- Fixed getDocsUrl() to use WebdavService.getPath() instead of hardcoded /_webdav string

- Fixed hasDocumentation() to use Files.exists() instead of new File().exists()
- getLocalPath() returns Path directly instead of converting to File
- Updated getSupplementaryFileBasenames() to use Files.list() instead of File.list()
- Refactored extractDocsFromZip() to use NIO Path
- Use FileUtil.copyDirectory(Path, Path) to copy docs from previous tool version

Author: vagisha

SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreController.java

@@ -100,6 +100,7 @@
 import java.net.URLDecoder;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.StandardCopyOption;
 import java.text.DateFormat;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
@@ -230,11 +231,11 @@ protected byte[] unzip(ZipInputStream stream)
         }
     }
 
-    protected static boolean extractDocsFromZip(File zipFile, File containerDir) throws IOException
+    protected static boolean extractDocsFromZip(Path zipFile, Path containerDir) throws IOException
     {
-        File docsDir = new File(containerDir, "docs");
+        Path docsDir = containerDir.resolve("docs");
         boolean extracted = false;
-        try (ZipFile zf = new ZipFile(zipFile))
+        try (ZipFile zf = new ZipFile(zipFile.toFile()))
         {
             Enumeration<? extends ZipEntry> entries = zf.entries();
             while (entries.hasMoreElements())
@@ -247,15 +248,14 @@ protected static boolean extractDocsFromZip(File zipFile, File containerDir) thr
                 String relativePath = name.substring("tool-inf/docs/".length());
                 if (relativePath.isEmpty())
                     continue;
-                File destFile = new File(docsDir, relativePath);
+                Path destPath = docsDir.resolve(relativePath).normalize();
                 // Zip-slip protection
-                if (!destFile.getCanonicalPath().startsWith(docsDir.getCanonicalPath() + File.separator))
+                if (!destPath.startsWith(docsDir.normalize()))
                     throw new IOException("Zip entry outside target directory: " + name);
-                Files.createDirectories(destFile.getParentFile().toPath());
-                try (InputStream in = zf.getInputStream(entry);
-                     FileOutputStream out = new FileOutputStream(destFile))
+                Files.createDirectories(destPath.getParent());
+                try (InputStream in = zf.getInputStream(entry))
                 {
-                    in.transferTo(out);
+                    Files.copy(in, destPath, StandardCopyOption.REPLACE_EXISTING);
                 }
                 extracted = true;
             }
@@ -265,12 +265,12 @@ protected static boolean extractDocsFromZip(File zipFile, File containerDir) thr
 
     public static File makeFile(Container c, String filename)
     {
-        return new File(getLocalPath(c), FileUtil.makeLegalName(filename));
+        return getLocalPath(c).resolve(FileUtil.makeLegalName(filename)).toFile();
     }
 
-    public static File getLocalPath(Container c)
+    public static Path getLocalPath(Container c)
     {
-        return FileContentService.get().getFileRootPath(c, FileContentService.ContentType.files).toFile();
+        return FileContentService.get().getFileRootPath(c, FileContentService.ContentType.files);
     }
 
     protected Container makeContainer(Container parent, String folderName, List<User> users, Role role) throws IOException
@@ -417,7 +417,7 @@ public static ArrayList<String> getToolRelevantUsers(SkylineTool tool, Role[] ro
         return new ArrayList<>(users);
     }
 
-    public static HashMap<String, String> getSupplementaryFiles(SkylineTool tool)
+    public static HashMap<String, String> getSupplementaryFiles(SkylineTool tool) throws IOException
     {
         // Store supporting files in map <url, icon url>
         final String[] knownExtensions = {"pdf", "zip"};
@@ -435,15 +435,15 @@ public static HashMap<String, String> getSupplementaryFiles(SkylineTool tool)
         return suppFiles;
     }
 
-    public static HashSet<String> getSupplementaryFileBasenames(SkylineTool tool)
+    public static HashSet<String> getSupplementaryFileBasenames(SkylineTool tool) throws IOException
     {
         HashSet<String> suppFiles = new HashSet<>();
-        File localToolDir = getLocalPath(tool.lookupContainer());
-        for (String suppFile : localToolDir.list())
+        Path localToolDir = getLocalPath(tool.lookupContainer());
+        try (var stream = Files.list(localToolDir))
         {
-            final String basename = new File(suppFile).getName();
-            if (!basename.startsWith(".") && !basename.equals(tool.getZipName()) && !basename.equals("icon.png") && !basename.equals("docs"))
-                suppFiles.add(suppFile);
+            stream.map(p -> p.getFileName().toString())
+                  .filter(name -> !name.startsWith(".") && !name.equals(tool.getZipName()) && !name.equals("icon.png") && !name.equals("docs"))
+                  .forEach(suppFiles::add);
         }
         return suppFiles;
     }
@@ -622,12 +622,12 @@ else if (!getContainer().hasPermission(getUser(), InsertPermission.class))
                         tool.writeIconToFile(makeFile(c, "icon.png"), "png");
 
                         // Extract docs from tool-inf/docs/ in the ZIP; carry forward from previous version if absent
-                        boolean hasDocs = extractDocsFromZip(storedZip, getLocalPath(c));
+                        boolean hasDocs = extractDocsFromZip(storedZip.toPath(), getLocalPath(c));
                         if (!hasDocs && existingVersionContainer != null)
                         {
-                            File oldDocs = new File(getLocalPath(existingVersionContainer), "docs");
-                            if (oldDocs.isDirectory())
-                                FileUtils.copyDirectory(oldDocs, new File(getLocalPath(c), "docs"));
+                            Path oldDocs = getLocalPath(existingVersionContainer).resolve("docs");
+                            if (Files.isDirectory(oldDocs))
+                                FileUtil.copyDirectory(oldDocs, getLocalPath(c).resolve("docs"));
                         }
 
                         if (copyFiles != null && existingVersionContainer != null)

SkylineToolsStore/src/org/labkey/skylinetoolsstore/model/SkylineTool.java

@@ -3,10 +3,15 @@
 import org.apache.commons.lang3.StringUtils;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.Entity;
+import org.labkey.api.files.FileContentService;
 import org.labkey.api.settings.AppProps;
 import org.labkey.api.util.Pair;
+import org.labkey.api.webdav.WebdavService;
 import org.labkey.skylinetoolsstore.SkylineToolsStoreController;
 
+import java.nio.file.Files;
+import java.nio.file.Path;
+
 import javax.imageio.ImageIO;
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
@@ -295,12 +300,17 @@ public String getFolderUrl()
 
     public boolean hasDocumentation()
     {
-        return new File(SkylineToolsStoreController.getLocalPath(lookupContainer()), "docs/index.html").exists();
+        Path localPath = SkylineToolsStoreController.getLocalPath(lookupContainer());
+        return localPath != null && Files.exists(localPath.resolve("docs/index.html"));
     }
 
     public String getDocsUrl()
     {
-        return AppProps.getInstance().getContextPath() + "/_webdav" + lookupContainer().getPath() + "/@files/docs/index.html";
+        org.labkey.api.util.Path path = WebdavService.getPath()
+                .append(lookupContainer().getParsedPath())
+                .append(FileContentService.FILES_LINK)
+                .append(new org.labkey.api.util.Path("docs", "index.html"));
+        return AppProps.getInstance().getContextPath() + path.encode();
     }
 
     public String getIconUrl()