download samples to the current working directory

steineggerlab · Aug 7, 2023 · 64ac3ee · 64ac3ee
1 parent b74db67
commit 64ac3ee
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Showing 2 changed files with 9 additions and 1 deletion.
diff --git a/src/envs/config/PathConfig.java b/src/envs/config/PathConfig.java
@@ -1,6 +1,7 @@
 package envs.config;
 
 import java.io.File;
+import java.nio.file.Paths;
 import java.util.Arrays;
 
 import envs.toolkit.ANSIHandler;
@@ -12,6 +13,7 @@
 
 public class PathConfig {
 	/* Environment */
+	public static final String CurrPath = Paths.get("").toAbsolutePath().toString() + File.separator;
 	public static final String JarPath = new File(UFCGMainPipeline.class.getProtectionDomain().getCodeSource().getLocation().getPath()).getParent() + File.separator;
 	public static String EnvironmentPath = "";
 	public static boolean EnvironmentPathSet = false;

diff --git a/src/module/DownloadModule.java b/src/module/DownloadModule.java
@@ -154,6 +154,8 @@ private void printManual() {
     private void checkStatus(){
         boolean ping = internetConnection();
         if(PathConfig.EnvironmentPathSet && !dirGiven) dir = PathConfig.EnvironmentPath;
+        String sampleDir = dir;
+        if(!dirGiven) sampleDir = PathConfig.CurrPath;
 
         System.out.println(ANSIHandler.wrapper(" System status", 'Y'));
         System.out.println(ANSIHandler.wrapper(" OS       : " + GenericConfig.OS, 'x'));
@@ -169,7 +171,7 @@ private void checkStatus(){
                 ANSIHandler.wrapper("OK", 'G') : ANSIHandler.wrapper("NO", 'R')));
         System.out.println(ANSIHandler.wrapper(" busco      ", 'x') + (new File(dir + "config/seq/busco/100957at4751.fa").exists() ?
                 ANSIHandler.wrapper("OK", 'G') : ANSIHandler.wrapper("NO", 'R')));
-        System.out.println(ANSIHandler.wrapper(" sample     ", 'x') + (new File(dir + "sample/meta_full.tsv").exists() ?
+        System.out.println(ANSIHandler.wrapper(" sample     ", 'x') + (new File(sampleDir + "sample/meta_full.tsv").exists() ?
                 ANSIHandler.wrapper("OK", 'G') : ANSIHandler.wrapper("NO", 'R')));
         System.out.println();
 
@@ -288,6 +290,10 @@ private void downloadBusco(){
         Prompt.print("Download success : target " + ANSIHandler.wrapper("busco", 'G'));
     }
     private void downloadSample(){
+        if(!dirGiven) {
+            dir = PathConfig.CurrPath;
+        }
+
         // download payload
         Prompt.print("Downloading sample package on " + ANSIHandler.wrapper(dir + "sample.tar.gz", 'y') + " ...");
         Shell.exec(String.format("wget -q -O %ssample.tar.gz https://ufcg.steineggerlab.workers.dev/payload/sample.tar.gz", dir));