Added documentation support to Skyline Tool Store

* Extract docs from tool-inf/docs/ in uploaded ZIPs and serve via WebDAV
* Carry forward docs from previous version when new ZIP has none
* Show "Online Documentation" link in Documentation box when docs exist
* Skip tool-inf/docs/ images during icon extraction
* Exclude docs dir from supplementary file listings
* Fall back to /home/support when no tool-specific support board exists

Co-Authored-By: Claude <noreply@anthropic.com>

Author: brendanx67

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

@@ -178,7 +178,8 @@ protected SkylineTool getToolFromZip(MultipartFile zip) throws IOException
             while ((zipEntry = zipStream.getNextEntry()) != null &&
                     (tool == null || tool.getIcon() == null))
             {
-                if (zipEntry.getName().toLowerCase().startsWith("tool-inf/"))
+                String entryLower = zipEntry.getName().toLowerCase();
+                if (entryLower.startsWith("tool-inf/") && !entryLower.startsWith("tool-inf/docs/"))
                 {
                     String lowerBaseName = new File(zipEntry.getName()).getName().toLowerCase();
 
@@ -229,6 +230,39 @@ protected byte[] unzip(ZipInputStream stream)
         }
     }
 
+    protected static boolean extractDocsFromZip(File zipFile, File containerDir) throws IOException
+    {
+        File docsDir = new File(containerDir, "docs");
+        boolean extracted = false;
+        try (ZipFile zf = new ZipFile(zipFile))
+        {
+            Enumeration<? extends ZipEntry> entries = zf.entries();
+            while (entries.hasMoreElements())
+            {
+                ZipEntry entry = entries.nextElement();
+                String name = entry.getName();
+                if (!name.toLowerCase().startsWith("tool-inf/docs/") || entry.isDirectory())
+                    continue;
+                // Strip "tool-inf/docs/" prefix to get relative path within docs dir
+                String relativePath = name.substring("tool-inf/docs/".length());
+                if (relativePath.isEmpty())
+                    continue;
+                File destFile = new File(docsDir, relativePath);
+                // Zip-slip protection
+                if (!destFile.getCanonicalPath().startsWith(docsDir.getCanonicalPath() + File.separator))
+                    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))
+                {
+                    in.transferTo(out);
+                }
+                extracted = true;
+            }
+        }
+        return extracted;
+    }
+
     public static File makeFile(Container c, String filename)
     {
         return new File(getLocalPath(c), FileUtil.makeLegalName(filename));
@@ -408,7 +442,7 @@ public static HashSet<String> getSupplementaryFileBasenames(SkylineTool tool)
         for (String suppFile : localToolDir.list())
         {
             final String basename = new File(suppFile).getName();
-            if (!basename.startsWith(".") && !basename.equals(tool.getZipName()) && !basename.equals("icon.png"))
+            if (!basename.startsWith(".") && !basename.equals(tool.getZipName()) && !basename.equals("icon.png") && !basename.equals("docs"))
                 suppFiles.add(suppFile);
         }
         return suppFiles;
@@ -583,9 +617,19 @@ else if (!getContainer().hasPermission(getUser(), InsertPermission.class))
                     {
                         Container c = makeContainer(getContainer(), folderName, toolOwnersUsers, RoleManager.getRole(EditorRole.class));
                         copyContainerPermissions(existingVersionContainer, c);
-                        zip.transferTo(makeFile(c, zip.getOriginalFilename()));
+                        File storedZip = makeFile(c, zip.getOriginalFilename());
+                        zip.transferTo(storedZip);
                         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));
+                        if (!hasDocs && existingVersionContainer != null)
+                        {
+                            File oldDocs = new File(getLocalPath(existingVersionContainer), "docs");
+                            if (oldDocs.isDirectory())
+                                FileUtils.copyDirectory(oldDocs, new File(getLocalPath(c), "docs"));
+                        }
+
                         if (copyFiles != null && existingVersionContainer != null)
                             for (String copyFile : copyFiles)
                                 FileUtils.copyFile(makeFile(existingVersionContainer, copyFile), makeFile(c, copyFile), true);

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

@@ -293,6 +293,16 @@ public String getFolderUrl()
         return AppProps.getInstance().getContextPath() + "/files" + lookupContainer().getPath() + "/";
     }
 
+    public boolean hasDocumentation()
+    {
+        return new File(SkylineToolsStoreController.getLocalPath(lookupContainer()), "docs/index.html").exists();
+    }
+
+    public String getDocsUrl()
+    {
+        return AppProps.getInstance().getContextPath() + "/_webdav" + lookupContainer().getPath() + "/@files/docs/index.html";
+    }
+
     public String getIconUrl()
     {
         return (SkylineToolsStoreController.makeFile(lookupContainer(), "icon.png").exists()) ?

SkylineToolsStore/src/org/labkey/skylinetoolsstore/view/SkylineToolDetails.jsp

@@ -1,4 +1,6 @@
 <%@ page import="org.apache.commons.lang3.StringUtils" %>
+<%@ page import="org.labkey.api.data.Container" %>
+<%@ page import="org.labkey.api.data.ContainerManager" %>
 <%@ page import="org.labkey.api.portal.ProjectUrls" %>
 <%@ page import="org.labkey.api.security.permissions.DeletePermission" %>
 <%@ page import="org.labkey.api.security.permissions.InsertPermission" %>
@@ -299,7 +301,17 @@ a { text-decoration: none; }
         </div>
 
         <button id="tool-support-board-btn" class="banner-button-small">Support Board</button>
-        <% addHandler("tool-support-board-btn", "click", "window.open(" + q(urlProvider(ProjectUrls.class).getBeginURL(getContainer().getChild("Support").getChild(tool.getName()))) + ", '_blank', 'noopener,noreferrer')"); %>
+        <%
+            Container supportContainer = getContainer().getChild("Support");
+            Container toolSupportBoard = supportContainer != null ? supportContainer.getChild(tool.getName()) : null;
+            Container supportTarget;
+            if (toolSupportBoard != null)
+                supportTarget = toolSupportBoard;
+            else
+                supportTarget = ContainerManager.getForPath("/home/support");
+            if (supportTarget != null)
+                addHandler("tool-support-board-btn", "click", "window.open(" + q(urlProvider(ProjectUrls.class).getBeginURL(supportTarget)) + ", '_blank', 'noopener,noreferrer')");
+        %>
     </div>
 <% if (toolEditor) { %>
     <div class="menuMouseArea sprocket">
@@ -332,9 +344,17 @@ a { text-decoration: none; }
     </div>
 </div>
 
-<% if (suppIter.hasNext()) { %>
+<% if (tool.hasDocumentation() || suppIter.hasNext()) { %>
 <div id="documentationbox" class="itemsbox">
     <legend>Documentation</legend>
+<% if (tool.hasDocumentation()) { %>
+    <div class="barItem">
+        <a href="<%=h(tool.getDocsUrl())%>" target="_blank" rel="noopener noreferrer">
+        <img src="<%= h(imgDir) %>link.png" alt="Documentation" />
+        <span>Online Documentation</span>
+        </a>
+    </div>
+<% } %>
 <%
     while (suppIter.hasNext()) {
         Map.Entry suppPair = (Map.Entry)suppIter.next();