/metanome/backend/input/database/ResultSetIterator.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package de.metanome.backend.input.sql;
+package de.metanome.backend.input.database;
 
 import com.google.common.collect.ImmutableList;
 

backend/src/main/java/de/metanome/backend/input/csv/DefaultFileInputGenerator.java → backend/src/main/java/de/metanome/backend/input/file/DefaultFileInputGenerator.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package de.metanome.backend.input.csv;
+package de.metanome.backend.input.file;
 
 import de.metanome.algorithm_integration.AlgorithmConfigurationException;
 import de.metanome.algorithm_integration.configuration.ConfigurationSettingFileInput;
@@ -29,7 +29,7 @@
 import java.io.FileReader;
 
 /**
- * Generator for {@link de.metanome.algorithm_integration.input.RelationalInput}s based on csv
+ * Generator for {@link de.metanome.algorithm_integration.input.RelationalInput}s based on file
  * files.
  * The setting holds all parameters to construct new {@link de.metanome.algorithm_integration.input.RelationalInput}s.
  * To adapt the parameters you have to adapt the setting.
@@ -44,7 +44,7 @@ public class DefaultFileInputGenerator implements FileInputGenerator {
   /**
    * Creates a DefaultFileInputGenerator with default settings.
    * The default setting is used to construct a new {@link de.metanome.algorithm_integration.input.RelationalInput}.
-   * @param inputFile the csv input file
+   * @param inputFile the file input file
    * @throws java.io.FileNotFoundException if the input file is not found
    */
   public DefaultFileInputGenerator(File inputFile) throws FileNotFoundException {
@@ -75,7 +75,7 @@ public RelationalInput generateNewCopy() throws InputGenerationException {
       throw new InputGenerationException(ExceptionParser.parse(e), e);
     } catch (InputIterationException e) {
       throw new InputGenerationException(
-          ExceptionParser.parse(e, "Could not iterate over the first line of the csv file"), e);
+          ExceptionParser.parse(e, "Could not iterate over the first line of the file file"), e);
     }
   }
 

backend/src/main/java/de/metanome/backend/input/csv/FileIterator.java → backend/src/main/java/de/metanome/backend/input/file/FileIterator.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package de.metanome.backend.input.csv;
+package de.metanome.backend.input.file;
 
 import au.com.bytecode.opencsv.CSVReader;
 
@@ -30,7 +30,7 @@
 import java.util.List;
 
 /**
- * {@link FileIterator}s are Iterators over lines in a csv file.
+ * {@link FileIterator}s are Iterators over lines in a file file.
  *
  * @author Jakob Zwiener
  */
@@ -149,7 +149,7 @@ protected List<String> readNextLine() throws InputIterationException {
       currentLineNumber++;
     } catch (IOException e) {
       throw new InputIterationException(
-          ExceptionParser.parse(e, "Could not read next line in csv file"), e);
+          ExceptionParser.parse(e, "Could not read next line in file file"), e);
     }
     if (lineArray == null) {
       return null;

backend/src/main/java/de/metanome/backend/results_db/FileInput.java

@@ -21,7 +21,7 @@
 import au.com.bytecode.opencsv.CSVParser;
 import au.com.bytecode.opencsv.CSVReader;
 
-import de.metanome.backend.input.csv.FileIterator;
+import de.metanome.backend.input.file.FileIterator;
 
 import java.io.Serializable;
 

backend/src/test/java/de/metanome/backend/algorithm_execution/AlgorithmExecutorTest.java

@@ -38,7 +38,7 @@
 import de.metanome.backend.configuration.ConfigurationValueListBox;
 import de.metanome.backend.configuration.ConfigurationValueRelationalInputGenerator;
 import de.metanome.backend.configuration.ConfigurationValueString;
-import de.metanome.backend.input.csv.FileFixture;
+import de.metanome.backend.input.file.FileFixture;
 import de.metanome.backend.resources.AlgorithmResource;
 import de.metanome.backend.resources.ExecutionResource;
 import de.metanome.backend.resources.FileInputResource;

backend/src/test/java/de/metanome/backend/configuration/DefaultConfigurationFactoryTest.java

@@ -30,7 +30,7 @@
 import de.metanome.algorithm_integration.configuration.ConfigurationSettingString;
 import de.metanome.algorithm_integration.input.InputGenerationException;
 import de.metanome.algorithm_integration.input.InputIterationException;
-import de.metanome.backend.input.csv.FileFixture;
+import de.metanome.backend.input.file.FileFixture;
 
 import org.junit.Before;
 import org.junit.Test;

backend/src/test/java/de/metanome/backend/input/DefaultRelationalInputGeneratorInitializerTest.java

@@ -24,7 +24,7 @@
 import de.metanome.algorithm_integration.input.InputIterationException;
 import de.metanome.algorithm_integration.input.RelationalInputGenerator;
 import de.metanome.backend.configuration.ConfigurationValueRelationalInputGenerator;
-import de.metanome.backend.input.csv.FileFixture;
+import de.metanome.backend.input.file.FileFixture;
 
 import org.junit.Test;
 import org.mockito.ArgumentCaptor;

backend/src/test/java/de/metanome/backend/input/sql/DefaultDatabaseConnectionGeneratorTest.java → backend/src/test/java/de/metanome/backend/input/database/DefaultDatabaseConnectionGeneratorTest.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package de.metanome.backend.input.sql;
+package de.metanome.backend.input.database;
 
 import de.metanome.algorithm_integration.input.InputGenerationException;
 
@@ -170,7 +170,7 @@ public void testGetSetResultSetConcurrency() {
 
   /**
    * Test method for {@link DefaultDatabaseConnectionGenerator#close()} <p/> The database connection
-   * generator should be closeable. After closing the sql iterator generator the underlying db
+   * generator should be closeable. After closing the database iterator generator the underlying db
    * connection should be closed.
    */
   @Test

backend/src/test/java/de/metanome/backend/input/sql/DefaultTableInputGeneratorTest.java → backend/src/test/java/de/metanome/backend/input/database/DefaultTableInputGeneratorTest.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package de.metanome.backend.input.sql;
+package de.metanome.backend.input.database;
 
 import de.metanome.algorithm_integration.input.InputGenerationException;
 
@@ -24,7 +24,7 @@
 import static org.mockito.Mockito.verify;
 
 /**
- * Tests for {@link de.metanome.backend.input.sql.DefaultTableInputGenerator}
+ * Tests for {@link de.metanome.backend.input.database.DefaultTableInputGenerator}
  *
  * @author Jakob Zwiener
  */

backend/src/test/java/de/metanome/backend/input/sql/ResultSetFixture.java → backend/src/test/java/de/metanome/backend/input/database/ResultSetFixture.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package de.metanome.backend.input.sql;
+package de.metanome.backend.input.database;
 
 import com.mysql.jdbc.ResultSetMetaData;
 

backend/src/test/java/de/metanome/backend/input/sql/ResultSetIteratorTest.java → backend/src/test/java/de/metanome/backend/input/database/ResultSetIteratorTest.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package de.metanome.backend.input.sql;
+package de.metanome.backend.input.database;
 
 import com.google.common.collect.ImmutableList;
 
@@ -176,7 +176,7 @@ public void testColumnNames() throws SQLException {
   }
 
   /**
-   * Test method for {@link ResultSetIterator#close()} <p/> The sql iterator should be closeable.
+   * Test method for {@link ResultSetIterator#close()} <p/> The database iterator should be closeable.
    * After closing the iterator, the underlying result set and statement should be closed.
    */
   @Test

backend/src/test/java/de/metanome/backend/input/sql/ResultSetTwoLinesFixture.java → backend/src/test/java/de/metanome/backend/input/database/ResultSetTwoLinesFixture.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package de.metanome.backend.input.sql;
+package de.metanome.backend.input.database;
 
 import com.google.common.collect.ImmutableList;
 

backend/src/test/java/de/metanome/backend/input/csv/CsvFileFixture.java → backend/src/test/java/de/metanome/backend/input/file/CsvFileFixture.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package de.metanome.backend.input.csv;
+package de.metanome.backend.input.file;
 
 import com.google.common.base.Joiner;
 import com.google.common.collect.ImmutableList;

backend/src/test/java/de/metanome/backend/input/csv/CsvFileNullValuesFixture.java → backend/src/test/java/de/metanome/backend/input/file/CsvFileNullValuesFixture.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package de.metanome.backend.input.csv;
+package de.metanome.backend.input.file;
 
 import com.google.common.base.Joiner;
 
@@ -28,7 +28,7 @@
 import java.util.List;
 
 /**
- * A fixture generating a csv file with 4 rows. Rows 2 and 4 have differing lengths (2 (short) and 4
+ * A fixture generating a file file with 4 rows. Rows 2 and 4 have differing lengths (2 (short) and 4
  * (long)).
  *
  * @author Tanja Bergmann

backend/src/test/java/de/metanome/backend/input/csv/CsvFileOneLineFixture.java → backend/src/test/java/de/metanome/backend/input/file/CsvFileOneLineFixture.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package de.metanome.backend.input.csv;
+package de.metanome.backend.input.file;
 
 import com.google.common.base.Joiner;
 import com.google.common.collect.ImmutableList;

backend/src/test/java/de/metanome/backend/input/csv/CsvFileShortLineFixture.java → backend/src/test/java/de/metanome/backend/input/file/CsvFileShortLineFixture.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package de.metanome.backend.input.csv;
+package de.metanome.backend.input.file;
 
 import com.google.common.base.Joiner;
 import com.google.common.collect.ImmutableList;
@@ -26,7 +26,7 @@
 import java.io.StringReader;
 
 /**
- * A fixture generating a csv file with 4 rows. Rows 2 and 4 have differing lengths (2 (short) and 4
+ * A fixture generating a file file with 4 rows. Rows 2 and 4 have differing lengths (2 (short) and 4
  * (long)).
  *
  * @author Jakob Zwiener

backend/src/test/java/de/metanome/backend/input/csv/CsvFileShortLineWithHeaderFixture.java → backend/src/test/java/de/metanome/backend/input/file/CsvFileShortLineWithHeaderFixture.java

@@ -14,15 +14,15 @@
  * limitations under the License.
  */
 
-package de.metanome.backend.input.csv;
+package de.metanome.backend.input.file;
 
 import de.metanome.algorithm_integration.configuration.ConfigurationSettingFileInput;
 import de.metanome.algorithm_integration.input.InputIterationException;
 
 import java.io.StringReader;
 
 /**
- * A fixture generating a csv file with a header and a short line.
+ * A fixture generating a file file with a header and a short line.
  *
  * @author Jakob Zwiener
  */

backend/src/test/java/de/metanome/backend/input/csv/DefaultFileInputGeneratorTest.java → backend/src/test/java/de/metanome/backend/input/file/DefaultFileInputGeneratorTest.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package de.metanome.backend.input.csv;
+package de.metanome.backend.input.file;
 
 import de.metanome.algorithm_integration.AlgorithmConfigurationException;
 import de.metanome.algorithm_integration.configuration.ConfigurationSettingFileInput;
@@ -54,7 +54,7 @@ public class DefaultFileInputGeneratorTest {
   @Before
   public void setUp() throws Exception {
     this.csvFileFixture = new CsvFileFixture();
-    this.expectedFile = csvFileFixture.getTestDataPath("test.csv");
+    this.expectedFile = csvFileFixture.getTestDataPath("test.file");
 
     this.expectedSeparator = CsvFileFixture.SEPARATOR;
     this.expectedQuotechar = CsvFileFixture.QUOTE_CHAR;
@@ -90,7 +90,7 @@ public void testConstructor() {
   }
 
   /**
-   * Test method for {@link de.metanome.backend.input.csv.DefaultFileInputGenerator#DefaultFileInputGenerator(de.metanome.algorithm_integration.configuration.ConfigurationSettingFileInput)}
+   * Test method for {@link de.metanome.backend.input.file.DefaultFileInputGenerator#DefaultFileInputGenerator(de.metanome.algorithm_integration.configuration.ConfigurationSettingFileInput)}
    *
    * The generator should store the file path correctly.
    * The generator should use a default setting.
@@ -114,7 +114,7 @@ public void testConstructorSetting() throws AlgorithmConfigurationException,
   /**
    * Test method for {@link DefaultFileInputGenerator#generateNewCopy()}
    *
-   * The generator should generate fresh csv files iterable from the start.
+   * The generator should generate fresh file files iterable from the start.
    */
   @Test
   public void testGenerateNewCsvFile() throws InputGenerationException, InputIterationException {