Added documentation support to Skyline Tool Store

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;
@@ -176,9 +177,10 @@ protected SkylineTool getToolFromZip(MultipartFile zip) throws IOException
         {
             ZipEntry zipEntry;
             while ((zipEntry = zipStream.getNextEntry()) != null &&
-                    (tool == null || tool.getIcon() == null))
+                    (tool == null || toolIcon == 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();
 
@@ -229,14 +231,46 @@ protected byte[] unzip(ZipInputStream stream)
         }
     }
 
+    protected static boolean extractDocsFromZip(Path zipFile, Path containerDir) throws IOException
+    {
+        Path docsDir = containerDir.resolve("docs");
+        boolean extracted = false;
+        try (ZipFile zf = new ZipFile(zipFile.toFile()))
+        {
+            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;
+                Path destPath = docsDir.resolve(relativePath).normalize();
+                // Zip-slip protection
+                if (!destPath.startsWith(docsDir.normalize()))
+                    throw new IOException("Zip entry outside target directory: " + name);
+                Files.createDirectories(destPath.getParent());
+                try (InputStream in = zf.getInputStream(entry))
+                {
+                    Files.copy(in, destPath, StandardCopyOption.REPLACE_EXISTING);
+                }
+                extracted = true;
+            }
+        }
+        return extracted;
+    }
+
     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
@@ -383,7 +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"};
@@ -401,15 +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"))
-                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;
     }
@@ -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.toPath(), getLocalPath(c));
+                        if (!hasDocs && existingVersionContainer != null)
+                        {
+                            Path oldDocs = getLocalPath(existingVersionContainer).resolve("docs");
+                            if (Files.isDirectory(oldDocs))
+                                FileUtil.copyDirectory(oldDocs, getLocalPath(c).resolve("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

@@ -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;
@@ -293,6 +298,21 @@ public String getFolderUrl()
         return AppProps.getInstance().getContextPath() + "/files" + lookupContainer().getPath() + "/";
     }
 
+    public boolean hasDocumentation()
+    {
+        Path localPath = SkylineToolsStoreController.getLocalPath(lookupContainer());
+        return localPath != null && Files.exists(localPath.resolve("docs/index.html"));
+    }
+
+    public String getDocsUrl()
+    {
+        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()
     {
         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" %>
@@ -298,8 +300,16 @@ a { text-decoration: none; }
 <% } %>
         </div>
 
+        <%
+            Container supportContainer = getContainer().getChild("Support");
+            Container toolSupportBoard = supportContainer != null ? supportContainer.getChild(tool.getName()) : null;
+            if (toolSupportBoard == null)
+                toolSupportBoard = ContainerManager.getForPath("/home/support");
+        %>
+        <% if (toolSupportBoard != null) { %>
         <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')"); %>
+        <% addHandler("tool-support-board-btn", "click", "window.open(" + q(urlProvider(ProjectUrls.class).getBeginURL(toolSupportBoard)) + ", '_blank', 'noopener,noreferrer')"); %>
+        <% } %>
     </div>
 <% if (toolEditor) { %>
     <div class="menuMouseArea sprocket">
@@ -332,9 +342,20 @@ a { text-decoration: none; }
     </div>
 </div>
 
-<% if (suppIter.hasNext()) { %>
+<%
+    boolean hasDocumentation = tool.hasDocumentation();
+%>
+<% if (hasDocumentation || suppIter.hasNext()) { %>
 <div id="documentationbox" class="itemsbox">
     <legend>Documentation</legend>
+<% if (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();

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

@@ -200,7 +200,7 @@
 
                 <div class="toolButtons">
 
-                    <button type="button" id="download-tool-btn-<%=tool.getRowId()%>" class="styled-button">Download</button>
+                    <button type="button" id="download-tool-btn-<%=tool.getRowId()%>" class="styled-button">Download <span class="visually-hidden"><%=h(tool.getName())%></span></button>
                     <% addHandler("download-tool-btn-" + tool.getRowId(), "click", "window.location.href = " + q(urlFor(SkylineToolsStoreController.DownloadToolAction.class).addParameter("id", tool.getRowId()))); %>
 <%
     if (suppFiles.size() == 1) {