com.actelion.research.util.IO Maven / Gradle / Ivy
/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/
package com.actelion.research.util;
import java.io.*;
import java.net.URL;
import java.nio.ByteBuffer;
import java.nio.channels.Channels;
import java.nio.channels.FileChannel;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
import java.text.DateFormat;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.text.SimpleDateFormat;
import java.util.*;
import com.actelion.research.io.StringReadChannel;
import com.actelion.research.util.datamodel.DoubleArray;
import com.actelion.research.util.datamodel.IntArray;
/**
* IO
* 2003 MvK: Start implementation
*/
public class IO {
// private static final NumberFormat NF = new DecimalFormat("000");
private static final int LIMIT_FILES_DIR = 10000;
public static final String SEP = System.getProperty("file.separator");
public static boolean canWriteAndDeleteInPath(File dir) throws IOException {
boolean w = false;
File f = File.createTempFile("test", ".txt", dir);
if(f.canWrite()){
w=true;
}
w = f.delete();
return w;
}
/**
* Do not forget to close BufferedReader
*
* @param sAbsolutePathIn
* path
* @return BufferedReader
*/
public static BufferedReader getBufferedReader(String sAbsolutePathIn) throws FileNotFoundException {
BufferedReader bufferedReader = null;
if (sAbsolutePathIn.length() > 0) {
FileInputStream fis = new FileInputStream(sAbsolutePathIn);
InputStreamReader isr = new InputStreamReader(fis, StandardCharsets.UTF_8);
bufferedReader = new BufferedReader(isr);
}
return bufferedReader;
}
/**
* A number is added to the base name of the file
*
* @param totalpath
* @return
*/
public static String getUniqueFileName(String totalpath) {
File fi = new File(totalpath);
return getUniqueFileName(fi, fi.getParentFile(), Formatter.dfI3).getAbsolutePath();
}
public static File getUniqueFileName(File fiIn) {
return getUniqueFileName(fiIn, fiIn.getParentFile());
}
public static File getUniqueFileName(String sFilename, String sDirDestination) {
return getUniqueFileName(new File(sFilename), new File(sDirDestination), Formatter.dfI3);
}
public static File getUniqueFileName(File file, File dirDestination) {
return getUniqueFileName(file, dirDestination, Formatter.dfI3);
}
/**
* If the file does not exists the input file is returned.
* @param file
* @param dirDestination
* @param df
* @return
*/
public static File getUniqueFileName(File file, File dirDestination, DecimalFormat df) {
String sFileName = file.getName();
File fiNew = new File(dirDestination, sFileName);
if(!fiNew.exists()){
return fiNew;
}
String sBaseName = getBaseName(file);
String sExtension = getExtension(file);
String sBaseNameNumber = sBaseName;
int cc = 1;
while (fiNew.isFile()) {
sBaseNameNumber = next(sBaseNameNumber, df);
sFileName = sBaseNameNumber + sExtension;
fiNew = new File(dirDestination, sFileName);
cc++;
if (cc > LIMIT_FILES_DIR) {
sFileName = null;
IOException ex = new IOException("To many files in this dir.");
ex.printStackTrace();
break;
}
}
return fiNew;
}
public static File getUniqueUserDir() throws IOException {
String sWorkdir = System.getProperty("user.home");
File dirParent = new File(sWorkdir);
return getUniqueDateDir(dirParent);
}
public static File getUniqueDateDir(File dirParent) throws IOException {
return getUniqueDateDir(dirParent, "");
}
public static File getUniqueDateDir(String appendix) throws IOException {
String sWorkdir = System.getProperty("user.home");
File dirParent = new File(sWorkdir);
return getUniqueDateDir(dirParent, appendix);
}
public static File getUniqueDateDir(File dirParent, String appendix) throws IOException {
Date d = new Date();
DateFormat df = new SimpleDateFormat("yyMMdd");
String sDate = df.format(d);
String name = sDate + appendix;
File dir = new File(dirParent, name);
int index = 1;
while(dir.exists()){
name = sDate + "_" + index + "_" + appendix;
index++;
dir = new File(dirParent, name);
}
if(!dir.mkdirs()){
String e = "Not possible to make dir " + dir.getAbsolutePath() + ".";
throw new IOException(e);
}
return dir;
}
public static File getUniqueDir(File dirParent, String suffix) throws IOException {
String name = suffix;
File dir = new File(dirParent, name);
int index = 1;
while(dir.exists()){
name = suffix+index;
index++;
dir = new File(dirParent, name);
}
if(!dir.mkdirs()){
String e = "Not possible to make dir " + dir.getAbsolutePath() + ".";
throw new IOException(e);
}
return dir;
}
/**
* Has to be the total path of the file or there will be errors.
* @param totalpath
* @return
*/
public static String getNextFileName(String totalpath) {
File fi = new File(totalpath);
return getUniqueFileName(fi, fi.getParentFile(), Formatter.dfI3).getAbsolutePath();
}
public static String next(String txt) {
return next(txt, Formatter.dfI3);
}
/**
*
* @param txt String with an integer num at the end. (blabla567)
* @return Adds one to the last number (blabla568).
* If no number in text 001 is added.
*/
public static String next(String txt, DecimalFormat dfExtern) {
String s = "";
int ind = -1;
for (int i = txt.length() - 1; i >= 0; i--) {
if (!Character.isDigit(txt.charAt(i))) {
ind = i;
break;
}
}
s = txt.substring(0, ind + 1);
String sN = txt.substring(ind + 1, txt.length());
NumberFormat nfName = dfExtern;
int num = 0;
if (sN.length() > 0) {
num = Integer.parseInt(sN);
String patFormat = "";
for (int i = 0; i < sN.length(); i++) {
patFormat += "0";
}
nfName = new DecimalFormat(patFormat);
}
num++;
s += nfName.format(num);
return s;
}
public static BufferedWriter getBuffWrite(String sAbsolutePathOut,
boolean bAppend) throws IOException {
BufferedWriter bufferedWriter = null;
if (sAbsolutePathOut.length() > 0) {
FileOutputStream fos = new FileOutputStream(sAbsolutePathOut, bAppend);
OutputStreamWriter isw = new OutputStreamWriter(fos);
bufferedWriter = new BufferedWriter(isw);
} else {
OutputStreamWriter isw = new OutputStreamWriter(System.out);
bufferedWriter = new BufferedWriter(isw);
}
return bufferedWriter;
}
/**
*
* @param str
* @return base name without extension.
*/
public static String getBaseName(String str) {
File fi = new File(str);
String name = fi.getName();
int iIndexStart = name.lastIndexOf('\\');
if(iIndexStart==-1){
iIndexStart = name.lastIndexOf(File.separator);
}
if(iIndexStart==-1){
iIndexStart = 0;
}
int iIndexEnd = name.lastIndexOf('.');
String sBaseName = "";
if(iIndexEnd == -1)
iIndexEnd = name.length();
sBaseName = name.substring(iIndexStart, iIndexEnd);
return sBaseName;
}
public static String getBaseName(File file) {
return getBaseName(file.getAbsolutePath());
}
/**
*
* @param file
* @return the part after the the last '.' inclusive the '.'.
* Returns String with length null when no extension found.
*/
public static String getExtension(File file) {
String sName = file.getName();
int iIndexStartName = sName.lastIndexOf(SEP) + 1;
int iIndexStartExtension = sName.lastIndexOf('.');
if(iIndexStartExtension==-1){
return "";
}
String sExtension = sName.substring(iIndexStartExtension);
return sExtension;
}
public static void mkdirs(String path) throws IOException {
mkdirs(new File(path));
}
public static void mkdirs(File dir) throws IOException {
if (!dir.exists()) {
if(!dir.mkdirs()){
throw new IOException("Not possible to make dir " + dir.getAbsolutePath() + ".");
}
}
}
public static void readBetweenTags(String sAbsolutePathIn,
String sTagStartRegEx,
String sTagEndRegEx,
Vector vecStringContent) {
try {
StringReadChannel channel = new StringReadChannel(Channels.newChannel(new FileInputStream(new File(sAbsolutePathIn))));
boolean bTagStartFound = false;
boolean bTagEndFound = false;
while (channel.hasMoreLines()) {
String sLine = channel.readLine();
if (sLine != null) {
if (sLine.matches(sTagStartRegEx)) {
bTagStartFound = true;
break;
}
}
}
if (bTagStartFound == true) {
while (channel.hasMoreLines()) {
String sLine = channel.readLine();
if (sLine != null) {
if (sLine.matches(sTagEndRegEx)) {
bTagEndFound = true;
break;
} else {
vecStringContent.addElement(sLine);
}
}
}
} else {
System.err.println("Tag: " + sTagStartRegEx + " not found");
(new RuntimeException()).printStackTrace();
}
channel.close();
if (!bTagEndFound) {
System.err.println("Tag: " + sTagEndRegEx + " not found");
(new RuntimeException()).printStackTrace();
}
} catch (IOException e) {
System.err.println(e);
} catch (Exception e) {
System.err.println(e);
}
}
/**
* Reads all lines after a given tag and stores the lines as Strings in a
* vector object.
*
* @param sAbsolutePathIn
* path of the input file
* @param sTagRegEx
* the tag as regular expression
* @param vecStringContent
* contains the result of the read in.
*/
public static void readFromTag(String sAbsolutePathIn, String sTagRegEx, Vector vecStringContent) {
try {
StringReadChannel channel = new StringReadChannel(Channels.newChannel(new FileInputStream(new File(sAbsolutePathIn))));
boolean bTagFound = false;
String sLine = "";
while (channel.hasMoreLines()) {
sLine = channel.readLine();
if (sLine != null) {
if (sLine.matches(sTagRegEx)) {
bTagFound = true;
break;
}
}
}
if (bTagFound == true) {
while (channel.hasMoreLines()) {
sLine = channel.readLine();
if (sLine != null) {
if (sLine.length() < 1) {
break;
} else {
vecStringContent.addElement(sLine);
}
}
}
} else {
System.err.println("Tag: " + sTagRegEx + " not found");
(new RuntimeException()).printStackTrace();
}
channel.close();
} catch (IOException e) {
System.err.println(e);
} catch (Exception e) {
System.err.println(e);
}
}
public static void skipUntilLineMatchesRegEx(InputStream in, String regex)throws Exception {
int limit = 10000;
int cc=0;
String line = readLine(in);
while(!line.matches(regex)){
line = readLine(in);
if(cc==limit) {
throw new Exception("Limit of " + limit + " lines exceeded.");
}
cc++;
}
}
public static String read(InputStream is) throws IOException {
BufferedReader reader = new BufferedReader(new InputStreamReader(is, StandardCharsets.UTF_8));
String line=null;
StringBuilder sb = new StringBuilder();
while ((line = reader.readLine())!=null) {
if(sb.length()>0)
sb.append("\n");
sb.append(line);
}
reader.close();
return sb.toString();
}
public static List readListIntger(File fiTxt) throws IOException {
Scanner scanner = new Scanner(fiTxt);
List li = new ArrayList();
while (scanner.hasNextInt()) {
li.add(scanner.nextInt());
}
scanner.close();
return li;
}
/**
* Reads a file that contains one int per line.
* @param fiIntLineWise
* @return
* @throws IOException
*/
public static int [] readLines2IntArray(File fiIntLineWise) throws IOException{
IntArray intArray = new IntArray();
BufferedReader br = new BufferedReader(new FileReader(fiIntLineWise));
String line = "";
while((line=br.readLine()) != null){
int val = Integer.parseInt(line);
intArray.add(val);
}
br.close();
return intArray.get();
}
public static double [] readLines2DoubleArray(File fiIntLineWise) throws IOException{
DoubleArray doubleArray = new DoubleArray();
BufferedReader br = new BufferedReader(new FileReader(fiIntLineWise));
String line = "";
while((line=br.readLine()) != null){
double v = Double.parseDouble(line);
doubleArray.add(v);
}
br.close();
return doubleArray.get();
}
public static String readLine(InputStream is) throws IOException {
StringBuilder sb = new StringBuilder();
int c = -1;
while((c = is.read()) != '\n'){
if(c==-1)
break;
sb.append((char)c);
}
String str = StringFunctions.removeCharacter(sb, '\r');
return str;
}
public static String read(File file) throws IOException {
BufferedReader reader = new BufferedReader(new FileReader(file));
String line=null;
StringBuilder sb = new StringBuilder();
while ((line = reader.readLine())!=null) {
if(sb.length()>0)
sb.append("\n");
sb.append(line);
}
reader.close();
return sb.toString();
}
public static String readLine(Reader is) throws IOException {
StringBuffer b = new StringBuffer();
int c=0;
c=is.read();
while((c != -1)&&(c != '\n')) {
b.append((char)c);
c=is.read();
}
return b.toString();
}
public static String readLine(FileChannel fc) throws IOException {
ByteBuffer buf = ByteBuffer.allocate(1000);
StringBuilder sb = new StringBuilder();
boolean bEOF=false;
boolean bEOLine=false;
long posFCPos = fc.position();
while (!bEOF){
buf.position(0);
int size = fc.read(buf);
if(size==-1){
break;
}
for (int i = 0; i < size; i++) {
int c = buf.get(i);
posFCPos++;
if(c==-1) {
bEOF=true;
} else {
if(c=='\n') {
fc.position(posFCPos);
bEOLine=true;
break;
} else {
sb.append((char)c);
}
}
}
if(bEOLine)
break;
}
return sb.toString();
}
public static List readLines2List(File file) throws IOException {
List li = new ArrayList();
BufferedReader reader = new BufferedReader(new FileReader(file));
String line = null;
while ((line = reader.readLine())!=null) {
li.add(line);
}
reader.close();
return li;
}
/**
* The stream is not closed.
* @param is
* @return
* @throws IOException
*/
public static List readLines2List(InputStream is) throws IOException {
List li = new ArrayList();
BufferedReader reader = new BufferedReader(new InputStreamReader(is, StandardCharsets.UTF_8));
String line = null;
while ((line = reader.readLine())!=null) {
li.add(line);
}
return li;
}
public static List readLines2List(List liFile) throws IOException {
List li = new ArrayList();
for (File fi : liFile) {
li.addAll(readLines2List(fi));
}
return li;
}
public static void write(String sAbsolutePathOut, String sContent) {
write(sAbsolutePathOut, sContent, true);
}
public static void write(String sAbsolutePathOut, String sContent, boolean bAppend) {
write(new File(sAbsolutePathOut), sContent, bAppend);
}
public static void write(File file, String sContent) {
write(file, sContent, false);
}
public static void write(File file, String sContent, boolean bAppend) {
try {
BufferedWriter bufferedWriter = new BufferedWriter(new FileWriter(file, bAppend));
bufferedWriter.write(sContent);
bufferedWriter.close();
} catch (IOException ex) {
throw new RuntimeException(ex);
}
}
public void write2Channel(FileChannel fc, String str) throws IOException {
ByteBuffer buf = ByteBuffer.allocate(str.length());
byte[] bytes = str.getBytes();
buf.put(bytes);
buf.flip();
fc.write(buf);
}
/**
* Writes each string in a separate line
* @param file
* @param li
* @throws IOException
*/
public static void write(File file, List li) throws IOException {
FileWriter fw = new FileWriter(file);
for (int i = 0; i < li.size(); i++) {
fw.write(li.get(i));
if(i li) throws IOException {
FileWriter fw = new FileWriter(file);
for (int i = 0; i < li.size(); i++) {
fw.write(li.get(i).toString());
if(i 0) {
sb.append(buf, 0, c);
}
return sb.toString();
}
public static String streamToString(InputStream is) throws IOException {
byte[] buf = new byte[512];
int c;
StringBuilder sb = new StringBuilder();
while(( c = is.read(buf)) > 0) {
sb.append(new String(buf, 0, c));
}
return sb.toString();
}
public static byte[] getBytes(File f) throws IOException {
FileInputStream is = new FileInputStream(f);
byte[] res = new byte[(int) f.length()];
is.read(res, 0, res.length);
is.close();
return res;
}
public static void bytesToFile(byte[] bytes, File f) throws IOException {
FileOutputStream os = new FileOutputStream(f);
os.write(bytes);
os.close();
}
public static void stringToFile(String s, File f) throws IOException {
try (FileWriter os = new FileWriter(f)) {
os.write(s);
}
}
public static String fileToString(File f) throws IOException {
return fileToString(f, Integer.MAX_VALUE);
}
public static String fileToString(File f, int maxSize) throws IOException {
try (FileReader reader = new FileReader(f)) {
return readerToString(reader, maxSize);
}
}
/**
* Redirects the streams, without closing them
* @param is
* @param os
* @throws IOException
*/
public static void redirect(InputStream is, OutputStream os) throws IOException {
byte[] buf = new byte[512];
int c;
while((c=is.read(buf))>0) {
os.write(buf, 0, c);
}
is.close();
}
/**
* Redirects the reader to the writer, without closing them
* @param is
* @param os
* @throws IOException
*/
public static void redirect(Reader is, Writer os) throws IOException {
char[] buf = new char[512];
int c;
while((c=is.read(buf))>0) {
os.write(buf, 0, c);
}
is.close();
}
public static void copy(File src, File dest) throws IOException {
InputStream is = null;
OutputStream os = null;
try {
is = new BufferedInputStream(new FileInputStream(src));
os = new BufferedOutputStream(new FileOutputStream(dest));
redirect(is, os);
} finally {
try {if(is!=null) is.close();}catch(Exception e){}
try {if(os!=null) os.close();}catch(Exception e){}
}
}
/**
* Debug instruction to view the relevant stacktrace
* @throws IOException
*/
public static void dumpStack() {
Exception e = new Exception("StackTrace");
Set dejaVu = Collections.newSetFromMap(new IdentityHashMap());
dejaVu.add(e);
synchronized (System.err) {
StackTraceElement[] trace = e.getStackTrace();
System.err.println("Exception "+e.getMessage());
for (StackTraceElement traceElement : trace) {
if(traceElement.getClassName().contains("com.actelion.research.util.IOUtils")) continue;
if(traceElement.getClassName().contains("com.actelion")) {
System.err.println("\tat " + traceElement);
}
}
if(e.getCause()!=null) {
System.err.println("Caused by "+e.getCause());
for (StackTraceElement traceElement : trace) {
if(traceElement.getClassName().contains("com.actelion.research.util.IOUtils.dumpStack")) continue;
if(traceElement.getClassName().contains("com.actelion")) {
System.err.println("\tat " + traceElement);
}
}
}
}
}
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