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CLI params as PATH, add basepath to functionsPath #14

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merged 3 commits into from
Jun 25, 2024
Merged

CLI params as PATH, add basepath to functionsPath #14

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854e4d4
fix: CLI params as PATH, add basepath to functionsPath
Apr 4, 2024
0c0eb3f
fix: basepath
Apr 9, 2024
0f8c2b2
Merge branch 'main' into fix-function-parameter-path
AuPath Jun 25, 2024
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66 changes: 33 additions & 33 deletions src/main/java/com/cefriel/template/Main.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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"})
Expand All @@ -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;
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@marioscrock marioscrock Apr 8, 2024 •
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@AuPath Directly parsed as Path by JCommander?

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Yes

@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"})
Expand All @@ -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 {

Expand All @@ -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);
}
}

Expand All @@ -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);
}
}
Expand All @@ -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
Expand All @@ -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)
Expand Down
5 changes: 2 additions & 3 deletions src/main/java/com/cefriel/template/TemplateMap.java
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Expand Up @@ -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
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/com/cefriel/template/io/Reader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@

package com.cefriel.template.io;

import java.nio.file.Path;
import java.util.List;
import java.util.Map;

Expand Down Expand Up @@ -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
Expand Down
4 changes: 1 addition & 3 deletions src/main/java/com/cefriel/template/io/csv/CSVReader.java
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Expand Up @@ -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;

Expand Down Expand Up @@ -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 {

}

Expand Down
4 changes: 2 additions & 2 deletions src/main/java/com/cefriel/template/io/json/JSONReader.java
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Expand Up @@ -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.*;

Expand Down Expand Up @@ -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");
}

Expand Down
10 changes: 4 additions & 6 deletions src/main/java/com/cefriel/template/io/rdf/RDFReader.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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);
}
Expand Down
9 changes: 6 additions & 3 deletions src/main/java/com/cefriel/template/io/sql/SQLReader.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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);
Expand All @@ -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) {
Expand Down
5 changes: 3 additions & 2 deletions src/main/java/com/cefriel/template/io/xml/XMLReader.java
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Expand Up @@ -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.*;
Expand Down Expand Up @@ -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();

Expand All @@ -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);
}
}
Expand Down