From 783d2f872ea256105d6c0a89897cc87aa0a4dde6 Mon Sep 17 00:00:00 2001
From: Ziheng Sun <zsun@gmu.edu>
Date: Mon, 16 Sep 2024 03:05:44 -0400
Subject: [PATCH] fix the symlink and bump

---
 pom.xml                                       |  2 +-
 .../com/gw/web/ResultBrowserController.java   | 22 ++++++++++++++++---
 src/main/resources/application.properties     |  1 +
 src/main/resources/static/js/gw.js            |  2 +-
 src/test/resources/application.properties     |  1 +
 5 files changed, 23 insertions(+), 5 deletions(-)

diff --git a/pom.xml b/pom.xml
index a9213cfb..9f9103a1 100644
--- a/pom.xml
+++ b/pom.xml
@@ -11,7 +11,7 @@
 	</parent>
 	<groupId>com.gw</groupId>
 	<artifactId>geoweaver</artifactId>
-	<version>1.7.1</version>
+	<version>1.7.3</version>
 	<name>geoweaver</name>
 	<description>A lightweight workflow management software for organizing data analysis workflows, 
 	preserving history of every workflow run, and improving scientist producitvity and workflow FAIRness,
diff --git a/src/main/java/com/gw/web/ResultBrowserController.java b/src/main/java/com/gw/web/ResultBrowserController.java
index 9416d977..5d0f3dc5 100644
--- a/src/main/java/com/gw/web/ResultBrowserController.java
+++ b/src/main/java/com/gw/web/ResultBrowserController.java
@@ -23,6 +23,7 @@
 import java.time.ZoneId;
 import java.time.format.DateTimeFormatter;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
@@ -33,6 +34,9 @@ public class ResultBrowserController {
 
     @Autowired BaseTool bt;
 
+    @Value("${geoweaver.follow_symlinks:false}")
+    boolean follow_symlinks;
+
     // Inject the directory path from application.properties
 
     // Endpoint to list image files in the directory
@@ -43,20 +47,32 @@ public List<Map<String, Object>> listFiles(@RequestParam(defaultValue = "") Stri
         
         // Navigate into the subfolder if it's provided
         Path rootLocation = Paths.get(resultfolder, subfolder);
+        System.out.println("Received " + subfolder);
+        
+        Stream<Path> walker = null;
+
+        if(follow_symlinks){
+            // 1: look at files in the current folder and subfolders
+            walker = Files.walk(rootLocation, 1, FileVisitOption.FOLLOW_LINKS);
+        }else{
+            walker = Files.walk(rootLocation, 1);
+        }
         
-        return Files.walk(rootLocation, 1) // 1: look at files in the current folder and subfolders
-                .map(path -> {
+        return walker.map(path -> {
                     Map<String, Object> fileDetails = new HashMap<>();
                     try {
+                        System.out.println(path);
                         Path relativePath = rootLocation.relativize(path);
                         String pathWithSubfolder = subfolder + "/" + relativePath.toString();
                         pathWithSubfolder = pathWithSubfolder.replaceAll("^/+","");
 
                         // Check if pathWithSubfolder contains any attempts to go up the directory
                         Path normalizedSubfolderPath = Paths.get(pathWithSubfolder).normalize();
+                        System.out.println("normalizedSubfolderPath = " + normalizedSubfolderPath);
                         if (normalizedSubfolderPath.startsWith("..")) {
                             throw new SecurityException("Attempt to access outside of the result folder is not allowed.");
                         }
+                        System.out.println("pathWithSubfolder = " + pathWithSubfolder);
                         
                         fileDetails.put("name", rootLocation.relativize(path).toString()); // Relative path
                         fileDetails.put("path", pathWithSubfolder); // Relative path
@@ -79,7 +95,7 @@ public List<Map<String, Object>> listFiles(@RequestParam(defaultValue = "") Stri
                         fileDetails.put("modified", formattedDateTime);
                     } catch (IOException e){
                         e.printStackTrace();
-                    }catch (SecurityException e) {
+                    } catch (SecurityException e) {
                         System.out.println("Error: " + (e.getMessage() != null ? e.getMessage() : "Unknown error occurred"));
                         throw e;
                     }
diff --git a/src/main/resources/application.properties b/src/main/resources/application.properties
index 983d11de..7c8b9111 100644
--- a/src/main/resources/application.properties
+++ b/src/main/resources/application.properties
@@ -95,5 +95,6 @@ geoweaver.allowed_ssh_hosts=*
 # list the allowed ssh clients. Input * if allowing all client IPs. Input localhost if only allowing access from local host.
 geoweaver.allowed_ssh_clients=*
 geoweaver.secret_properties_path=cc_secret.properties
+geoweaver.follow_symlinks=true
 
 
diff --git a/src/main/resources/static/js/gw.js b/src/main/resources/static/js/gw.js
index 808ca7a8..fbc7978d 100644
--- a/src/main/resources/static/js/gw.js
+++ b/src/main/resources/static/js/gw.js
@@ -9,7 +9,7 @@ edu = {
         sponsor:
           "ESIPLab incubator project, NASA ACCESS project, NSF Geoinformatics project, NSF Cybertraining project",
 
-        version: "1.7.2",
+        version: "1.7.3",
 
         author: "open source contributors",
 
diff --git a/src/test/resources/application.properties b/src/test/resources/application.properties
index 4a7ce87c..7fcd83b8 100644
--- a/src/test/resources/application.properties
+++ b/src/test/resources/application.properties
@@ -74,6 +74,7 @@ geoweaver.upload_file_path=temp
 geoweaver.temp_file_path=temp
 geoweaver.workspace=~/gw-workspace
 geoweaver.result_file_path=results
+geoweaver.follow_symlinks=true
 
 # list the allowed ssh hosts. Input * if allowing all hosts. Input localhost if only allowing the local host.
 geoweaver.allowed_ssh_hosts=*