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#28 - use real path if symbolic links are given
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@endixk
endixk committed Jul 5, 2024
1 parent dc192c9 commit f426ac3
Showing 1 changed file with 81 additions and 3 deletions.
84 changes: 81 additions & 3 deletions src/envs/config/PathConfig.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
package envs.config;

import java.io.File;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Arrays;

Expand Down Expand Up @@ -34,7 +36,14 @@ public static int setFastBlockSearchPath(String path) {
try {
Prompt.talk("fastBlockSearch binary check : " + ANSIHandler.wrapper(path, 'B'));
String[] exec = Shell.exec("file -b " + path);
if(!exec[0].contains("exec") && !exec[0].contains("link")) {
if(exec[0].contains("link")) {
// symbolic link given, get the real path
Path link = Files.readSymbolicLink(Paths.get(path));
Path real = link.toRealPath().toAbsolutePath();
Prompt.talk("Symbolic link detected : " + ANSIHandler.wrapper(path, 'B') + " -> " + ANSIHandler.wrapper(real.toString(), 'B'));
return setFastBlockSearchPath(real.toString());
}
if(!exec[0].contains("exec")) {
ExceptionHandler.pass(path);
ExceptionHandler.handle(ExceptionHandler.INVALID_BINARY);
return 1;
Expand All @@ -55,7 +64,14 @@ public static int setAugustusPath(String path) {
try {
Prompt.talk("AUGUSTUS binary check : " + ANSIHandler.wrapper(path, 'B'));
String[] exec = Shell.exec("file -b " + path);
if(!exec[0].contains("exec") && !exec[0].contains("link")) {
if(exec[0].contains("link")) {
// symbolic link given, get the real path
Path link = Files.readSymbolicLink(Paths.get(path));
Path real = link.toRealPath().toAbsolutePath();
Prompt.talk("Symbolic link detected : " + ANSIHandler.wrapper(path, 'B') + " -> " + ANSIHandler.wrapper(real.toString(), 'B'));
return setAugustusPath(real.toString());
}
if(!exec[0].contains("exec")) {
ExceptionHandler.pass(path);
ExceptionHandler.handle(ExceptionHandler.INVALID_BINARY);
return 1;
Expand All @@ -77,7 +93,14 @@ public static int setHmmsearchPath(String path) {
try {
Prompt.talk("hmmsearch binary check : " + ANSIHandler.wrapper(path, 'B'));
String[] exec = Shell.exec("file -b " + path);
if(!exec[0].contains("exec") && !exec[0].contains("link")) {
if(exec[0].contains("link")) {
// symbolic link given, get the real path
Path link = Files.readSymbolicLink(Paths.get(path));
Path real = link.toRealPath().toAbsolutePath();
Prompt.talk("Symbolic link detected : " + ANSIHandler.wrapper(path, 'B') + " -> " + ANSIHandler.wrapper(real.toString(), 'B'));
return setHmmsearchPath(real.toString());
}
if(!exec[0].contains("exec")) {
ExceptionHandler.pass(path);
ExceptionHandler.handle(ExceptionHandler.INVALID_BINARY);
return 1;
Expand All @@ -98,6 +121,13 @@ public static int setMMseqsPath(String path) {
try {
Prompt.talk("MMseqs binary check : " + ANSIHandler.wrapper(path, 'B'));
String[] exec = Shell.exec("file -b " + path);
if(exec[0].contains("link")) {
// symbolic link given, get the real path
Path link = Files.readSymbolicLink(Paths.get(path));
Path real = link.toRealPath().toAbsolutePath();
Prompt.talk("Symbolic link detected : " + ANSIHandler.wrapper(path, 'B') + " -> " + ANSIHandler.wrapper(real.toString(), 'B'));
return setMMseqsPath(real.toString());
}
if(!exec[0].contains("exec") && !exec[0].contains("link")) {
ExceptionHandler.pass(path);
ExceptionHandler.handle(ExceptionHandler.INVALID_BINARY);
Expand All @@ -119,6 +149,14 @@ public static void setTrinityPath(String path) {
try {
Prompt.talk("Trinity binary check : " + ANSIHandler.wrapper(path, 'B'));
String[] exec = Shell.exec("file -b " + path);
if(exec[0].contains("link")) {
// symbolic link given, get the real path
Path link = Files.readSymbolicLink(Paths.get(path));
Path real = link.toRealPath().toAbsolutePath();
Prompt.talk("Symbolic link detected : " + ANSIHandler.wrapper(path, 'B') + " -> " + ANSIHandler.wrapper(real.toString(), 'B'));
setTrinityPath(real.toString());
return;
}
if(!exec[0].contains("exec") && !exec[0].contains("link")) {
ExceptionHandler.pass(path);
ExceptionHandler.handle(ExceptionHandler.INVALID_BINARY);
Expand All @@ -140,6 +178,14 @@ public static int setInputPath(String path) {
try {
Prompt.talk("Input file check : " + ANSIHandler.wrapper(path, 'B'));
String[] exec = Shell.exec("file -b " + path);
if(exec[0].contains("link")) {
// symbolic link given, get the real path
Path link = Files.readSymbolicLink(Paths.get(path));
Path real = link.toRealPath().toAbsolutePath();
Prompt.talk("Symbolic link detected : " + ANSIHandler.wrapper(path, 'B') + " -> " + ANSIHandler.wrapper(real.toString(), 'B'));
return setInputPath(real.toString());
}

if(exec[0].contains("directory")) InputIsFolder = true;
Prompt.talk("Input argument : " + ANSIHandler.wrapper(exec[0], 'B'));

Expand All @@ -166,6 +212,14 @@ public static void checkInputFile(String path) {
Prompt.talk("Input file check : " + ANSIHandler.wrapper(path, 'B'));
String[] exec = Shell.exec("file -b " + path);
Prompt.talk("Input argument : " + ANSIHandler.wrapper(exec[0], 'B'));
if(exec[0].contains("link")) {
// symbolic link given, get the real path
Path link = Files.readSymbolicLink(Paths.get(path));
Path real = link.toRealPath().toAbsolutePath();
Prompt.talk("Symbolic link detected : " + ANSIHandler.wrapper(path, 'B') + " -> " + ANSIHandler.wrapper(real.toString(), 'B'));
checkInputFile(real.toString());
return;
}
if(exec[0].contains("directory") | exec[0].startsWith("cannot")) {
ExceptionHandler.pass(path);
ExceptionHandler.handle(ExceptionHandler.INVALID_FILE);
Expand Down Expand Up @@ -229,6 +283,14 @@ public static int checkOutputPath() {
public static int setTempPath(String path) {
try {
Prompt.talk("Temporary directory check : " + ANSIHandler.wrapper(path, 'B'));
String[] exec = Shell.exec("file -b " + path);
if(exec[0].contains("link")) {
// symbolic link given, get the real path
Path link = Files.readSymbolicLink(Paths.get(path));
Path real = link.toRealPath().toAbsolutePath();
Prompt.talk("Symbolic link detected : " + ANSIHandler.wrapper(path, 'B') + " -> " + ANSIHandler.wrapper(real.toString(), 'B'));
return setTempPath(real.toString());
}
File output = new File(path);
if(output.exists()) {
if(!output.canWrite()) {
Expand Down Expand Up @@ -262,6 +324,14 @@ public static int setMetaPath(String path) {
try {
Prompt.talk("Metadata file check : " + ANSIHandler.wrapper(path, 'B'));
String[] exec = Shell.exec("file -b " + path);
if(exec[0].contains("link")) {
// symbolic link given, get the real path
Path link = Files.readSymbolicLink(Paths.get(path));
Path real = link.toRealPath().toAbsolutePath();
Prompt.talk("Symbolic link detected : " + ANSIHandler.wrapper(path, 'B') + " -> " + ANSIHandler.wrapper(real.toString(), 'B'));
setMetaPath(real.toString());
return 0;
}
if(!exec[0].contains("text")) {
ExceptionHandler.pass(path);
ExceptionHandler.handle(ExceptionHandler.INVALID_FILE);
Expand Down Expand Up @@ -405,6 +475,14 @@ public static int setAugustusConfig(String path) {
try {
Prompt.talk("AUGUSTUS-PPX config file check : " + ANSIHandler.wrapper(path, 'B'));
String[] exec = Shell.exec("file -b " + path);
if(exec[0].contains("link")) {
// symbolic link given, get the real path
Path link = Files.readSymbolicLink(Paths.get(path));
Path real = link.toRealPath().toAbsolutePath();
Prompt.talk("Symbolic link detected : " + ANSIHandler.wrapper(path, 'B') + " -> " + ANSIHandler.wrapper(real.toString(), 'B'));
setAugustusConfig(real.toString());
return 0;
}
if(!exec[0].contains("text")) {
ExceptionHandler.pass(path);
ExceptionHandler.handle(ExceptionHandler.INVALID_FILE);
Expand Down

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