File Issues: Greatest Hits, 2006-2015

- When relinking a missing stored file, copy it into the attachment's
  storage directory automatically
  - Previously, selecting a file outside the attachment subdir would
    just result in a missing attachment, since it only looks for stored
    files within the subdir
- Display an error message if a Windows shortcut (.lnk) is added via
  drag-and-drop or via a file dialog on non-Windows systems, until we
  can figure out how to determine the original file
  - Shortcuts can cause errors during syncing, for unclear reasons
  - Neither nsIFile::copyToFollowingLinks() nor nsIFile::target work for
    me to get the original file, even when nsIFile::isSymlink() returns
    true
  - Windows file dialogs seem to automatically resolve shortcuts, so
    it's only an issue there for drag-and-drop
- Disallow hidden files from being selected in relink dialog
  - I think some people on Windows with hidden files shown relink the
    .zotero* files that show up when they click Locate, which causes
    file sync errors. Which brings us to...
- Fix file sync errors for *.lnk and .zotero* files
- Ignore existing .zotero* attachment files, treating the files as
  missing instead to encourage relinking
- Strip leading period in getValidFileName() to prevent added files from
  being hidden
    - This allows hidden files to be added explicitly; they just won't
      stay that way in the storage directory

(These things should have tests, but that will have to happen on the 5.0
branch.)

chrome/content/zotero/webpagedump/common.js

@@ -644,7 +644,7 @@ var wpdCommon = {
 
 		aDir.initWithPath(destdir);
 
-		aFile.copyTo(aDir, destfile);
+		aFile.copyToFollowingLinks(aDir, destfile);
 		return true; // Added by Dan S. for Zotero
 	},
 

chrome/content/zotero/xpcom/attachments.js

@@ -55,6 +55,10 @@ Zotero.Attachments = new function(){
 			throw ("'" + file.leafName + "' must be a file in Zotero.Attachments.importFromFile()");
 		}
 		
+		if (file.leafName.endsWith(".lnk")) {
+			throw new Error("Cannot add Windows shortcut");
+		}
+		
 		Zotero.DB.beginTransaction();
 		
 		try {
@@ -165,7 +169,7 @@ Zotero.Attachments = new function(){
 			var storageDir = Zotero.getStorageDirectory();
 			var destDir = this.getStorageDirectory(itemID);
 			_moveOrphanedDirectory(destDir);
-			file.parent.copyTo(storageDir, destDir.leafName);
+			file.parent.copyToFollowingLinks(storageDir, destDir.leafName);
 			
 			// Point to copied file
 			var newFile = destDir.clone();

chrome/content/zotero/xpcom/data/item.js

@@ -2863,6 +2863,11 @@ Zotero.Item.prototype.getFile = function(row, skipExistsCheck) {
 			if (Zotero.isWin || path.indexOf('/') != -1) {
 				path = Zotero.File.getValidFileName(path, true);
 			}
+			// Ignore .zotero* files that were relinked before we started blocking them
+			if (path.startsWith(".zotero")) {
+				Zotero.debug("Ignoring attachment file " + path, 2);
+				return false;
+			}
 			var file = Zotero.Attachments.getStorageDirectory(this.id);
 			file.QueryInterface(Components.interfaces.nsILocalFile);
 			file.setRelativeDescriptor(file, path);
@@ -3109,15 +3114,47 @@ Zotero.Item.prototype.relinkAttachmentFile = function(file, skipItemUpdate) {
 		throw('Cannot relink linked URL in Zotero.Items.relinkAttachmentFile()');
 	}
 	
+	if (file.leafName.endsWith(".lnk")) {
+		throw new Error("Cannot relink to Windows shortcut");
+	}
+	
 	var newName = Zotero.File.getValidFileName(file.leafName);
 	if (!newName) {
 		throw ("No valid characters in filename after filtering in Zotero.Item.relinkAttachmentFile()");
 	}
 	
-	// Rename file to filtered name if necessary
-	if (file.leafName != newName) {
-		Zotero.debug("Renaming file '" + file.leafName + "' to '" + newName + "'");
-		file.moveTo(null, newName);
+	try {
+		// If selected file isn't in the attachment's storage directory,
+		// copy it in and use that one instead
+		var storageDir = Zotero.Attachments.getStorageDirectory(this.id);
+		if (this.isImportedAttachment() && !file.parent.equals(storageDir)) {
+			// If file with same name already exists in the storage directory,
+			// move it out of the way
+			let targetFile = storageDir.clone();
+			targetFile.append(newName);
+			let renamedFile;
+			if (targetFile.exists()) {
+				renamedFile = targetFile.clone();
+				renamedFile.moveTo(null, newName + ".bak");
+			}
+			
+			Zotero.File.copyToUnique(file, targetFile);
+			file = targetFile;
+			
+			// Delete backup file
+			if (renamedFile) {
+				renamedFile.remove(false);
+			}
+		}
+		// Rename file to filtered name if necessary
+		else if (file.leafName != newName) {
+			Zotero.debug("Renaming file '" + file.leafName + "' to '" + newName + "'");
+			file.moveTo(null, newName);
+		}
+	}
+	catch (e) {
+		Zotero.logError(e);
+		return false;
 	}
 	
 	var path = Zotero.Attachments.getPath(file, linkMode);
@@ -3128,7 +3165,7 @@ Zotero.Item.prototype.relinkAttachmentFile = function(file, skipItemUpdate) {
 		skipClientDateModifiedUpdate: skipItemUpdate
 	});
 	
-	return false;
+	return true;
 }
 
 
@@ -3342,7 +3379,8 @@ Zotero.Item.prototype.__defineGetter__('attachmentPath', function () {
 	
 	var sql = "SELECT path FROM itemAttachments WHERE itemID=?";
 	var path = Zotero.DB.valueQuery(sql, this.id);
-	if (!path) {
+	// Ignore .zotero* files that were relinked before we started blocking them
+	if (!path || path.startsWith('.zotero')) {
 		path = '';
 	}
 	this._attachmentPath = path;

chrome/content/zotero/xpcom/file.js

@@ -426,7 +426,7 @@ Zotero.File = new function(){
 		newFile.remove(null);
 		
 		// Copy file to unique name
-		file.copyTo(newFile.parent, newName);
+		file.copyToFollowingLinks(newFile.parent, newName);
 		return newFile;
 	}
 	
@@ -442,7 +442,7 @@ Zotero.File = new function(){
 		while (otherFiles.hasMoreElements()) {
 			var file = otherFiles.getNext();
 			file.QueryInterface(Components.interfaces.nsIFile);
-			file.copyTo(newDir, null);
+			file.copyToFollowingLinks(newDir, null);
 		}
 	}
 	
@@ -505,6 +505,8 @@ Zotero.File = new function(){
 			// Strip characters not valid in XML, since they won't sync and they're probably unwanted
 			fileName = fileName.replace(/[\u0000-\u0008\u000b\u000c\u000e-\u001f\ud800-\udfff\ufffe\uffff]/g, '');
 		}
+		// Don't allow hidden files
+		fileName = fileName.replace(/^\./, '');
 		// Don't allow blank or illegal filenames
 		if (!fileName || fileName == '.' || fileName == '..') {
 			fileName = '_';

chrome/content/zotero/xpcom/itemTreeView.js

@@ -2810,7 +2810,7 @@ Zotero.ItemTreeView.fileDragDataProvider.prototype = {
 							}
 						}
 						
-						parentDir.copyTo(destDir, newName ? newName : dirName);
+						parentDir.copyToFollowingLinks(destDir, newName ? newName : dirName);
 						
 						// Store nsIFile
 						if (useTemp) {
@@ -2851,7 +2851,7 @@ Zotero.ItemTreeView.fileDragDataProvider.prototype = {
 							}
 						}
 						
-						file.copyTo(destDir, newName ? newName : null);
+						file.copyToFollowingLinks(destDir, newName ? newName : null);
 						
 						// Store nsIFile
 						if (useTemp) {
@@ -3219,6 +3219,14 @@ Zotero.ItemTreeView.prototype.drop = function(row, orient, dataTransfer) {
 						var itemID = Zotero.Attachments.linkFromFile(file, sourceItemID);
 					}
 					else {
+						if (file.leafName.endsWith(".lnk")) {
+							let wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
+							   .getService(Components.interfaces.nsIWindowMediator);
+							let win = wm.getMostRecentWindow("navigator:browser");
+							win.ZoteroPane.displayCannotAddShortcutMessage(file.path);
+							Zotero.DB.commitTransaction();
+							continue;
+						}
 						var itemID = Zotero.Attachments.importFromFile(file, sourceItemID, targetLibraryID);
 						// If moving, delete original file
 						if (dragData.dropEffect == 'move') {

chrome/content/zotero/xpcom/storage.js

@@ -1486,6 +1486,10 @@ Zotero.Sync.Storage = new function () {
 		if (!file) {
 			throw ("Empty path for item " + item.key + " in " + funcName);
 		}
+		// Don't save Windows aliases
+		if (file.leafName.endsWith('.lnk')) {
+			return false;
+		}
 		
 		var fileName = file.leafName;
 		var renamed = false;
@@ -1899,8 +1903,9 @@ Zotero.Sync.Storage = new function () {
 			params.push(Zotero.Sync.Storage.SYNC_STATE_TO_DOWNLOAD);
 		}
 		sql += ") "
-			// Skip attachments with empty path, which can't be saved
-			+ "AND path!=''";
+			// Skip attachments with empty path, which can't be saved, and files with .zotero*
+			// paths, which have somehow ended up in some users' libraries
+			+ "AND path!='' AND path NOT LIKE 'storage:.zotero%'";
 		var itemIDs = Zotero.DB.columnQuery(sql, params);
 		if (!itemIDs) {
 			return [];

chrome/content/zotero/zoteroPane.js

@@ -3116,8 +3116,16 @@ var ZoteroPane = new function()
 				var attachmentID;
 				if(link)
 					attachmentID = Zotero.Attachments.linkFromFile(file, id);
-				else
+				else {
+					if (file.leafName.endsWith(".lnk")) {
+						let wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
+						.getService(Components.interfaces.nsIWindowMediator);
+						let win = wm.getMostRecentWindow("navigator:browser");
+						win.ZoteroPane.displayCannotAddShortcutMessage(file.path);
+						continue;
+					}
 					attachmentID = Zotero.Attachments.importFromFile(file, id, libraryID);
+				}
 			
 				if(attachmentID && !id)
 				{
@@ -3757,6 +3765,16 @@ var ZoteroPane = new function()
 	}
 	
 	
+	// TODO: Figure out a functioning way to get the original path and just copy the real file
+	this.displayCannotAddShortcutMessage = function (path) {
+		Zotero.alert(
+			null,
+			Zotero.getString("general.error"),
+			Zotero.getString("file.error.cannotAddShortcut") + (path ? "\n\n" + path : "")
+		);
+	}
+	
+	
 	function showAttachmentNotFoundDialog(itemID, noLocate) {
 		var ps = Components.classes["@mozilla.org/embedcomp/prompt-service;1"].
 				createInstance(Components.interfaces.nsIPromptService);
@@ -3951,25 +3969,43 @@ var ZoteroPane = new function()
 			throw('Item ' + itemID + ' not found in ZoteroPane_Local.relinkAttachment()');
 		}
 		
-		var nsIFilePicker = Components.interfaces.nsIFilePicker;
-		var fp = Components.classes["@mozilla.org/filepicker;1"]
-					.createInstance(nsIFilePicker);
-		fp.init(window, Zotero.getString('pane.item.attachments.select'), nsIFilePicker.modeOpen);
-		
-		
-		var file = item.getFile(false, true);
-		var dir = Zotero.File.getClosestDirectory(file);
-		if (dir) {
-			dir.QueryInterface(Components.interfaces.nsILocalFile);
-			fp.displayDirectory = dir;
-		}
-		
-		fp.appendFilters(Components.interfaces.nsIFilePicker.filterAll);
-		
-		if (fp.show() == nsIFilePicker.returnOK) {
-			var file = fp.file;
-			file.QueryInterface(Components.interfaces.nsILocalFile);
-			item.relinkAttachmentFile(file);
+		while (true) {
+			var nsIFilePicker = Components.interfaces.nsIFilePicker;
+			var fp = Components.classes["@mozilla.org/filepicker;1"]
+						.createInstance(nsIFilePicker);
+			fp.init(window, Zotero.getString('pane.item.attachments.select'), nsIFilePicker.modeOpen);
+			
+			
+			var file = item.getFile(false, true);
+			var dir = Zotero.File.getClosestDirectory(file);
+			if (dir) {
+				dir.QueryInterface(Components.interfaces.nsILocalFile);
+				fp.displayDirectory = dir;
+			}
+			
+			fp.appendFilters(Components.interfaces.nsIFilePicker.filterAll);
+			
+			if (fp.show() == nsIFilePicker.returnOK) {
+				let file = fp.file;
+				file.QueryInterface(Components.interfaces.nsILocalFile);
+				
+				// Disallow hidden files
+				// TODO: Display a message
+				if (file.leafName.startsWith('.')) {
+					continue;
+				}
+				
+				// Disallow Windows shortcuts
+				if (file.leafName.endsWith(".lnk")) {
+					this.displayCannotAddShortcutMessage(file.path);
+					continue;
+				}
+				
+				item.relinkAttachmentFile(file);
+				break;
+			}
+			
+			break;
 		}
 	}
 	

chrome/locale/en-US/zotero/zotero.properties

@@ -963,6 +963,7 @@ file.accessError.message.windows	= Check that the file is not currently in use,
 file.accessError.message.other		= Check that the file is not currently in use and that its permissions allow write access.
 file.accessError.restart			= Restarting your computer or disabling security software may also help.
 file.accessError.showParentDir		= Show Parent Directory
+file.error.cannotAddShortcut       = Shortcut files cannot be added directly. Please select the original file.
 
 lookup.failure.title				= Lookup Failed
 lookup.failure.description			= Zotero could not find a record for the specified identifier. Please verify the identifier and try again.