Merge pull request #14 from cefriel/fix-function-parameter-path

CLI params as PATH, add basepath to functionsPath

src/main/java/com/cefriel/template/Main.java

@@ -19,25 +19,24 @@
 import com.beust.jcommander.Parameter;
 import com.cefriel.template.io.Formatter;
 import com.cefriel.template.io.Reader;
-import com.cefriel.template.io.json.JSONReader;
-import com.cefriel.template.io.sql.SQLReader;
-import com.cefriel.template.utils.*;
+import com.cefriel.template.utils.TemplateFunctions;
+import com.cefriel.template.utils.Util;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import javax.tools.JavaCompiler;
 import javax.tools.ToolProvider;
 import java.io.File;
 import java.io.FileWriter;
+import java.io.IOException;
 import java.net.URL;
 import java.net.URLClassLoader;
+import java.nio.file.DirectoryStream;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.time.Instant;
-import java.util.*;
-
-import static com.cefriel.template.utils.Util.validInputFormat;
+import java.util.List;
 
 public class Main {
 	@Parameter(names={"--template","-t"})
@@ -50,13 +49,13 @@ public class Main {
 	@Parameter(names={"--baseiri","-iri"})
 	private String baseIri = "http://www.cefriel.com/data/";
 	@Parameter(names={"--basepath","-b"})
-	private String basePath;
+	private Path basePath;
 	@Parameter(names={"--output","-o"})
-	private String destinationPath = "output.txt";
+	private Path destinationPath = Path.of("output.txt");
 	@Parameter(names={"--key-value","-kv"})
-	private String keyValuePairsPath;
+	private Path keyValuePairsPath;
 	@Parameter(names={"--key-value-csv","-kvc"})
-	private String keyValueCsvPath;
+	private Path keyValueCsvPath;
 	@Parameter(names={"--format","-f"})
 	private String format;
 	@Parameter(names={"--trim","-tr"})
@@ -74,18 +73,17 @@ public class Main {
 	@Parameter(names={"--contextIRI","-c"})
 	private String context;
 	@Parameter(names={"--query","-q"})
-	private String queryPath;
+	private Path queryPath;
 	@Parameter(names={"--debug-query","-dq"})
 	private boolean debugQuery;
 	@Parameter(names={"--verbose","-v"})
 	private boolean verbose;
 	@Parameter(names={"--time","-tm"})
-	private String timePath;
+	private Path timePath;
 	@Parameter(names={"--functions","-fun"})
-	private String functionsPath;
-
-    private final Logger log = LoggerFactory.getLogger(Main.class);
+	private Path functionsPath;
 
+	private final Logger log = LoggerFactory.getLogger(Main.class);
 
 	public static void main(String ... argv) throws Exception {
 
@@ -102,21 +100,22 @@ public static void main(String ... argv) throws Exception {
 
 	public void updateBasePath(){
 		if (basePath != null) {
-			basePath = basePath.endsWith("/") ? basePath : basePath + "/";
-			templatePath = Path.of(basePath + templatePath.toString());
+		    templatePath = basePath.resolve(templatePath);
 			if (inputFilesPaths != null)
 				for (int i = 0; i < inputFilesPaths.size(); i++)
 					if(inputFilesPaths.get(i) != null)
-						inputFilesPaths.set(i, Path.of(basePath.toString() + inputFilesPaths.get(i)));
-			destinationPath = basePath + destinationPath;
+						inputFilesPaths.set(i, basePath.resolve(inputFilesPaths.get(i)));
+			destinationPath = basePath.resolve(destinationPath);
 			if (queryPath != null)
-				queryPath = basePath + queryPath;
+				queryPath = basePath.resolve(queryPath);
 			if (keyValueCsvPath != null)
-				keyValueCsvPath = basePath + keyValueCsvPath;
+				keyValueCsvPath = basePath.resolve(keyValueCsvPath);
 			if (keyValuePairsPath != null)
-				keyValuePairsPath = basePath + keyValuePairsPath;
+				keyValuePairsPath = basePath.resolve(keyValuePairsPath);
 			if (timePath != null)
-				timePath = basePath + timePath;
+				timePath = basePath.resolve(timePath);
+			if (functionsPath != null)
+				functionsPath = basePath.resolve(functionsPath);
 		}
 	}
 
@@ -130,7 +129,7 @@ public void exec() throws Exception {
 				if (queryPath == null)
 					log.error("Provide a query using the --query option");
 				else {
-					String debugQueryFromFile = Files.readString(Paths.get(queryPath));
+					String debugQueryFromFile = Files.readString(queryPath);
 					reader.debugQuery(debugQueryFromFile, destinationPath);
 				}
 			}
@@ -149,17 +148,18 @@ public void exec() throws Exception {
 		Formatter formatter = null;
 		if(format != null) {
 			formatter = Util.createFormatter(format);
-			if(reader != null) 
+			if(reader != null)
 				reader.setOutputFormat(format);
 		}
 
+
 		TemplateFunctions templateFunctions = new TemplateFunctions();
 		if (functionsPath != null) {
 			JavaCompiler compiler = ToolProvider.getSystemJavaCompiler();
-			File utilsFile = new File(functionsPath);
+			File utilsFile = functionsPath.toFile();
 			compiler.run(null, null, null, utilsFile.getPath());
-
-			File classDir = new File(utilsFile.getParent());
+			File classDir = functionsPath.getParent() != null ?
+					functionsPath.getParent().toFile() : Path.of("./").resolve(functionsPath).toFile();
 			URLClassLoader classLoader = URLClassLoader.newInstance(new URL[]{(classDir).toURI().toURL()});
 
 			// List all the files in the directory and identify the class file
@@ -178,20 +178,20 @@ public void exec() throws Exception {
 		}
 
 		if(timePath != null)
-			try (FileWriter pw = new FileWriter(timePath, true)) {
+			try (FileWriter pw = new FileWriter(timePath.toFile(), true)) {
 				long start = Instant.now().toEpochMilli();
 				if(queryPath != null)
-					tl.executeMappingParametric(reader, templatePath, templateInResources, trimTemplate, Paths.get(queryPath), Paths.get(destinationPath), templateMap, formatter, templateFunctions);
+					tl.executeMappingParametric(reader, templatePath, templateInResources, trimTemplate, queryPath, destinationPath, templateMap, formatter, templateFunctions);
 				else
-					tl.executeMapping(reader, templatePath, templateInResources, trimTemplate, Paths.get(destinationPath), templateMap, formatter, templateFunctions);
+					tl.executeMapping(reader, templatePath, templateInResources, trimTemplate, destinationPath, templateMap, formatter, templateFunctions);
 				long duration = Instant.now().toEpochMilli() - start;
 				pw.write(templatePath + "," + destinationPath + "," + duration + "\n");
 			}
 		else{
 			if(queryPath != null)
-				tl.executeMappingParametric(reader, templatePath, templateInResources, trimTemplate, Paths.get(queryPath), Paths.get(destinationPath), templateMap, formatter, templateFunctions);
+				tl.executeMappingParametric(reader, templatePath, templateInResources, trimTemplate, queryPath, destinationPath, templateMap, formatter, templateFunctions);
 			else
-				tl.executeMapping(reader, templatePath, templateInResources, trimTemplate, Paths.get(destinationPath), templateMap, formatter, templateFunctions);
+				tl.executeMapping(reader, templatePath, templateInResources, trimTemplate, destinationPath, templateMap, formatter, templateFunctions);
 		}
 
 		if(reader != null)

src/main/java/com/cefriel/template/TemplateMap.java

@@ -35,9 +35,8 @@
 
 public class TemplateMap extends HashMap<String, String> {
     private static final Logger log = LoggerFactory.getLogger(TemplateMap.class);
-    public TemplateMap(String filePath, boolean isCsv) throws IOException {
-        Path path = FileSystems.getDefault().getPath(filePath);
-        Stream<String> lines = Files.lines(path);
+    public TemplateMap(Path filePath, boolean isCsv) throws IOException {
+        Stream<String> lines = Files.lines(filePath);
         if (isCsv)
             putAll(parseCsvMap(lines));
         else

src/main/java/com/cefriel/template/io/Reader.java

@@ -16,6 +16,7 @@
 
 package com.cefriel.template.io;
 
+import java.nio.file.Path;
 import java.util.List;
 import java.util.Map;
 
@@ -51,7 +52,7 @@ public interface Reader {
      * @param destinationPath The path of the destination file
      * @throws Exception
      */
-    void debugQuery(String query, String destinationPath) throws Exception;
+    void debugQuery(String query, Path destinationPath) throws Exception;
 
     /**
      * If {@code verbose} is set, debug information about executed queries are logged

src/main/java/com/cefriel/template/io/csv/CSVReader.java

@@ -17,8 +17,6 @@
 package com.cefriel.template.io.csv;
 
 import com.cefriel.template.io.Reader;
-import de.siegmar.fastcsv.reader.CsvReader;
-import de.siegmar.fastcsv.reader.CsvRow;
 import de.siegmar.fastcsv.reader.NamedCsvReader;
 import de.siegmar.fastcsv.reader.NamedCsvRow;
 
@@ -70,7 +68,7 @@ public List<Map<String, String>> getDataframe(String query) {
     }
 
     @Override
-    public void debugQuery(String query, String destinationPath) throws Exception {
+    public void debugQuery(String query, Path destinationPath) throws Exception {
 
     }
 

src/main/java/com/cefriel/template/io/json/JSONReader.java

@@ -26,9 +26,9 @@
 import org.slf4j.LoggerFactory;
 
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.nio.file.Files;
+import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.*;
 
@@ -136,7 +136,7 @@ public List<Map<String, String>> getDataframe() throws Exception {
     }
 
     @Override
-    public void debugQuery(String query, String destinationPath) throws Exception {
+    public void debugQuery(String query, Path destinationPath) throws Exception {
         log.warn("Debug operation not implemented");
     }
 

src/main/java/com/cefriel/template/io/rdf/RDFReader.java

@@ -15,10 +15,8 @@
  */
 package com.cefriel.template.io.rdf;
 
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.StringReader;
+import java.io.*;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.time.Duration;
 import java.time.Instant;
@@ -223,8 +221,8 @@ private List<Map<String, String>> getDataframeXMLEscaped(List<Map<String, String
      * @param destinationPath File to save the results of the SPARQL query
      * @throws IOException If an error occurs in handling the files
      */
-    public void debugQuery(String query, String destinationPath) throws IOException {
-        SPARQLResultsTSVWriter writer = new SPARQLResultsTSVWriter(new FileOutputStream(destinationPath));
+    public void debugQuery(String query, Path destinationPath) throws IOException {
+        SPARQLResultsTSVWriter writer = new SPARQLResultsTSVWriter(new BufferedOutputStream(Files.newOutputStream(destinationPath)));
         try (RepositoryConnection con = this.repository.getConnection()) {
             con.prepareTupleQuery(query).evaluate(writer);
         }

src/main/java/com/cefriel/template/io/sql/SQLReader.java

@@ -23,6 +23,8 @@
 import org.slf4j.LoggerFactory;
 
 import java.io.*;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.security.InvalidParameterException;
 import java.sql.*;
 import java.sql.Statement;
@@ -196,13 +198,14 @@ private void queryResultToWriter(Writer writer, ResultSet resultSet) throws SQLE
      * @param destinationPath File to save the results of the SQL query
      * @throws IOException If an error occurs in handling the files
      */
-    public void debugQuery(String query, String destinationPath) throws IOException {
 
+    public void debugQuery(String query, Path destinationPath) throws IOException {        
         String queryCheck = query.toLowerCase();
         if (queryCheck.contains("select")) {
             try (ResultSet resultSet = executeQuery(query)) {
-                try (FileWriter writer = new FileWriter(destinationPath)) {
+               try (BufferedWriter writer = new BufferedWriter(Files.newBufferedWriter(destinationPath))) {
                     queryResultToWriter(writer, resultSet);
+
                 }
             } catch (SQLException e) {
                 log.error(e.getMessage(), e);
@@ -213,7 +216,7 @@ public void debugQuery(String query, String destinationPath) throws IOException
                 try {
                     PreparedStatement preparedStatement = conn.prepareStatement(q);
                     ResultSet resultSet = preparedStatement.executeQuery();
-                    try (FileWriter writer = new FileWriter(destinationPath)) {
+                    try (BufferedWriter writer = new BufferedWriter(Files.newBufferedWriter(destinationPath))) {
                         queryResultToWriter(writer, resultSet);
                     }
                 } catch (SQLException e) {

src/main/java/com/cefriel/template/io/xml/XMLReader.java

@@ -37,6 +37,7 @@
 import java.io.PrintWriter;
 import java.io.StringReader;
 import java.nio.file.Files;
+import java.nio.file.Path;
 import java.time.Duration;
 import java.time.Instant;
 import java.util.*;
@@ -163,7 +164,7 @@ public List<Map<String, String>> getDataframe() throws Exception {
     }
 
     @Override
-    public void debugQuery(String query, String destinationPath) throws Exception {
+    public void debugQuery(String query, Path destinationPath) throws Exception {
         List<Map<String, String>> result = getDataframe(query);
         StringBuilder sb = new StringBuilder();
 
@@ -186,7 +187,7 @@ public void debugQuery(String query, String destinationPath) throws Exception {
             }
             sb.setLength(sb.length() - 1);
 
-            try (PrintWriter out = new PrintWriter(destinationPath)) {
+            try (PrintWriter out = new PrintWriter(destinationPath.toString())) {
                 out.println(sb);
             }
         }