Zotero File Storage megacommit

- Group file sync via Zotero File Storage
- Split file syncing into separate modules for ZFS and WebDAV
- Dragging items between libraries copies child notes, snapshots/files, and links based on checkboxes for each (enabled by default) in the Zotero preferences
- Sync errors now trigger an exclamation/error icon separate from the sync icon, with a popup window displaying the error and an option to report it
- Various errors that could cause perpetual sync icon spinning now stop the sync properly
- Zotero.Utilities.md5(str) is now md5(strOrFile, base64)
- doPost(), doHead(), and retrieveSource() now takes a headers parameter instead of requestContentType
- doHead() can now accept an nsIURI (with login credentials), is a background request, and isn't cached
- When library access or file writing access is denied during sync, display a warning and then reset local group to server version
- Perform additional steps (e.g., removing local groups) when switching sync users to prevent errors
- Compare hash as well as mod time when checking for modified local files
- Don't trigger notifications when removing groups from the client
- Clear relation links to items in removed groups
- Zotero.Item.attachmentHash property to get file MD5
- importFromFile() now takes libraryID as a third parameter
- Zotero.Attachments.getNumFiles() returns the number of files in the attachment directory
- Zotero.Attachments.copyAttachmentToLibrary() copies an attachment item, including files, to another library
- Removed Zotero.File.getFileHash() in favor of updated Zotero.Utilities.md5()
- Zotero.File.copyDirectory(dir, newDir) copies all files from dir into newDir
- Preferences shuffling: OpenURL to Advanced, import/export character set options to Export, "Include URLs of paper articles in references" to Styles
- Other stuff I don't remember

Suffice it to say, this could use testing.

chrome/content/zotero/overlay.js

@@ -177,11 +177,25 @@ var ZoteroPane = new function()
 				);
 				
 				if (index == 0) {
-					Zotero.Sync.Server.sync(function () {
+					Zotero.Sync.Server.sync({
-						pr.alert(
+						onSuccess: function () {
-							"Restore Completed",
+							Zotero.Sync.Runner.setSyncIcon();
-							"The local Zotero database has been successfully restored."
+							
-						);
+							pr.alert(
+								"Restore Completed",
+								"The local Zotero database has been successfully restored."
+							);
+						},
+						
+						onError: function (msg) {
+							pr.alert(
+								"Restore Failed",
+								"An error occurred while restoring from the server:\n\n"
+									+ msg
+							);
+							
+							Zotero.Sync.Runner.error(msg);
+						}
 					});
 				}
 			}, 1000);
@@ -898,7 +912,7 @@ var ZoteroPane = new function()
 		if (!tagSelector.getAttribute('collapsed') ||
 				tagSelector.getAttribute('collapsed') == 'false') {
 			Zotero.debug('Updating tag selector with current tags');
-			if (itemGroup.isEditable()) {
+			if (itemGroup.editable) {
 				tagSelector.mode = 'edit';
 			}
 			else {
@@ -2281,7 +2295,7 @@ var ZoteroPane = new function()
 		var disabled = Zotero.locked;
 		if (!disabled && self.collectionsView.selection && self.collectionsView.selection.count) {
 			var itemGroup = self.collectionsView._getItemAtRow(self.collectionsView.selection.currentIndex);
-			disabled = !itemGroup.isEditable()
+			disabled = !itemGroup.editable;
 		}
 		for each(var menuitem in menu.firstChild.childNodes) {
 			menuitem.disabled = disabled;
@@ -2837,7 +2851,26 @@ var ZoteroPane = new function()
 		}
 		
 		var itemGroup = this.collectionsView._getItemAtRow(row);
-		return itemGroup.isEditable();
+		return itemGroup.editable;
+	}
+	
+	
+	/**
+	 * Test if the user can edit the currently selected library/collection,
+	 * and display an error if not
+	 *
+	 * @param	{Integer}	[row]
+	 *
+	 * @return	{Boolean}		TRUE if user can edit, FALSE if not
+	 */
+	this.canEditFiles = function (row) {
+		// Currently selected row
+		if (row === undefined) {
+			row = this.collectionsView.selection.currentIndex;
+		}
+		
+		var itemGroup = this.collectionsView._getItemAtRow(row);
+		return itemGroup.filesEditable;
 	}
 	
 	
@@ -2999,12 +3032,6 @@ var ZoteroPane = new function()
 	this.setLastSyncStatus = function (tooltip) {
 		var label = tooltip.firstChild.nextSibling;
 		
-		var msg = Zotero.Sync.Runner.lastSyncError;
-		if (msg) {
-			label.value = 'Last error: ' + msg; // TODO: localize
-			return;
-		}
-		
 		var lastSyncTime = Zotero.Sync.Server.lastLocalSyncTime;
 		// TODO: localize
 		msg = 'Last sync: ';

chrome/content/zotero/overlay.xul

@@ -164,8 +164,8 @@
 								<menuitem hidden="true" label="  Reset Client" oncommand="Zotero.Sync.Server.resetClient()"/>
 								<menuitem label="Storage Debugging" disabled="true"/>
 								<menuitem hidden="true" label="  Reset Storage History" oncommand="Zotero.Sync.Storage.resetAllSyncStates()"/>
-								<menuitem label="  Purge Deleted Storage Files" oncommand="Zotero.Sync.Storage.purgeDeletedStorageFiles(function(results) { Zotero.debug(results); })"/>
+								<menuitem label="  Purge Deleted Storage Files" oncommand="Zotero.Sync.Storage.purgeDeletedStorageFiles('webdav', function(results) { Zotero.debug(results); })"/>
-								<menuitem label="  Purge Orphaned Storage Files" oncommand="Zotero.Sync.Storage.purgeOrphanedStorageFiles(function(results) { Zotero.debug(results); })"/>
+								<menuitem label="  Purge Orphaned Storage Files" oncommand="Zotero.Sync.Storage.purgeOrphanedStorageFiles('webdav', function(results) { Zotero.debug(results); })"/>
 								<menuseparator id="zotero-tb-actions-separator"/>
 								<menuitem id="zotero-tb-actions-prefs" label="&zotero.toolbar.preferences.label;"
 									oncommand="ZoteroPane.openPreferences()"/>
@@ -375,6 +375,7 @@
 							</grid>
 						</tooltip>
 					</hbox>
+					<toolbarbutton id="zotero-tb-sync-warning" hidden="true"/>
 					<toolbarbutton id="zotero-tb-sync" class="zotero-tb-button" tooltip="_child"
 							oncommand="Zotero.Sync.Server.canAutoResetClient = true; Zotero.Sync.Runner.sync()">
 						<tooltip

chrome/content/zotero/preferences/preferences.js

@@ -42,7 +42,7 @@ function init()
 		rows[i].firstChild.nextSibling.value = Zotero.isMac ? 'Cmd+Shift+' : 'Ctrl+Alt+';
 	}
 	
-	updateStorageSettings();
+	updateStorageSettings(null, null, true);
 	refreshStylesList();
 	refreshProxyList();
 	populateQuickCopyList();
@@ -171,43 +171,85 @@ function populateOpenURLResolvers() {
 //
 // Sync
 //
-/*
+function updateStorageSettings(enabled, protocol, skipWarnings) {
-function updateSyncStatus() {
+	if (enabled === null) {
-	var disabled = !Zotero.Sync.Server.enabled;
+		enabled = document.getElementById('pref-storage-enabled').value;
+	}
 	
-	var radioGroup = document.getElementById('zotero-reset').firstChild;
+	var oldProtocol = document.getElementById('pref-storage-protocol').value;
-	radioGroup.disabled = disabled;
+	if (protocol === null) {
-	var labels = radioGroup.getElementsByTagName('label');
+		protocol = oldProtocol;
-	for each(var label in labels) {
-		label.disabled = disabled;
 	}
-	var labels = radioGroup.getElementsByTagName('description');
+	
-	for each(var label in labels) {
+	var protocolMenu = document.getElementById('storage-protocol');
-		label.disabled = disabled;
+	var settings = document.getElementById('storage-webdav-settings');
+	var sep = document.getElementById('storage-separator');
+	
+	if (!enabled || protocol == 'zotero') {
+		settings.hidden = true;
+		sep.hidden = false;
+	}
+	else {
+		settings.hidden = false;
+		sep.hidden = true;
+	}
+	
+	protocolMenu.disabled = !enabled;
+	
+	if (!skipWarnings) {
+		// WARN if going between
+	}
+	
+	if (oldProtocol == 'zotero' && protocol == 'webdav') {
+		var sql = "SELECT COUNT(*) FROM version WHERE schema='storage_zfs'";
+		if (Zotero.DB.valueQuery(sql)) {
+			var pr = Components.classes["@mozilla.org/network/default-prompt;1"]
+						.getService(Components.interfaces.nsIPrompt);
+			var buttonFlags = (pr.BUTTON_POS_0) * (pr.BUTTON_TITLE_IS_STRING)
+								+ (pr.BUTTON_POS_1) * (pr.BUTTON_TITLE_IS_STRING)
+								+ pr.BUTTON_DELAY_ENABLE;
+			var account = Zotero.Sync.Server.username;
+			var index = pr.confirmEx(
+				// TODO: localize
+				"Purge Attachment Files on Zotero Servers?",
+				
+				"If you plan to use WebDAV for file syncing and you previously synced attachment files in My Library "
+					+ "to the Zotero servers, you can purge those files from the Zotero servers to give you more "
+					+ "storage space for groups.\n\n"
+					+ "You can purge files at any time from your account settings on zotero.org.",
+				buttonFlags,
+				"Purge Files Now",
+				"Do Not Purge", null, null, {}
+			);
+			
+			if (index == 0) {
+				var sql = "INSERT OR IGNORE INTO settings VALUES (?,?,?)";
+				Zotero.DB.query(sql, ['storage', 'zfsPurge', 'user']);
+				
+				Zotero.Sync.Storage.purgeDeletedStorageFiles('zfs', function (success) {
+					if (success) {
+						pr.alert(
+							Zotero.getString("general.success"),
+							"Attachment files from your personal library have been removed from the Zotero servers."
+						);
+					}
+					else {
+						pr.alert(
+							Zotero.getString("general.error"),
+							"An error occurred. Please try again later."
+						);
+					}
+				});
+			}
+		}
 	}
-	document.getElementById('zotero-reset-button').disabled = disabled;
 }
-*/
 
-function updateStorageSettings(value) {
+
-	if (!value) {
-		value = document.getElementById('pref-storage-protocol').value;
-	}
-	var prefix = document.getElementById('storage-url-prefix');
-	switch (value) {
-		case 'webdav':
-			prefix.value = 'http://';
-			break;
-		
-		case 'webdavs':
-			prefix.value = 'https://';
-			break;
-	}
-}
 
 function unverifyStorageServer() {
-	Zotero.Sync.Storage.clearSettingsCache();
 	Zotero.Prefs.set('sync.storage.verified', false);
+	Zotero.Sync.Storage.resetAllSyncStates(null, true, false);
 }
 
 function verifyStorageServer() {
@@ -220,7 +262,7 @@ function verifyStorageServer() {
 	var usernameField = document.getElementById("storage-username");
 	var passwordField = document.getElementById("storage-password");
 	
-	var callback = function (uri, status, authRequired) {
+	var callback = function (uri, status) {
 		verifyButton.hidden = false;
 		abortButton.hidden = true;
 		progressMeter.hidden = true;
@@ -245,13 +287,13 @@ function verifyStorageServer() {
 				break;
 		}
 		
-		Zotero.Sync.Storage.checkServerCallback(uri, status, authRequired, window);
+		Zotero.Sync.Storage.checkServerCallback(uri, status, window);
 	}
 	
 	verifyButton.hidden = true;
 	abortButton.hidden = false;
 	progressMeter.hidden = false;
-	var requestHolder = Zotero.Sync.Storage.checkServer(callback);
+	var requestHolder = Zotero.Sync.Storage.checkServer('webdav', callback);
 	abortButton.onclick = function () {
 		if (requestHolder.request) {
 			requestHolder.request.onreadystatechange = undefined;

chrome/content/zotero/preferences/preferences.xul

@@ -38,7 +38,8 @@ To add a new preference:
 
 -->
 <prefwindow id="zotero-prefs" title="&zotero.preferences.title;" onload="moveToAlertPosition(); init()" onunload="Zotero_Preferences.onUnload()"
-		windowtype="zotero:pref" xmlns="http://www.mozilla.org/keymaster/gatekeeper/there.is.only.xul">
+		windowtype="zotero:pref" xmlns="http://www.mozilla.org/keymaster/gatekeeper/there.is.only.xul"
+		style="min-height: 600px">
 	
 	<prefpane id="zotero-prefpane-general"
 						label="&zotero.preferences.prefpane.general;"
@@ -54,8 +55,10 @@ To add a new preference:
 			<preference id="pref-automaticSnapshots" name="extensions.zotero.automaticSnapshots" type="bool"/>
 			<preference id="pref-downloadAssociatedFiles" name="extensions.zotero.downloadAssociatedFiles" type="bool"/>
 			<preference id="pref-automaticTags" name="extensions.zotero.automaticTags" type="bool"/>
-			<preference id="pref-openURL-resolver" name="extensions.zotero.openURL.resolver" type="string"/>
+			
-			<preference id="pref-openURL-version" name="extensions.zotero.openURL.version" type="string"/>
+			<preference id="pref-groups-copyChildNotes" name="extensions.zotero.groups.copyChildNotes" type="bool"/>
+			<preference id="pref-groups-copyChildFileAttachments" name="extensions.zotero.groups.copyChildFileAttachments" type="bool"/>
+			<preference id="pref-groups-copyChildLinks" name="extensions.zotero.groups.copyChildLinks" type="bool"/>
 		</preferences>
 		
 		<groupbox>
@@ -138,31 +141,18 @@ To add a new preference:
 		</groupbox>
 		
 		<groupbox>
-			<caption label="&zotero.preferences.openurl.caption;"/>
+			<caption label="Groups"/>
 			
-			<button id="openURLSearchButton" label="&zotero.preferences.openurl.search;" oncommand="populateOpenURLResolvers()"/>
+			<!-- TODO: localize -->
-			<menulist id="openURLMenu" oncommand="onOpenURLSelected();">
+			<label value="When copying items between libraries, include:"/>
-				<menupopup>
+			<vbox style="margin-left: 2em">
-					<menuseparator/>
+				<checkbox label="child notes" preference="pref-groups-copyChildNotes"/>
-					<menuitem label="&zotero.preferences.openurl.custom;" value="custom" selected="true"/>
+				<checkbox label="child snapshots and imported files" preference="pref-groups-copyChildFileAttachments"/>
-				</menupopup>
+				<checkbox label="child links" preference="pref-groups-copyChildLinks"/>
-			</menulist>
+			</vbox>
-			
-			<hbox align="center">
-				<label value="&zotero.preferences.openurl.server;"/>
-				<textbox id="openURLServerField" flex="1" oninput="onOpenURLCustomized();" preference="pref-openURL-resolver"/>
-			</hbox>
-		
-			<hbox align="center">
-				<label value="&zotero.preferences.openurl.version;" control="openURLVersionMenu"/>
-				<menulist id="openURLVersionMenu" oncommand="onOpenURLCustomized();" preference="pref-openURL-version">
-					<menupopup>
-						<menuitem label="0.1" value="0.1"/>
-						<menuitem label="1.0" value="1.0"/>
-					</menupopup>
-				</menulist>
-			</hbox>
 		</groupbox>
+		
+		<separator/>
 	</prefpane>
 	
 	
@@ -174,10 +164,12 @@ To add a new preference:
 		<preferences>
 			<preference id="pref-sync-autosync" name="extensions.zotero.sync.autoSync" type="bool"/>
 			<preference id="pref-sync-username" name="extensions.zotero.sync.server.username" type="string" instantApply="true"/>
-			<preference id="pref-storage-protocol" name="extensions.zotero.sync.storage.protocol" type="string"/>
 			<preference id="pref-storage-enabled" name="extensions.zotero.sync.storage.enabled" type="bool"/>
+			<preference id="pref-storage-protocol" name="extensions.zotero.sync.storage.protocol" type="string" onchange="unverifyStorageServer()"/>
+			<preference id="pref-storage-scheme" name="extensions.zotero.sync.storage.scheme" type="string"/>
 			<preference id="pref-storage-url" name="extensions.zotero.sync.storage.url" type="string" instantApply="true"/>
 			<preference id="pref-storage-username" name="extensions.zotero.sync.storage.username" type="string" instantApply="true"/>
+			<preference id="pref-group-storage-enabled" name="extensions.zotero.sync.storage.groups.enabled" type="bool"/>
 		</preferences>
 		
 		<!-- This doesn't wrap without an explicit width, for some reason -->
@@ -250,50 +242,44 @@ To add a new preference:
 					</groupbox>
 					
 					
+					<!-- TODO: localize -->
 					<groupbox>
-						<caption label="Storage Server"/>
+						<caption label="File Syncing"/>
 						
-						<hbox>
+						<!-- My Library -->
-							<checkbox label="Enable file syncing" preference="pref-storage-enabled"/>
+						<hbox style="margin: 0">
+							<checkbox label="Sync attachment files in My Library using" preference="pref-storage-enabled" oncommand="updateStorageSettings(this.checked, null)"/>
+							<menulist id="storage-protocol" style="margin-left: .5em" preference="pref-storage-protocol" oncommand="updateStorageSettings(null, this.value)">
+								<menupopup>
+									<menuitem label="Zotero" value="zotero"/>
+									<menuitem label="WebDAV" value="webdav"/>
+								</menupopup>
+							</menulist>
 						</hbox>
 						
-						<separator class="thin"/>
+						<stack id="storage-webdav-settings" style="margin-top: .5em; margin-bottom: .8em; border: 1px gray solid; -moz-border-radius: 3px">
-						<hbox align="center">
+						<!-- Background shading -->
-							<label value="A" style="margin-right: 0"/>
+						<box style="background: black; opacity:.03"/>
-							<label value="WebDAV server" class="text-link" href="http://zotero.org/support/sync#file_syncing" style="margin-left: .25em; margin-right: .25em"/>
-							<label value="is currently required to sync attachment files." style="margin-left: 0"/>
-						</hbox>
 						
-						<separator class="thin"/>
+						<grid style="padding: .7em .4em .7em 0">
-						<label value="Syncing of attachment files in group libraries is not currently supported."/>
-						
-						<separator/>
-						
-						<grid id="storage-settings">
 							<columns>
 								<column/>
 								<column flex="1"/>
 							</columns>
 							
 							<rows>
-								<row>
-									<label value="Protocol:"/>
-									<hbox>
-										<menulist id="storage-url-protocol"
-												preference="pref-storage-protocol"
-												onsynctopreference="updateStorageSettings(this.value); unverifyStorageServer();">
-											<menupopup>
-												<menuitem label="WebDAV" value="webdav"/>
-												<!-- TODO: localize -->
-												<menuitem label="WebDAV (Secure)" value="webdavs"/>
-											</menupopup>
-										</menulist>
-									</hbox>
-								</row>
 								<row>
 									<label value="URL:"/>
 									<hbox>
-										<label id="storage-url-prefix"/>
+										<menulist id="storage-url-prefix"
+												preference="pref-storage-scheme"
+												onsynctopreference="unverifyStorageServer()" style="padding: 0; width: 7em">
+											<menupopup>
+												<menuitem label="http" value="http" style="padding: 0"/>
+												<menuitem label="https" value="https" style="padding: 0"/>
+											</menupopup>
+										</menulist>
+										<label value="://"/>
 										<textbox id="storage-url" flex="1"
 											preference="pref-storage-url"
 											onkeypress="if (Zotero.isMac &amp;&amp; event.keyCode == 13) { this.blur(); verifyStorageServer(); }"
@@ -309,7 +295,7 @@ To add a new preference:
 											preference="pref-storage-username"
 											onkeypress="if (Zotero.isMac &amp;&amp; event.keyCode == 13) { this.blur(); setTimeout('verifyStorageServer();', 1); }"
 											onsynctopreference="unverifyStorageServer();"
-											onchange="var pass = document.getElementById('storage-password'); if (pass.value) { Zotero.Sync.Storage.password = pass.value; }"/>
+											onchange="var pass = document.getElementById('storage-password'); if (pass.value) { Zotero.Sync.Storage.Session.WebDAV.prototype.password = pass.value; }"/>
 									</hbox>
 								</row>
 								<row>
@@ -318,7 +304,7 @@ To add a new preference:
 										<textbox id="storage-password" flex="0" type="password"
 											onkeypress="if (Zotero.isMac &amp;&amp; event.keyCode == 13) { this.blur(); setTimeout('verifyStorageServer();', 1); }"
 											oninput="unverifyStorageServer()"
-											onchange="Zotero.Sync.Storage.password = this.value"/>
+											onchange="Zotero.Sync.Storage.Session.WebDAV.prototype.password = this.value"/>
 									</hbox>
 								</row>
 								<row>
@@ -333,6 +319,20 @@ To add a new preference:
 								</row>
 							</rows>
 						</grid>
+						
+						</stack>
+						
+						<separator id="storage-separator" class="thin"/>
+						
+						<!-- Group Libraries -->
+						<checkbox label="Sync attachment files in group libraries using Zotero File Storage"
+								preference="pref-group-storage-enabled"/>
+						
+						<separator class="thin"/>
+						
+						<hbox style="margin-top:.3em">
+							<label class="text-link" style="margin-left: 0" value="About File Syncing" href="http://zotero.org/support/file_sync"/>
+						</hbox>
 					</groupbox>
 				</tabpanel>
 				
@@ -377,7 +377,7 @@ To add a new preference:
 						</groupbox>
 						
 						<groupbox>
-							<caption label="Storage Server"/>
+							<caption label="File Syncing"/>
 							
 							<grid>
 								<columns>
@@ -404,6 +404,8 @@ To add a new preference:
 				</tabpanel>
 			</tabpanels>
 		</tabbox>
+		
+		<separator/>
 	</prefpane>
 	
 	
@@ -492,6 +494,8 @@ To add a new preference:
 				</rows>
 			</grid>
 		</groupbox>
+		
+		<separator/>
 	</prefpane>
 	
 	
@@ -499,21 +503,10 @@ To add a new preference:
 						label="&zotero.preferences.prefpane.export;"
 						image="chrome://zotero/skin/prefs-export.png">
 		<preferences>
-			<preference id="pref-export-citePaperJournalArticleURL" name="extensions.zotero.export.citePaperJournalArticleURL" type="bool"/>
 			<preference id="pref-quickCopy-setting" name="extensions.zotero.export.quickCopy.setting" type="string"/>
 			<preference id="pref-quickCopy-dragLimit" name="extensions.zotero.export.quickCopy.dragLimit" type="int"/>
 		</preferences>
 		
-		<groupbox>
-			<caption label="&zotero.preferences.citationOptions.caption;"/>
-			
-			<checkbox label="&zotero.preferences.export.citePaperJournalArticleURL;" preference="pref-export-citePaperJournalArticleURL"/>
-			<!-- This doesn't wrap without an explicit width, for some reason -->
-			<label id="export-citePaperJournalArticleURL" width="45em">
-				&zotero.preferences.export.citePaperJournalArticleURL.description;
-			</label>
-		</groupbox>
-		
 		<groupbox>
 			<caption label="&zotero.preferences.quickCopy.caption;"/>
 			
@@ -548,23 +541,38 @@ To add a new preference:
 				<button label="+" onclick="showQuickCopySiteEditor()"/>
 			</hbox>
 			
-			<separator/>
-			
 			<!-- TODO: localize -->
 			<hbox align="center">
 				<label value="Disable Quick Copy when dragging more than"/>
 				<textbox preference="pref-quickCopy-dragLimit" size="3"/>
 				<label value="items" flex="1"/>
 			</hbox>
-			
-			<separator/>
 		</groupbox>
+		
+		<groupbox>
+			<caption label="&zotero.preferences.charset;"/>
+			
+			<checkbox id="zotero-export-displayCharsetOption" label="&zotero.preferences.charset.displayExportOption;"
+				preference="pref-export-displayCharsetOption"/>
+			
+			<hbox align="center">
+				<label value="&zotero.preferences.charset.importCharset;:" control="zotero-import-charsetMenu"/>
+				<menulist id="zotero-import-charsetMenu" preference="pref-import-charset"/>
+			</hbox>
+		</groupbox>
+		
+		<separator/>
 	</prefpane>
 	
 	
 	<prefpane id="zotero-prefpane-styles"
 						label="&zotero.preferences.prefpane.styles;"
 						image="chrome://zotero/skin/prefs-styles.png">
+		
+		<preferences>
+			<preference id="pref-styles-citePaperJournalArticleURL" name="extensions.zotero.export.citePaperJournalArticleURL" type="bool"/>
+		</preferences>
+		
 		<groupbox flex="1">
 			<caption label="&zotero.preferences.styles.styleManager;"/>
 			
@@ -579,13 +587,24 @@ To add a new preference:
 				<treechildren id="styleManager-rows"/>
 			</tree>
 			<separator class="thin"/>
-			<hbox pack="end">
+			<hbox align="center" flex="1">
+				<label class="text-link" href="http://www.zotero.org/styles/" value="&zotero.preferences.export.getAdditionalStyles;" flex="1"/>
 				<button disabled="true" id="styleManager-delete" label="-" onclick="deleteStyle()"/>
 				<button label="+" onclick="addStyle()"/>
 			</hbox>
-			<separator/>
-			<label class="text-link" href="http://www.zotero.org/styles/" value="&zotero.preferences.export.getAdditionalStyles;"/>
 		</groupbox>
+		
+		<groupbox>
+			<caption label="&zotero.preferences.citationOptions.caption;"/>
+			
+			<checkbox label="&zotero.preferences.export.citePaperJournalArticleURL;" preference="pref-styles-citePaperJournalArticleURL"/>
+			<!-- This doesn't wrap without an explicit width, for some reason -->
+			<label id="export-citePaperJournalArticleURL" width="45em">
+				&zotero.preferences.export.citePaperJournalArticleURL.description;
+			</label>
+		</groupbox>
+		
+		<separator/>
 	</prefpane>
 	
 	
@@ -621,6 +640,8 @@ To add a new preference:
 				<button label="+" onclick="showProxyEditor()"/>
 			</hbox>
 		</groupbox>
+		
+		<separator/>
 	</prefpane>
 	
 	
@@ -714,6 +735,8 @@ To add a new preference:
 		<checkbox label="&zotero.preferences.keys.overrideGlobal;" preference="pref-keys-overrideGlobal"/>
 		
 		<label class="statusLine" value="&zotero.preferences.keys.changesTakeEffect;"/>
+		
+		<separator/>
 	</prefpane>
 	
 	
@@ -726,6 +749,8 @@ To add a new preference:
 			<preference id="pref-export-displayCharsetOption" name="extensions.zotero.export.displayCharsetOption" type="bool"/>
 			<preference id="pref-debug-output-enableAfterRestart" name="extensions.zotero.debug.store" type="bool"/>
 			<preference id="pref-import-charset" name="extensions.zotero.import.charset" type="string"/>
+			<preference id="pref-openURL-resolver" name="extensions.zotero.openURL.resolver" type="string"/>
+			<preference id="pref-openURL-version" name="extensions.zotero.openURL.version" type="string"/>
 		</preferences>
 		
 		<groupbox>
@@ -750,9 +775,6 @@ To add a new preference:
 			
 			<hbox>
 				<button label="&zotero.preferences.dbMaintenance.integrityCheck;" oncommand="runIntegrityCheck()"/>
-			</hbox>
-			
-			<hbox>
 				<button label="&zotero.preferences.dbMaintenance.resetTranslatorsAndStyles;" oncommand="resetTranslatorsAndStyles()"/>
 			</hbox>
 		</groupbox>
@@ -782,16 +804,38 @@ To add a new preference:
 		</groupbox>
 		
 		<groupbox>
-			<caption label="&zotero.preferences.charset;"/>
+			<caption label="&zotero.preferences.openurl.caption;"/>
-			
-			<checkbox id="zotero-export-displayCharsetOption" label="&zotero.preferences.charset.displayExportOption;"
-				preference="pref-export-displayCharsetOption"/>
 			
 			<hbox align="center">
-				<label value="&zotero.preferences.charset.importCharset;:" control="zotero-import-charsetMenu"/>
+				<!-- vbox prevents some weird vertical stretching of the menulist -->
-				<menulist id="zotero-import-charsetMenu" preference="pref-import-charset"/>
+				<vbox flex="1">
+					<menulist id="openURLMenu" oncommand="onOpenURLSelected();">
+						<menupopup>
+							<menuseparator/>
+							<menuitem label="&zotero.preferences.openurl.custom;" value="custom" selected="true"/>
+						</menupopup>
+					</menulist>
+				</vbox>
+				<button id="openURLSearchButton" label="&zotero.preferences.openurl.search;" oncommand="populateOpenURLResolvers()"/>
+			</hbox>
+			
+			<hbox align="center">
+				<label value="&zotero.preferences.openurl.server;"/>
+				<textbox id="openURLServerField" flex="1" oninput="onOpenURLCustomized();" preference="pref-openURL-resolver"/>
+			</hbox>
+		
+			<hbox align="center">
+				<label value="&zotero.preferences.openurl.version;" control="openURLVersionMenu"/>
+				<menulist id="openURLVersionMenu" oncommand="onOpenURLCustomized();" preference="pref-openURL-version">
+					<menupopup>
+						<menuitem label="0.1" value="0.1"/>
+						<menuitem label="1.0" value="1.0"/>
+					</menupopup>
+				</menulist>
 			</hbox>
 		</groupbox>
+		
+		<separator/>
 	</prefpane>
 	
 	<!-- These mess up the prefwindow (more) if they come before the prefpanes

chrome/content/zotero/xpcom/attachments.js

@@ -43,7 +43,7 @@ Zotero.Attachments = new function(){
 	var self = this;
 	
 	
-	function importFromFile(file, sourceItemID){
+	function importFromFile(file, sourceItemID, libraryID) {
 		Zotero.debug('Importing attachment from file');
 		
 		var title = file.leafName;
@@ -61,6 +61,9 @@ Zotero.Attachments = new function(){
 				var parentItem = Zotero.Items.get(sourceItemID);
 				attachmentItem.libraryID = parentItem.libraryID;
 			}
+			else if (libraryID) {
+				attachmentItem.libraryID = libraryID;
+			}
 			attachmentItem.setField('title', title);
 			attachmentItem.setSource(sourceItemID);
 			attachmentItem.attachmentLinkMode = this.LINK_MODE_IMPORTED_FILE;
@@ -979,6 +982,54 @@ Zotero.Attachments = new function(){
 	}
 	
 	
+	/**
+	 * Returns the number of files in the attachment directory
+	 *
+	 * Only counts if MIME type is text/html
+	 *
+	 * @param	{Zotero.Item}	item	Attachment item
+	 */
+	this.getNumFiles = function (item) {
+		var funcName = "Zotero.Attachments.getNumFiles()";
+		
+		if (!item.isAttachment()) {
+			throw ("Item is not an attachment in " + funcName);
+		}
+		
+		var linkMode = item.attachmentLinkMode;
+		switch (linkMode) {
+			case Zotero.Attachments.LINK_MODE_IMPORTED_URL:
+			case Zotero.Attachments.LINK_MODE_IMPORTED_FILE:
+				break;
+			
+			default:
+				throw ("Invalid attachment link mode in " + funcName);
+		}
+		
+		if (item.attachmentMIMEType != 'text/html') {
+			return 1;
+		}
+		
+		var file = item.getFile();
+		if (!file) {
+			throw ("File not found in " + funcName);
+		}
+		
+		var numFiles = 0;
+		var parentDir = file.parent;
+		var files = parentDir.directoryEntries;
+		while (files.hasMoreElements()) {
+			file = files.getNext();
+			file.QueryInterface(Components.interfaces.nsIFile);
+			if (file.leafName.indexOf('.') == 0) {
+				continue;
+			}
+			numFiles++;
+		}
+		return numFiles;
+	}
+	
+	
 	/**
 	 * @param	{Zotero.Item}	item
 	 * @param	{Boolean}		[skipHidden=FALSE]	Don't count hidden files
@@ -1026,6 +1077,45 @@ Zotero.Attachments = new function(){
 	}
 	
 	
+	/**
+	 * Copy attachment item, including files, to another library
+	 */
+	this.copyAttachmentToLibrary = function (attachment, libraryID, sourceItemID) {
+		var linkMode = attachment.attachmentLinkMode;
+		
+		if (attachment.libraryID == libraryID) {
+			throw ("Attachment is already in library " + libraryID);
+		}
+		
+		var newAttachment = new Zotero.Item('attachment');
+		newAttachment.libraryID = libraryID;
+		// Link mode needs to be set when saving new attachment
+		newAttachment.attachmentLinkMode = linkMode;
+		if (attachment.isImportedAttachment()) {
+			// Attachment path isn't copied over by clone() if libraryID is different
+			newAttachment.attachmentPath = attachment.attachmentPath;
+		}
+		// DEBUG: save here because clone() doesn't currently work on unsaved tagged items
+		var id = newAttachment.save();
+		newAttachment = Zotero.Items.get(id);
+		attachment.clone(false, newAttachment);
+		if (sourceItemID) {
+			newAttachment.setSource(sourceItemID);
+		}
+		newAttachment.save();
+		
+		// Copy over files
+		if (newAttachment.isImportedAttachment()) {
+			var dir = Zotero.Attachments.getStorageDirectory(attachment.id);
+			var newDir = Zotero.Attachments.createDirectoryForItem(newAttachment.id);
+			Zotero.File.copyDirectory(dir, newDir);
+		}
+		
+		attachment.addLinkedItem(newAttachment);
+		return newAttachment.id;
+	}
+	
+	
 	function _getFileNameFromURL(url, mimeType){
 		var nsIURL = Components.classes["@mozilla.org/network/standard-url;1"]
 					.createInstance(Components.interfaces.nsIURL);

chrome/content/zotero/xpcom/collectionTreeView.js

@@ -326,9 +326,14 @@ Zotero.CollectionTreeView.prototype.notify = function(action, type, ids)
 					break;
 				
 				case 'group':
-					if (this._groupRowMap[ids[i]] != null) {
+					//if (this._groupRowMap[ids[i]] != null) {
-						rows.push(this._groupRowMap[ids[i]]);
+					//	rows.push(this._groupRowMap[ids[i]]);
-					}
+					//}
+					
+					// For now, just reload if a group is removed, since otherwise
+					// we'd have to remove collections too
+					this.reload();
+					this.rememberSelection(savedSelection);
 					break;
 			}
 		}
@@ -635,7 +640,7 @@ Zotero.CollectionTreeView.prototype.isSelectable = function (row, col) {
 
 
 Zotero.CollectionTreeView.prototype.__defineGetter__('editable', function () {
-	return this._getItemAtRow(this.selection.currentIndex).isEditable();
+	return this._getItemAtRow(this.selection.currentIndex).editable;
 });
 
 
@@ -1029,16 +1034,15 @@ Zotero.CollectionTreeView.prototype.canDrop = function(row, orient, dragData)
 	{
 		var itemGroup = this._getItemAtRow(row); //the collection we are dragging over
 		
-		if (!itemGroup.isEditable()) {
+		if (!itemGroup.editable) {
 			return false;
 		}
 		
 		if (dataType == 'zotero/item') {
-
 			if(itemGroup.isBucket()) {
 				return true;
 			}
-
+			
 			var ids = data;
 			var items = Zotero.Items.get(ids);
 			var skip = true;
@@ -1048,10 +1052,13 @@ Zotero.CollectionTreeView.prototype.canDrop = function(row, orient, dragData)
 					return false
 				}
 				
-				// TODO: for now, only allow regular items to be dragged to groups
+				if (itemGroup.isWithinGroup() && item.isAttachment()) {
-				if (itemGroup.isWithinGroup() && itemGroup.ref.libraryID != item.libraryID
+					// Linked files can't be added to groups
-						&& !item.isRegularItem()) {
+					if (item.attachmentLinkMode == Zotero.Attachments.LINK_MODE_LINKED_FILE) {
-					return false;
+						return false;
+					}
+					skip = false;
+					continue;
 				}
 				
 				// TODO: for now, skip items that are already linked
@@ -1070,7 +1077,7 @@ Zotero.CollectionTreeView.prototype.canDrop = function(row, orient, dragData)
 					continue;
 				}
 				
-				// Allow drag of group items to library
+				// Allow drag of group items to personal library
 				if (item.libraryID && (itemGroup.isLibrary()
 						|| itemGroup.isCollection() && !itemGroup.isWithinGroup())) {
 					// TODO: for now, skip items that are already linked
@@ -1106,10 +1113,17 @@ Zotero.CollectionTreeView.prototype.canDrop = function(row, orient, dragData)
 			if (itemGroup.isSearch()) {
 				return false;
 			}
-			// Don't allow folder drag
+			if (dataType == 'application/x-moz-file') {
-			if (dataType == 'application/x-moz-file' && data[0].isDirectory()) {
+				// Don't allow folder drag
-				return false;
+				if (data[0].isDirectory()) {
+					return false;
+				}
+				// Don't allow drop if no permissions
+				if (!itemGroup.filesEditable) {
+					return false;
+				}
 			}
+			
 			return true;
 		}
 		else if (dataType == 'zotero/collection') {
@@ -1179,7 +1193,7 @@ Zotero.CollectionTreeView.prototype.drop = function(row, orient)
 		else {
 			var targetLibraryID = null;
 		}
-
+		
 		if(itemGroup.isBucket()) {
 			itemGroup.ref.uploadItems(ids);
 			return;
@@ -1263,12 +1277,19 @@ Zotero.CollectionTreeView.prototype.drop = function(row, orient)
 					*/
 				}
 				
+				// Standalone attachment
+				if (item.isAttachment()) {
+					var id = Zotero.Attachments.copyAttachmentToLibrary(item, targetLibraryID);
+					newIDs.push(id);
+					continue;
+				}
+				
 				// Create new unsaved clone item in target library
 				var newItem = new Zotero.Item(item.itemTypeID);
 				newItem.libraryID = targetLibraryID;
 				// DEBUG: save here because clone() doesn't currently work on unsaved tagged items
 				var id = newItem.save();
-				var newItem = Zotero.Items.get(id);
+				newItem = Zotero.Items.get(id);
 				item.clone(false, newItem);
 				newItem.save();
 				//var id = newItem.save();
@@ -1277,6 +1298,62 @@ Zotero.CollectionTreeView.prototype.drop = function(row, orient)
 				// Record link
 				item.addLinkedItem(newItem);
 				newIDs.push(id);
+				
+				if (item.isNote()) {
+					continue;
+				}
+				
+				// For regular items, add child items if prefs and permissions allow
+				
+				// Child notes
+				if (Zotero.Prefs.get('groups.copyChildNotes')) {
+					var noteIDs = item.getNotes();
+					var notes = Zotero.Items.get(noteIDs);
+					for each(var note in notes) {
+						var newNote = new Zotero.Item('note');
+						newNote.libraryID = targetLibraryID;
+						// DEBUG: save here because clone() doesn't currently work on unsaved tagged items
+						var id = newNote.save();
+						newNote = Zotero.Items.get(id);
+						note.clone(false, newNote);
+						newNote.setSource(newItem.id);
+						newNote.save();
+						
+						note.addLinkedItem(newNote);
+					}
+				}
+				
+				// Child attachments
+				var copyChildLinks = Zotero.Prefs.get('groups.copyChildLinks');
+				var copyChildFileAttachments = Zotero.Prefs.get('groups.copyChildFileAttachments');
+				if (copyChildLinks || copyChildFileAttachments) {
+					var attachmentIDs = item.getAttachments();
+					var attachments = Zotero.Items.get(attachmentIDs);
+					for each(var attachment in attachments) {
+						var linkMode = attachment.attachmentLinkMode;
+						
+						// Skip linked files
+						if (linkMode == Zotero.Attachments.LINK_MODE_LINKED_FILE) {
+							continue;
+						}
+						
+						// Skip imported files if we don't have pref and permissions
+						if (linkMode == Zotero.Attachments.LINK_MODE_LINKED_URL) {
+							if (!copyChildLinks) {
+								Zotero.debug("Skipping child link attachment on drag");
+								continue;
+							}
+						}
+						else {
+							if (!copyChildFileAttachments || !itemGroup.filesEditable) {
+								Zotero.debug("Skipping child file attachment on drag");
+								continue;
+							}
+						}
+						
+						var id = Zotero.Attachments.copyAttachmentToLibrary(attachment, targetLibraryID, newItem.id);
+					}
+				}
 			}
 			
 			if (toReconcile.length) {
@@ -1342,12 +1419,11 @@ Zotero.CollectionTreeView.prototype.drop = function(row, orient)
 		return;
 	}
 	else if (dataType == 'text/x-moz-url' || dataType == 'application/x-moz-file') {
-		// FIXME: temporarily disable dragging in of files
+		if (itemGroup.isWithinGroup()) {
-		if (dataType == 'application/x-moz-file' && itemGroup.isWithinGroup()) {
+			var targetLibraryID = itemGroup.ref.libraryID;
-			var ps = Components.classes["@mozilla.org/embedcomp/prompt-service;1"]
+		}
-									.getService(Components.interfaces.nsIPromptService);
+		else {
-			ps.alert(null, "", "Files cannot currently be added to group libraries.");
+			var targetLibraryID = null;
-			return;
 		}
 		
 		if (itemGroup.isCollection()) {
@@ -1398,7 +1474,7 @@ Zotero.CollectionTreeView.prototype.drop = function(row, orient)
 				
 				try {
 					Zotero.DB.beginTransaction();
-					var itemID = Zotero.Attachments.importFromFile(file, false);
+					var itemID = Zotero.Attachments.importFromFile(file, false, targetLibraryID);
 					if (parentCollectionID) {
 						var col = Zotero.Collections.get(parentCollectionID);
 						if (col) {
@@ -1545,11 +1621,10 @@ Zotero.ItemGroup.prototype.isWithinGroup = function () {
 	return this.ref && !!this.ref.libraryID;
 }
 
-Zotero.ItemGroup.prototype.isEditable = function () {
+Zotero.ItemGroup.prototype.__defineGetter__('editable', function () {
 	if (this.isTrash() || this.isShare()) {
 		return false;
 	}
-	
 	if (!this.isWithinGroup()) {
 		return true;
 	}
@@ -1564,12 +1639,33 @@ Zotero.ItemGroup.prototype.isEditable = function () {
 			var group = Zotero.Groups.get(groupID);
 			return group.editable;
 		}
-		else {
+		throw ("Unknown library type '" + type + "' in Zotero.ItemGroup.editable");
-			throw ("Unknown library type '" + type + "' in Zotero.ItemGroup.isEditable()");
-		}
 	}
-}
+	return false;
+});
 
+Zotero.ItemGroup.prototype.__defineGetter__('filesEditable', function () {
+	if (this.isTrash() || this.isShare()) {
+		return false;
+	}
+	if (!this.isWithinGroup()) {
+		return true;
+	}
+	var libraryID = this.ref.libraryID;
+	if (this.isGroup()) {
+		return this.ref.filesEditable;
+	}
+	if (this.isCollection()) {
+		var type = Zotero.Libraries.getType(libraryID);
+		if (type == 'group') {
+			var groupID = Zotero.Groups.getGroupIDFromLibraryID(libraryID);
+			var group = Zotero.Groups.get(groupID);
+			return group.filesEditable;
+		}
+		throw ("Unknown library type '" + type + "' in Zotero.ItemGroup.filesEditable");
+	}
+	return false;
+});
 
 Zotero.ItemGroup.prototype.getName = function()
 {

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

@@ -327,7 +327,7 @@ Zotero.DataObjects = function (object, objectPlural, id, table) {
 	
 	
 	this.editCheck = function (obj) {
-		if (!Zotero.Sync.Server.syncInProgress && !this.isEditable(obj)) {
+		if (!Zotero.Sync.Server.syncInProgress && !Zotero.Sync.Storage.syncInProgress && !this.isEditable(obj)) {
 			throw ("Cannot edit " + this._ZDO_object + " in read-only Zotero library");
 		}
 	}

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

@@ -286,6 +286,10 @@ Zotero.Group.prototype.save = function () {
 * Deletes group and all descendant objects
 **/
 Zotero.Group.prototype.erase = function() {
+	// Don't send notifications for items and other groups objects that are deleted,
+	// since we're really only removing the group from the client
+	var notifierDisabled = Zotero.Notifier.disable();
+	
 	Zotero.DB.beginTransaction();
 	
 	var sql, ids, obj;
@@ -331,6 +335,9 @@ Zotero.Group.prototype.erase = function() {
 	sql = "DELETE FROM syncDeleteLog WHERE libraryID=?";
 	Zotero.DB.query(sql, this.libraryID);
 	
+	var prefix = "groups/" + this.id;
+	Zotero.Relations.eraseByPathPrefix(prefix);
+	
 	// Delete group
 	sql = "DELETE FROM groups WHERE groupID=?";
 	ids = Zotero.DB.query(sql, this.id)
@@ -342,6 +349,10 @@ Zotero.Group.prototype.erase = function() {
 	
 	Zotero.DB.commitTransaction();
 	
+	if (notifierDisabled) {
+		Zotero.Notifier.enable();
+	}
+	
 	Zotero.Notifier.trigger('delete', 'group', this.id, notifierData);
 }
 

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

@@ -2540,28 +2540,16 @@ Zotero.Item.prototype.getFile = function(row, skipExistsCheck) {
 /**
  * _row_ is optional itemAttachments row if available to skip queries
  */
-Zotero.Item.prototype.getFilename = function (row) {
+Zotero.Item.prototype.getFilename = function () {
 	if (!this.isAttachment()) {
 		throw ("getFileName() can only be called on attachment items in Zotero.Item.getFilename()");
 	}
 	
-	if (!row) {
+	if (this.attachmentLinkMode == Zotero.Attachments.LINK_MODE_LINKED_URL) {
-		var row = {
-			linkMode: this.attachmentLinkMode,
-			path: this.attachmentPath
-		};
-	}
-	
-	if (row.linkMode == Zotero.Attachments.LINK_MODE_LINKED_URL) {
 		throw ("getFilename() cannot be called on link attachments in Zotero.Item.getFilename()");
 	}
 	
-	if (this.isImportedAttachment()) {
+	var file = this.getFile(null, true);
-		var matches = row.path.match("^storage:(.+)$");
-		return matches[1];
-	}
-	
-	var file = this.getFile();
 	if (!file) {
 		return false;
 	}
@@ -2602,10 +2590,12 @@ Zotero.Item.prototype.renameAttachmentFile = function(newName, overwrite) {
 		}
 		
 		file.moveTo(null, newName);
-		// Update mod time so the file syncs
+		// Update mod time and clear hash so the file syncs
 		dest.lastModifiedTime = new Date();
 		this.relinkAttachmentFile(dest);
 		
+		Zotero.Sync.Storage.setSyncedHash(this.id, null, false);
+		
 		return true;
 	}
 	catch (e) {
@@ -2947,6 +2937,32 @@ Zotero.Item.prototype.__defineGetter__('attachmentModificationTime', function ()
 });
 
 
+/**
+ * MD5 hash of an attachment file
+ *
+ * Note: This is the hash of the file itself, not the last-known hash
+ * of the file on the storage server as stored in the database
+ *
+ * @return	{String}		MD5 hash of file as hex string
+ */
+Zotero.Item.prototype.__defineGetter__('attachmentHash', function () {
+	if (!this.isAttachment()) {
+		return undefined;
+	}
+	
+	if (!this.id) {
+		return undefined;
+	}
+	
+	var file = this.getFile();
+	if (!file) {
+		return undefined;
+	}
+	
+	return Zotero.Utilities.prototype.md5(file);
+});
+
+
 /**
  * Return plain text of attachment content
  *

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

@@ -421,7 +421,6 @@ Zotero.Items = new function() {
 				var item = this.get(id);
 				if (!item) {
 					Zotero.debug('Item ' + id + ' does not exist in Items.erase()!', 1);
-					Zotero.Notifier.trigger('delete', 'item', id);
 					continue;
 				}
 				item.erase(eraseChildren); // calls unload()

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

@@ -6,6 +6,7 @@ Zotero.Relations = new function () {
 		owl: 'http://www.w3.org/2002/07/owl#'
 	};
 	
+	var _prefix = "http://zotero.org/";
 	
 	this.get = function (id) {
 		if (typeof id != 'number') {
@@ -76,6 +77,37 @@ Zotero.Relations = new function () {
 	}
 	
 	
+	this.updateUser = function (fromUserID, fromLibraryID, toUserID, toLibraryID) {
+		if (!fromUserID) {
+			throw ("Invalid source userID " + fromUserID + " in Zotero.Relations.updateUserID");
+		}
+		if (!fromLibraryID) {
+			throw ("Invalid source libraryID " + fromLibraryID + " in Zotero.Relations.updateUserID");
+		}
+		if (!toUserID) {
+			throw ("Invalid target userID " + toUserID + " in Zotero.Relations.updateUserID");
+		}
+		if (!toLibraryID) {
+			throw ("Invalid target libraryID " + toLibraryID + " in Zotero.Relations.updateUserID");
+		}
+		
+		Zotero.DB.beginTransaction();
+		
+		var sql = "UPDATE relations SET libraryID=? WHERE libraryID=?";
+		Zotero.DB.query(sql, [fromLibraryID, toLibraryID]);
+		
+		sql = "UPDATE relations SET "
+				+ "subject=REPLACE(subject, 'zotero.org/users/" + fromUserID + "', "
+					+ "'zotero.org/users/" + toUserID + "'), "
+				+ "object=REPLACE(object, 'zotero.org/users/" + fromUserID + "', "
+					+ "'zotero.org/users/" + toUserID + "') "
+					+ "WHERE predicate='owl:sameAs'";
+		Zotero.DB.query(sql);
+		
+		Zotero.DB.commitTransaction();
+	}
+	
+	
 	this.add = function (libraryID, subject, predicate, object) {
 		predicate = _getPrefixAndValue(predicate).join(':');
 		
@@ -109,6 +141,13 @@ Zotero.Relations = new function () {
 	}
 	
 	
+	this.eraseByPathPrefix = function (prefix) {
+		prefix = _prefix + prefix + '%';
+		sql = "DELETE FROM relations WHERE subject LIKE ? OR object LIKE ?";
+		Zotero.DB.query(sql, [prefix, prefix]);
+	}
+	
+	
 	this.xmlToRelation = function (xml) {
 		var relation = new Zotero.Relation;
 		var libraryID = xml.@libraryID.toString();

chrome/content/zotero/xpcom/db.js

@@ -421,7 +421,9 @@ Zotero.DBConnection.prototype.getLastErrorString = function () {
 Zotero.DBConnection.prototype.beginTransaction = function () {
 	// TODO: limit to Zotero.DB, not all Zotero.DBConnections?
 	if (Zotero.waiting) {
-		throw ("Cannot access database layer during active Zotero.wait()");
+		var msg = "Cannot access database layer during active Zotero.wait()";
+		Zotero.debug(msg, 2);
+		throw (msg);
 	}
 	
 	var db = this._getDBConnection();

chrome/content/zotero/xpcom/error.js

@@ -1,6 +1,7 @@
-Zotero.Error = function (message, error) {
+Zotero.Error = function (message, error, data) {
 	this.name = "ZOTERO_ERROR";
 	this.message = message;
+	this.data = data;
 	if (parseInt(error) == error) {
 		this.error = error;
 	}
@@ -14,6 +15,11 @@ Zotero.Error.ERROR_MISSING_OBJECT = 1;
 Zotero.Error.ERROR_FULL_SYNC_REQUIRED = 2;
 Zotero.Error.ERROR_SYNC_USERNAME_NOT_SET = 3;
 Zotero.Error.ERROR_INVALID_SYNC_LOGIN = 4;
+Zotero.Error.ERROR_ZFS_OVER_QUOTA = 5;
+Zotero.Error.ERROR_ZFS_UPLOAD_QUEUE_LIMIT = 6;
+Zotero.Error.ERROR_ZFS_FILE_EDITING_DENIED = 7;
+//Zotero.Error.ERROR_SYNC_EMPTY_RESPONSE_FROM_SERVER = 6;
+//Zotero.Error.ERROR_SYNC_INVALID_RESPONSE_FROM_SERVER = 7;
 
 Zotero.Error.prototype.toString = function () {
 	return this.message;

chrome/content/zotero/xpcom/file.js

@@ -148,25 +148,6 @@ Zotero.File = new function(){
 	}
 	
 	
-	/**
-	 * @param	{nsIFile}	file
-	 * @return	{String}			Base-64 representation of MD5 hash
-	 */
-	this.getFileHash = function (file) {
-		var fis = Components.classes["@mozilla.org/network/file-input-stream;1"]
-					.createInstance(Components.interfaces.nsIFileInputStream);
-		fis.init(file, -1, -1, false);
-		
-		var hash = Components.classes["@mozilla.org/security/hash;1"].
-				createInstance(Components.interfaces.nsICryptoHash);
-		hash.init(Components.interfaces.nsICryptoHash.MD5);
-		hash.updateFromStream(fis, 4294967295); // PR_UINT32_MAX
-		hash = hash.finish(true);
-		fis.close();
-		return hash;
-	}
-	
-	
 	/*
 	 * Write string to a file, overwriting existing file if necessary
 	 */
@@ -199,6 +180,19 @@ Zotero.File = new function(){
 	}
 	
 	
+	/**
+	 * Copies all files from dir into newDir
+	 */
+	this.copyDirectory = function (dir, newDir) {
+		var otherFiles = dir.directoryEntries;
+		while (otherFiles.hasMoreElements()) {
+			var file = otherFiles.getNext();
+			file.QueryInterface(Components.interfaces.nsIFile);
+			file.copyTo(newDir, null);
+		}
+	}
+	
+	
 	this.createDirectoryIfMissing = function (dir) {
 		if (!dir.exists() || !dir.isDirectory()) {
 			if (dir.exists() && !dir.isDirectory()) {

chrome/content/zotero/xpcom/itemTreeView.js

@@ -2218,16 +2218,8 @@ Zotero.ItemTreeView.prototype.drop = function(row, orient)
 		}
 	}
 	else if (dataType == 'text/x-moz-url' || dataType == 'application/x-moz-file') {
-		// FIXME: temporarily disable dragging in of files
-		if (dataType == 'application/x-moz-file' && itemGroup.isWithinGroup()) {
-			var ps = Components.classes["@mozilla.org/embedcomp/prompt-service;1"]
-									.getService(Components.interfaces.nsIPromptService);
-			ps.alert(null, "", "Files cannot currently be added to group libraries.");
-			return;
-		}
-		
 		// Disallow drop into read-only libraries
-		if (!itemGroup.isEditable()) {
+		if (!itemGroup.editable) {
 			var wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
 					   .getService(Components.interfaces.nsIWindowMediator);
 			var win = wm.getMostRecentWindow("navigator:browser");
@@ -2235,6 +2227,13 @@ Zotero.ItemTreeView.prototype.drop = function(row, orient)
 			return;
 		}
 		
+		if (itemGroup.isWithinGroup()) {
+			var targetLibraryID = itemGroup.ref.libraryID;
+		}
+		else {
+			var targetLibraryID = null;
+		}
+		
 		var sourceItemID = false;
 		var parentCollectionID = false;
 		
@@ -2245,9 +2244,6 @@ Zotero.ItemTreeView.prototype.drop = function(row, orient)
 		else if (itemGroup.isCollection()) {
 			var parentCollectionID = itemGroup.ref.id;
 		}
-		else if (itemGroup.isLibrary(true)) {
-			var libraryID = itemGroup.ref.libraryID;
-		}
 		
 		var unlock = Zotero.Notifier.begin(true);
 		try {
@@ -2278,15 +2274,10 @@ Zotero.ItemTreeView.prototype.drop = function(row, orient)
 					
 					// Still string, so remote URL
 					if (typeof file == 'string') {
-						if (sourceItemID) {
+						var wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
-							Zotero.Attachments.importFromURL(url, sourceItemID);
+								   .getService(Components.interfaces.nsIWindowMediator);
-						}
+						var win = wm.getMostRecentWindow("navigator:browser");
-						else {
+						win.ZoteroPane.addItemFromURL(url, 'temporaryPDFHack', row); // TODO: don't do this
-							var wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
-									   .getService(Components.interfaces.nsIWindowMediator);
-							var win = wm.getMostRecentWindow("navigator:browser");
-							win.ZoteroPane.addItemFromURL(url, 'temporaryPDFHack'); // TODO: don't do this
-						}
 						continue;
 					}
 					
@@ -2295,7 +2286,7 @@ Zotero.ItemTreeView.prototype.drop = function(row, orient)
 				
 				try {
 					Zotero.DB.beginTransaction();
-					var itemID = Zotero.Attachments.importFromFile(file, sourceItemID);
+					var itemID = Zotero.Attachments.importFromFile(file, sourceItemID, targetLibraryID);
 					if (parentCollectionID) {
 						var col = Zotero.Collections.get(parentCollectionID);
 						if (col) {

chrome/content/zotero/xpcom/schema.js

@@ -2451,6 +2451,21 @@ Zotero.Schema = new function(){
 					Zotero.DB.query("CREATE INDEX IF NOT EXISTS itemData_fieldID ON itemData(fieldID)");
 				}
 				
+				if (i==63) {
+					Zotero.DB.query("ALTER TABLE itemAttachments ADD COLUMN storageHash TEXT");
+					
+					var protocol = Zotero.Prefs.get('sync.storage.protocol');
+					if (protocol == 'webdav') {
+						Zotero.Prefs.set('sync.storage.scheme', 'http');
+					}
+					else {
+						Zotero.Prefs.set('sync.storage.protocol', 'webdav');
+						Zotero.Prefs.set('sync.storage.scheme', 'https');
+					}
+					
+					Zotero.DB.query("UPDATE version SET schema='storage_webdav' WHERE schema='storage'");
+				}
+				
 				Zotero.wait();
 			}
 			

chrome/content/zotero/xpcom/storage/session.js

@@ -0,0 +1,166 @@
+Zotero.Sync.Storage.Session = function (module, callbacks) {
+	switch (module) {
+		case 'webdav':
+			this._session = new Zotero.Sync.Storage.Session.WebDAV(callbacks);
+			break;
+			
+		case 'zfs':
+			this._session = new Zotero.Sync.Storage.Session.ZFS(callbacks);
+			break;
+		
+		default:
+			throw ("Invalid storage session module '" + module + "'");
+	}
+	
+	this.module = module;
+	this.onError = callbacks.onError;
+}
+
+Zotero.Sync.Storage.Session.prototype.__defineGetter__('name', function () this._session.name);
+Zotero.Sync.Storage.Session.prototype.__defineGetter__('includeUserFiles', function () this._session.includeUserFiles);
+Zotero.Sync.Storage.Session.prototype.__defineGetter__('includeGroupFiles', function () this._session.includeGroupFiles);
+
+Zotero.Sync.Storage.Session.prototype.__defineGetter__('enabled', function () {
+	try {
+		return this._session.enabled;
+	}
+	catch (e) {
+		this.onError(e);
+	}
+});
+
+Zotero.Sync.Storage.Session.prototype.__defineGetter__('verified', function () {
+	try {
+		return this._session.verified;
+	}
+	catch (e) {
+		this.onError(e);
+	}
+});
+
+Zotero.Sync.Storage.Session.prototype.__defineGetter__('active', function () {
+	try {
+		return this._session.active;
+	}
+	catch (e) {
+		this.onError(e);
+	}
+});
+
+Zotero.Sync.Storage.Session.prototype.__defineGetter__('username', function () {
+	try {
+		return this._session.username;
+	}
+	catch (e) {
+		this.onError(e);
+	}
+});
+
+Zotero.Sync.Storage.Session.prototype.__defineGetter__('password', function () {
+	try {
+		return this._session.password;
+	}
+	catch (e) {
+		this.onError(e);
+	}
+});
+
+Zotero.Sync.Storage.Session.prototype.__defineSetter__('password', function (val) {
+	try {
+		this._session.password = val;
+	}
+	catch (e) {
+		this.onError(e);
+	}
+});
+
+
+Zotero.Sync.Storage.Session.prototype.initFromPrefs = function () {
+	try {
+		return this._session.init();
+	}
+	catch (e) {
+		this.onError(e);
+	}
+}
+
+Zotero.Sync.Storage.Session.prototype.initFromPrefs = function () {
+	try {
+		return this._session.initFromPrefs();
+	}
+	catch (e) {
+		this.onError(e);
+	}
+}
+
+Zotero.Sync.Storage.Session.prototype.downloadFile = function (request) {
+	try {
+		this._session.downloadFile(request);
+	}
+	catch (e) {
+		this.onError(e);
+	}
+}
+
+Zotero.Sync.Storage.Session.prototype.uploadFile = function (request) {
+	try {
+		this._session.uploadFile(request);
+	}
+	catch (e) {
+		this.onError(e);
+	}
+}
+
+Zotero.Sync.Storage.Session.prototype.getLastSyncTime = function (callback) {
+	try {
+		this._session.getLastSyncTime(callback);
+	}
+	catch (e) {
+		this.onError(e);
+	}
+}
+
+Zotero.Sync.Storage.Session.prototype.setLastSyncTime = function (callback, useLastSyncTime) {
+	try {
+		this._session.setLastSyncTime(callback, useLastSyncTime);
+	}
+	catch (e) {
+		this.onError(e);
+	}
+}
+
+Zotero.Sync.Storage.Session.prototype.checkServer = function (callback) {
+	try {
+		this._session.checkServer(callback);
+	}
+	catch (e) {
+		this.onError(e);
+	}
+}
+
+Zotero.Sync.Storage.Session.prototype.checkServerCallback = function (uri, status, authRequired, window, skipSuccessMessage) {
+	try {
+		return this._session.checkServerCallback(uri, status, authRequired, window, skipSuccessMessage);
+	}
+	catch (e) {
+		this.onError(e);
+	}
+}
+
+Zotero.Sync.Storage.Session.prototype.purgeDeletedStorageFiles = function (callback) {
+	try {
+		this._session.purgeDeletedStorageFiles(callback);
+	}
+	catch (e) {
+		this.onError(e);
+	}
+}
+
+Zotero.Sync.Storage.Session.prototype.purgeOrphanedStorageFiles = function (callback) {
+	try {
+		this._session.purgeOrphanedStorageFiles(callback);
+	}
+	catch (e) {
+		this.onError(e);
+	}
+}

chrome/content/zotero/xpcom/storage/zfs.js

@@ -0,0 +1,852 @@
+Zotero.Sync.Storage.Session.ZFS = function (callbacks) {
+	this.onChangesMade = callbacks.onChangesMade ? callbacks.onChangesMade : function () {};
+	this.onError = callbacks.onError ? callbacks.onError : function () {};
+	
+	this._rootURI;
+	this._userURI;
+	this._cachedCredentials = false;
+	this._lastSyncTime = null;
+}
+
+Zotero.Sync.Storage.Session.ZFS.prototype.name = "ZFS";
+
+Zotero.Sync.Storage.Session.ZFS.prototype.__defineGetter__('includeUserFiles', function () {
+	return Zotero.Prefs.get("sync.storage.enabled") && Zotero.Prefs.get("sync.storage.protocol") == 'zotero';
+});
+
+Zotero.Sync.Storage.Session.ZFS.prototype.__defineGetter__('includeGroupFiles', function () {
+	return Zotero.Prefs.get("sync.storage.groups.enabled");
+});
+
+Zotero.Sync.Storage.Session.ZFS.prototype.__defineGetter__('enabled', function () {
+	return this.includeUserFiles || this.includeGroupFiles;
+});
+
+Zotero.Sync.Storage.Session.ZFS.prototype.__defineGetter__('active', function () {
+	return this.enabled;
+});
+
+
+Zotero.Sync.Storage.Session.ZFS.prototype.__defineGetter__('rootURI', function () {
+	if (!this._rootURI) {
+		throw ("Root URI not initialized in Zotero.Sync.Storage.Session.ZFS.rootURI");
+	}
+	return this._rootURI.clone();
+});
+
+Zotero.Sync.Storage.Session.ZFS.prototype.__defineGetter__('userURI', function () {
+	if (!this._userURI) {
+		throw ("User URI not initialized in Zotero.Sync.Storage.Session.ZFS.userURI");
+	}
+	return this._userURI.clone();
+});
+
+Zotero.Sync.Storage.Session.ZFS.prototype.init = function (url, username, password) {
+	var ios = Components.classes["@mozilla.org/network/io-service;1"].
+				getService(Components.interfaces.nsIIOService);
+	try {
+		var uri = ios.newURI(url, null, null);
+		if (username) {
+			uri.username = username;
+			uri.password = password;
+		}
+	}
+	catch (e) {
+		Zotero.debug(e);
+		Components.utils.reportError(e);
+		return false;
+	}
+	this._rootURI = uri;
+	
+	uri = uri.clone();
+	uri.spec += 'users/' + Zotero.userID + '/';
+	this._userURI = uri;
+	
+	return true;
+}
+
+
+Zotero.Sync.Storage.Session.ZFS.prototype.initFromPrefs = function () {
+	var url = ZOTERO_CONFIG.API_URL;
+	var username = Zotero.Sync.Server.username;
+	var password = Zotero.Sync.Server.password;
+	return this.init(url, username, password);
+}
+
+
+/**
+ * Get file metadata on storage server
+ *
+ * @param	{Zotero.Item}	item
+ * @param	{Function}		callback		Callback f(item, etag)
+ */
+Zotero.Sync.Storage.Session.ZFS.prototype._getStorageFileInfo = function (item, callback) {
+	var uri = this._getItemURI(item);
+	
+	var self = this;
+	
+	Zotero.Utilities.HTTP.doHead(uri, function (req) {
+		var funcName = "Zotero.Sync.Storage.Session.ZFS._getStorageFileInfo()";
+		
+		if (req.status == 404) {
+			callback(item, false);
+			return;
+		}
+		else if (req.status != 200) {
+			Zotero.debug(req.responseText);
+			self.onError("Unexpected status code " + req.status + " in " + funcName);
+			return;
+		}
+		
+		var info = {};
+		info.hash = req.getResponseHeader('ETag');
+		info.filename = req.getResponseHeader('X-Zotero-Filename');
+		info.mtime = req.getResponseHeader('X-Zotero-Modification-Time');
+		info.compressed = req.getResponseHeader('X-Zotero-Compressed') == 'Yes';
+		Zotero.debug(info);
+		
+		if (!info) {
+			callback(item, false);
+			return;
+		}
+		
+		callback(item, info);
+	});
+}
+
+
+/**
+ * Begin download process for individual file
+ *
+ * @param	{Zotero.Sync.Storage.Request}	[request]
+ */
+Zotero.Sync.Storage.Session.ZFS.prototype.downloadFile = function (request) {
+	var item = Zotero.Sync.Storage.getItemFromRequestName(request.name);
+	if (!item) {
+		throw ("Item '" + request.name + "' not found in Zotero.Sync.Storage.Session.ZFS.downloadFile()");
+	}
+	
+	var self = this;
+	
+	// Retrieve file info from server to store locally afterwards
+	this._getStorageFileInfo(item, function (item, info) {
+		if (!request.isRunning()) {
+			Zotero.debug("Download request '" + request.name
+				+ "' is no longer running after getting remote file info");
+			return;
+		}
+		
+		if (!info) {
+			Zotero.debug("Remote file not found for item " + item.libraryID + "/" + item.key);
+			request.finish();
+			return;
+		}
+		
+		try {
+			var syncModTime = info.mtime;
+			var syncHash = info.hash;
+			
+			var file = item.getFile();
+			// Skip download if local file exists and matches mod time
+			if (file && file.exists()) {
+				if (syncModTime == Math.round(file.lastModifiedTime / 1000)) {
+					Zotero.debug("File mod time matches remote file -- skipping download");
+					
+					Zotero.DB.beginTransaction();
+					var syncState = Zotero.Sync.Storage.getSyncState(item.id);
+					//var updateItem = syncState != 1;
+					var updateItem = false;
+					Zotero.Sync.Storage.setSyncedModificationTime(item.id, syncModTime, updateItem);
+					Zotero.Sync.Storage.setSyncState(item.id, Zotero.Sync.Storage.SYNC_STATE_IN_SYNC);
+					Zotero.DB.commitTransaction();
+					self.onChangesMade();
+					request.finish();
+					return;
+				}
+				// If not compressed, check hash, in case only timestamp changed
+				else if (!info.compressed && Zotero.Utilities.prototype.md5(file) == syncHash) {
+					Zotero.debug("File hash matches remote file -- skipping download");
+					
+					Zotero.DB.beginTransaction();
+					var syncState = Zotero.Sync.Storage.getSyncState(item.id);
+					//var updateItem = syncState != 1;
+					var updateItem = false;
+					if (!info.compressed) {
+						Zotero.Sync.Storage.setSyncedHash(item.id, syncHash, false);
+					}
+					Zotero.Sync.Storage.setSyncedModificationTime(item.id, syncModTime, updateItem);
+					Zotero.Sync.Storage.setSyncState(item.id, Zotero.Sync.Storage.SYNC_STATE_IN_SYNC);
+					Zotero.DB.commitTransaction();
+					self.onChangesMade();
+					request.finish();
+					return;
+				}
+			}
+			
+			var destFile = Zotero.getTempDirectory();
+			if (info.compressed) {
+				destFile.append(item.key + '.zip.tmp');
+			}
+			else {
+				destFile.append(item.key + '.tmp');
+				if (destFile.exists()) {
+					destFile.remove(false);
+				}
+			}
+			if (destFile.exists()) {
+				destFile.remove(false);
+			}
+			
+			var listener = new Zotero.Sync.Storage.StreamListener(
+				{
+					onStart: function (request, data) {
+						if (data.request.isFinished()) {
+							Zotero.debug("Download request " + data.request.name
+								+ " stopped before download started -- closing channel");
+							request.cancel(0x804b0002); // NS_BINDING_ABORTED
+							return;
+						}
+					},
+					onProgress: function (a, b, c) {
+						request.onProgress(a, b, c)
+					},
+					onStop: function (request, status, response, data) {
+						if (status != 200) {
+							self.onError("Unexpected status code " + status
+								+ " for request " + data.request.name + " in Zotero.Sync.Storage.Session.ZFS.downloadFile()");
+							return;
+						}
+						
+						// Don't try to process if the request has been cancelled
+						if (data.request.isFinished()) {
+							Zotero.debug("Download request " + data.request.name
+								+ " is no longer running after file download");
+							return;
+						}
+						
+						Zotero.debug("Finished download of " + destFile.path);
+						
+						try {
+							Zotero.Sync.Storage.processDownload(data);
+							data.request.finish();
+						}
+						catch (e) {
+							self.onError(e);
+						}
+					},
+					request: request,
+					item: item,
+					compressed: info.compressed,
+					syncModTime: syncModTime,
+					syncHash: syncHash
+				}
+			);
+			
+			var uri = self._getItemURI(item);
+			
+			// Don't display password in console
+			var disp = uri.clone();
+			if (disp.password) {
+				disp.password = "********";
+			}
+			
+			Zotero.debug('Saving ' + disp.spec + ' with saveURI()');
+			const nsIWBP = Components.interfaces.nsIWebBrowserPersist;
+			var wbp = Components
+				.classes["@mozilla.org/embedding/browser/nsWebBrowserPersist;1"]
+				.createInstance(nsIWBP);
+			wbp.persistFlags = nsIWBP.PERSIST_FLAGS_BYPASS_CACHE;
+			
+			wbp.progressListener = listener;
+			wbp.saveURI(uri, null, null, null, null, destFile);
+		}
+		catch (e) {
+			self.onError(e);
+		}
+	});
+}
+
+
+Zotero.Sync.Storage.Session.ZFS.prototype.uploadFile = function (request) {
+	var self = this;
+	var item = Zotero.Sync.Storage.getItemFromRequestName(request.name);
+	if (Zotero.Attachments.getNumFiles(item) > 1) {
+		Zotero.Sync.Storage.createUploadFile(request, function (data) { self._processUploadFile(data); });
+	}
+	else {
+		this._processUploadFile({ request: request });
+	}
+}
+
+
+/**
+ * Upload the file to the server
+ *
+ * @param	{Object}		Object with 'request' property
+ * @return	{void}
+ */
+Zotero.Sync.Storage.Session.ZFS.prototype._processUploadFile = function (data) {
+	/*
+	_updateSizeMultiplier(
+		(100 - Zotero.Sync.Storage.compressionTracker.ratio) / 100
+	);
+	*/
+	
+	var request = data.request;
+	var item = Zotero.Sync.Storage.getItemFromRequestName(request.name);
+	
+	var self = this;
+	
+	this._getStorageFileInfo(item, function (item, info) {
+		if (request.isFinished()) {
+			Zotero.debug("Upload request '" + request.name
+				+ "' is no longer running after getting file info");
+			return;
+		}
+		
+		try {
+			// Check for conflict
+			if (Zotero.Sync.Storage.getSyncState(item.id)
+					!= Zotero.Sync.Storage.SYNC_STATE_FORCE_UPLOAD) {
+				if (info) {
+					// Remote mod time
+					var mtime = info.mtime;
+					// Local file time
+					var fmtime = item.attachmentModificationTime;
+					
+					if (fmtime == mtime) {
+						Zotero.debug("File mod time matches remote file -- skipping upload");
+						
+						Zotero.debug(Zotero.Sync.Storage.getSyncedModificationTime(item.id));
+						
+						Zotero.DB.beginTransaction();
+						var syncState = Zotero.Sync.Storage.getSyncState(item.id);
+						//Zotero.Sync.Storage.setSyncedModificationTime(item.id, fmtime, true);
+						Zotero.Sync.Storage.setSyncedModificationTime(item.id, fmtime);
+						Zotero.Sync.Storage.setSyncState(item.id, Zotero.Sync.Storage.SYNC_STATE_IN_SYNC);
+						Zotero.DB.commitTransaction();
+						self.onChangesMade();
+						request.finish();
+						return;
+					}
+					
+					var smtime = Zotero.Sync.Storage.getSyncedModificationTime(item.id);
+					if (smtime != mtime) {
+						var localData = { modTime: fmtime };
+						var remoteData = { modTime: mtime };
+						Zotero.Sync.Storage.QueueManager.addConflict(
+							request.name, localData, remoteData
+						);
+						Zotero.debug("Conflict -- last synced file mod time "
+							+ "does not match time on storage server"
+							+ " (" + smtime + " != " + mtime + ")");
+						request.finish();
+						return;
+					}
+				}
+				else {
+					Zotero.debug("Remote file not found for item " + item.id);
+				}
+			}
+			
+			self._getFileUploadParameters(
+				item,
+				function (item, target, uploadKey, params) {
+					try {
+						self._postFile(request, item, target, uploadKey, params);
+					}
+					catch (e) {
+						self.onError(e);
+					}
+				},
+				function () {
+					self._updateItemFileInfo(item);
+					request.finish();
+				}
+			);
+		}
+		catch (e) {
+			self.onError(e);
+		}
+	});
+}
+
+
+/**
+ * Get mod time of file on storage server
+ *
+ * @param	{Zotero.Item}					item
+ * @param	{Function}		uploadCallback					Callback f(request, item, target, params)
+ * @param	{Function}		existsCallback					Callback f() to call when file already exists
+ *																on server and uploading isn't necessary
+ */
+Zotero.Sync.Storage.Session.ZFS.prototype._getFileUploadParameters = function (item, uploadCallback, existsCallback) {
+	var uri = this._getItemURI(item);
+	
+	if (Zotero.Attachments.getNumFiles(item) > 1) {
+		var file = Zotero.getTempDirectory();
+		var filename = item.key + '.zip';
+		file.append(filename);
+		uri.spec = uri.spec;
+		var zip = true;
+	}
+	else {
+		var file = item.getFile();
+		var filename = file.leafName;
+		var zip = false;
+	}
+	
+	var mtime = item.attachmentModificationTime;
+	var hash = Zotero.Utilities.prototype.md5(file);
+	
+	var body = "md5=" + hash + "&filename=" + encodeURIComponent(filename)
+				+ "&filesize=" + file.fileSize + "&mtime=" + mtime;
+	if (zip) {
+		body += "&zip=1";
+	}
+	
+	var self = this;
+	
+	Zotero.Utilities.HTTP.doPost(uri, body, function (req) {
+		var funcName = "Zotero.Sync.Storage.Session.ZFS._getFileUploadParameters()";
+		
+		if (req.status == 413) {
+			var retry = req.getResponseHeader('Retry-After');
+			if (retry) {
+				var minutes = Math.round(retry / 60);
+				var e = new Zotero.Error("You have too many queued uploads. Please try again in " + minutes + " minutes.", "ZFS_UPLOAD_QUEUE_LIMIT");
+				self.onError(e);
+			}
+			else {
+				Zotero.debug(req.responseText);
+				var e = new Zotero.Error("File would exceed Zotero File Storage quota", "ZFS_OVER_QUOTA");
+				self.onError(e);
+			}
+			return;
+		}
+		else if (req.status == 403) {
+			Zotero.debug(req.responseText);
+			
+			var groupID = Zotero.Groups.getGroupIDFromLibraryID(item.libraryID);
+			var e = new Zotero.Error("File editing denied for group", "ZFS_FILE_EDITING_DENIED", { groupID: groupID });
+			self.onError(e);
+			return;
+		}
+		else if (req.status != 200) {
+			Zotero.debug(req.responseText);
+			self.onError("Unexpected status code " + req.status + " in " + funcName);
+			return;
+		}
+		
+		Zotero.debug(req.responseText);
+		
+		try {
+			// Strip XML declaration and convert to E4X
+			var xml = new XML(req.responseText.replace(/<\?xml.*\?>/, ''));
+		}
+		catch (e) {
+			self.onError("Invalid response retrieving file upload parameters");
+			return;
+		}
+		
+		if (xml.name() != 'upload' && xml.name() != 'exists') {
+			self.onError("Invalid response retrieving file upload parameters");
+			return;
+		}
+		// File was already available, so uploading isn't required
+		if (xml.name() == 'exists') {
+			existsCallback();
+			return;
+		}
+		
+		var url = xml.url.toString();
+		var uploadKey = xml.key.toString();
+		var params = {}, p = '';
+		for each(var param in xml.params.children()) {
+			params[param.name()] = param.toString();
+		}
+		Zotero.debug(params);
+		uploadCallback(item, url, uploadKey, params);
+	});
+}
+
+
+Zotero.Sync.Storage.Session.ZFS.prototype._postFile = function (request, item, url, uploadKey, params) {
+	if (request.isFinished()) {
+		Zotero.debug("Upload request " + request.name + " is no longer running after getting upload parameters");
+		return;
+	}
+	
+	var file = this._getUploadFile(item);
+	
+	// TODO: make sure this doesn't appear in file
+	var boundary = "---------------------------" + Math.random().toString().substr(2);
+	
+	var mis = Components.classes["@mozilla.org/io/multiplex-input-stream;1"]
+				.createInstance(Components.interfaces.nsIMultiplexInputStream);
+	
+	// Add parameters
+	for (var key in params) {
+		var storage = Components.classes["@mozilla.org/storagestream;1"]
+						.createInstance(Components.interfaces.nsIStorageStream);
+		storage.init(4096, 4294967295, null); // PR_UINT32_MAX
+		var out = storage.getOutputStream(0);
+		
+		var conv = Components.classes["@mozilla.org/intl/converter-output-stream;1"]
+						.createInstance(Components.interfaces.nsIConverterOutputStream);
+		conv.init(out, null, 4096, "?");
+		
+		var str = "--" + boundary + '\r\nContent-Disposition: form-data; name="' + key + '"'
+					+ '\r\n\r\n' + params[key] + '\r\n';
+		conv.writeString(str);
+		conv.close();
+		
+		var instr = storage.newInputStream(0);
+		mis.appendStream(instr);
+	}
+	
+	// Add file
+	var sis = Components.classes["@mozilla.org/io/string-input-stream;1"]
+				.createInstance(Components.interfaces.nsIStringInputStream);
+	var str = "--" + boundary + '\r\nContent-Disposition: form-data; name="file"\r\n\r\n';
+	sis.setData(str, -1);
+	mis.appendStream(sis);
+	
+	var fis = Components.classes["@mozilla.org/network/file-input-stream;1"]
+				.createInstance(Components.interfaces.nsIFileInputStream);
+	fis.init(file, 0x01, 0, Components.interfaces.nsIFileInputStream.CLOSE_ON_EOF);
+	
+	var bis = Components.classes["@mozilla.org/network/buffered-input-stream;1"]
+				.createInstance(Components.interfaces.nsIBufferedInputStream)
+	bis.init(fis, 64 * 1024);
+	mis.appendStream(bis);
+	
+	// End request
+	var sis = Components.classes["@mozilla.org/io/string-input-stream;1"]
+				.createInstance(Components.interfaces.nsIStringInputStream);
+	var str = "\r\n--" + boundary + "--";
+	sis.setData(str, -1);
+	mis.appendStream(sis);
+	
+	
+/*	var cstream = Components.classes["@mozilla.org/intl/converter-input-stream;1"].
+	createInstance(Components.interfaces.nsIConverterInputStream);
+	cstream.init(mis, "UTF-8", 0, 0); // you can use another encoding here if you wish
+	
+	let (str = {}) {
+		cstream.readString(-1, str); // read the whole file and put it in str.value
+		data = str.value;
+	}
+	cstream.close(); // this closes fstream
+	alert(data);
+*/	
+	
+	var ios = Components.classes["@mozilla.org/network/io-service;1"].
+				getService(Components.interfaces.nsIIOService);
+	var uri = ios.newURI(url, null, null);
+	var channel = ios.newChannelFromURI(uri);
+	
+	channel.QueryInterface(Components.interfaces.nsIUploadChannel);
+	channel.setUploadStream(mis, "multipart/form-data", -1);
+	channel.QueryInterface(Components.interfaces.nsIHttpChannel);
+	channel.requestMethod = 'POST';
+	channel.allowPipelining = false;
+	channel.setRequestHeader('Keep-Alive', '', false);
+	channel.setRequestHeader('Connection', '', false);
+	channel.setRequestHeader("Content-Type", "multipart/form-data; boundary=" + boundary, false);
+	//channel.setRequestHeader('Date', date, false);
+	
+	var self = this;
+	
+	request.setChannel(channel);
+	
+	var listener = new Zotero.Sync.Storage.StreamListener(
+		{
+			onProgress: function (a, b, c) {
+				request.onProgress(a, b, c);
+			},
+			onStop: function (httpRequest, status, response, data) { self._onUploadComplete(httpRequest, status, response, data); },
+			onCancel: function (httpRequest, status, data) { self._onUploadCancel(httpRequest, status, data); },
+			request: request,
+			item: item,
+			uploadKey: uploadKey,
+			streams: [mis]
+		}
+	);
+	channel.notificationCallbacks = listener;
+	
+	var dispURI = uri.clone();
+	if (dispURI.password) {
+		dispURI.password = '********';
+	}
+	Zotero.debug("HTTP POST of " + file.leafName + " to " + dispURI.spec);
+	
+	channel.asyncOpen(listener, null);
+}
+
+
+Zotero.Sync.Storage.Session.ZFS.prototype._onUploadComplete = function (httpRequest, status, response, data) {
+	var request = data.request;
+	var item = data.item;
+	var uploadKey = data.uploadKey;
+	
+	Zotero.debug("Upload of attachment " + item.key
+		+ " finished with status code " + status);
+	
+	Zotero.debug(response);
+	
+	switch (status) {
+		case 201:
+			break;
+		
+		default:
+			this.onError("Unexpected file upload status " + status
+				+ " in Zotero.Sync.Storage._onUploadComplete()");
+			return;
+	}
+	
+	var uri = this._getItemURI(item);
+	var body = "update=" + uploadKey + "&mtime=" + item.attachmentModificationTime;
+	
+	var self = this;
+	
+	// Register upload on server
+	Zotero.Utilities.HTTP.doPost(uri, body, function (req) {
+		Zotero.debug(req.responseText);
+		
+		if (req.status != 204) {
+			self.onError("Unexpected file registration status " + status
+				+ " in Zotero.Sync.Storage._onUploadComplete()");
+			return;
+		}
+		
+		self._updateItemFileInfo(item);
+		request.finish();
+	});
+}
+
+
+Zotero.Sync.Storage.Session.ZFS.prototype._updateItemFileInfo = function (item) {
+	// Mark as changed locally
+	Zotero.DB.beginTransaction();
+	Zotero.Sync.Storage.setSyncState(item.id, Zotero.Sync.Storage.SYNC_STATE_IN_SYNC);
+	
+	// Store file mod time
+	var mtime = item.attachmentModificationTime;
+	Zotero.Sync.Storage.setSyncedModificationTime(item.id, mtime, false);
+	
+	// Store file hash of individual files
+	if (Zotero.Attachments.getNumFiles(item) == 1) {
+		var hash = item.attachmentHash;
+		Zotero.Sync.Storage.setSyncedHash(item.id, hash, true);
+	}
+	
+	Zotero.DB.commitTransaction();
+	
+	try {
+		if (Zotero.Attachments.getNumFiles(item) > 1) {
+			var file = Zotero.getTempDirectory();
+			file.append(item.key + '.zip');
+			file.remove(false);
+		}
+	}
+	catch (e) {
+		Components.utils.reportError(e);
+	}
+	
+	this.onChangesMade();
+}
+
+
+Zotero.Sync.Storage.Session.ZFS.prototype._onUploadCancel = function (httpRequest, status, data) {
+	var request = data.request;
+	var item = data.item;
+	
+	Zotero.debug("Upload of attachment " + item.key + " cancelled with status code " + status);
+	
+	try {
+		if (Zotero.Attachments.getNumFiles(item) > 1) {
+			var file = Zotero.getTempDirectory();
+			file.append(item.key + '.zip');
+			file.remove(false);
+		}
+	}
+	catch (e) {
+		Components.utils.reportError(e);
+	}
+	
+	request.finish();
+}
+
+
+Zotero.Sync.Storage.Session.ZFS.prototype.getLastSyncTime = function (callback) {
+	var uri = this.userURI;
+	var successFileURI = uri.clone();
+	successFileURI.spec += "laststoragesync?auth=1";
+	
+	var self = this;
+	
+	// Cache the credentials
+	if (!this._cachedCredentials) {
+		var uri = this.rootURI;
+		// TODO: move to root uri
+		uri.spec += "?auth=1";
+		Zotero.Utilities.HTTP.doHead(uri, function (req) {
+			if (req.status != 200) {
+				self.onError("Unexpected status code " + req.status + " caching "
+					+ "authentication credentials in Zotero.Sync.Storage.Session.ZFS.getLastSyncTime()");
+				return;
+			}
+			self._cachedCredentials = true;
+			self.getLastSyncTime(callback);
+		});
+		return;
+	}
+	
+	Zotero.Utilities.HTTP.doGet(successFileURI, function (req) {
+		if (req.responseText) {
+			Zotero.debug(req.responseText);
+		}
+		Zotero.debug(req.status);
+		
+		if (req.status != 200 && req.status != 404) {
+			self.onError("Unexpected status code " + req.status + " getting "
+				+ "last file sync time");
+			return;
+		}
+		
+		var ts = req.responseText;
+		var date = new Date(req.responseText * 1000);
+		Zotero.debug("Last successful storage sync was " + date);
+		self._lastSyncTime = ts;
+		callback(ts);
+	});
+}
+
+
+Zotero.Sync.Storage.Session.ZFS.prototype.setLastSyncTime = function (callback, useLastSyncTime) {
+	if (useLastSyncTime) {
+		var sql = "REPLACE INTO version VALUES ('storage_zfs', ?)";
+		Zotero.DB.query(sql, { int: this._lastSyncTime });
+		
+		this._lastSyncTime = null;
+		this._cachedCredentials = false;
+		
+		if (callback) {
+			callback();
+		}
+		return;
+	}
+	this._lastSyncTime = null;
+	
+	var uri = this.userURI;
+	var successFileURI = uri.clone();
+	successFileURI.spec += "laststoragesync?auth=1";
+	
+	var self = this;
+	
+	Zotero.Utilities.HTTP.doPost(successFileURI, "", function (req) {
+		Zotero.debug(req.responseText);
+		Zotero.debug(req.status);
+		
+		if (req.status != 200) {
+			self.onError("Unexpected status code " + req.status + " setting "
+				+ "last file sync time");
+			return;
+		}
+		
+		var ts = req.responseText;
+		
+		var sql = "REPLACE INTO version VALUES ('storage_zfs', ?)";
+		Zotero.DB.query(sql, { int: ts });
+		
+		self._cachedCredentials = false;
+		
+		if (callback) {
+			callback();
+		}
+	});
+}
+
+
+Zotero.Sync.Storage.Session.ZFS.prototype.purgeDeletedStorageFiles = function (callback) {
+	// If we don't have a user id we've never synced and don't need to bother
+	if (!Zotero.userID) {
+		return;
+	}
+	
+	var sql = "SELECT value FROM settings WHERE setting=? AND key=?";
+	var values = Zotero.DB.columnQuery(sql, ['storage', 'zfsPurge']);
+	if (!values) {
+		return;
+	}
+	
+	Zotero.debug("Unlinking synced files on ZFS");
+	
+	var uri = this.userURI;
+	uri.spec += "removestoragefiles?";
+	for each(var value in values) {
+		switch (value) {
+			case 'user':
+				uri.spec += "user=1&";
+				break;
+				
+			case 'group':
+				uri.spec += "group=1&";
+				break;
+			
+			default:
+				throw ("Invalid zfsPurge value '" + value + "' in ZFS purgeDeletedStorageFiles()");
+		}
+	}
+	uri.spec = uri.spec.substr(0, uri.spec.length - 1);
+	
+	var self = this;
+	
+	Zotero.Utilities.HTTP.doPost(uri, "", function (xmlhttp) {
+		if (xmlhttp.status != 204) {
+			if (callback) {
+				callback(false);
+			}
+			self.onError("Unexpected status code " + xmlhttp.status + " purging ZFS files");
+		}
+		
+		var sql = "DELETE FROM settings WHERE setting=? AND key=?";
+		Zotero.DB.query(sql, ['storage', 'zfsPurge']);
+		
+		if (callback) {
+			callback(true);
+		}
+	});
+}
+
+
+//
+// Private methods
+//
+
+/**
+ * Get the storage URI for an item
+ *
+ * @inner
+ * @param	{Zotero.Item}
+ * @return	{nsIURI}					URI of file on storage server
+ */
+Zotero.Sync.Storage.Session.ZFS.prototype._getItemURI = function (item) {
+	var uri = this.rootURI;
+	uri.spec += Zotero.URI.getItemPath(item) + '/file?auth=1';
+	return uri;
+}
+
+
+Zotero.Sync.Storage.Session.ZFS.prototype._getUploadFile = function (item) {
+	if (Zotero.Attachments.getNumFiles(item) > 1) {
+		var file = Zotero.getTempDirectory();
+		var filename = item.key + '.zip';
+		file.append(filename);
+	}
+	else {
+		var file = item.getFile();
+	}
+	return file;
+}

chrome/content/zotero/xpcom/sync.js

@@ -118,7 +118,7 @@ Zotero.Sync = new function() {
 	}
 	
 	
-	/**                                                          
+	/**
 	 * @param	{Date}	lastSyncDate	JS Date object
 	 * @param	{Zotero.Sync.Server.ObjectKeySet}
 	 * @return	TRUE if found, FALSE if none, or -1 if last sync time is before start of log
@@ -443,30 +443,28 @@ Zotero.Sync.EventListener = new function () {
 
 
 Zotero.Sync.Runner = new function () {
-	this.__defineGetter__("lastSyncError", function () {
-		return _lastSyncError;
-	});
-	
 	this.__defineGetter__("background", function () {
 		return _background;
 	});
 	
-	var _lastSyncError;
 	var _autoSyncTimer;
 	var _queue;
 	var _running;
 	var _background;
 	
+	var _warning = null;
+	
 	this.init = function () {
 		this.EventListener.init();
 		this.IdleListener.init();
 	}
 	
 	this.sync = function (background) {
+		_warning = null;
+		
 		if (Zotero.Utilities.HTTP.browserIsOffline()){
-			_lastSyncError = "Browser is offline"; // TODO: localize
 			this.clearSyncTimeout(); // DEBUG: necessary?
-			this.setSyncIcon('error');
+			this.setSyncIcon('error', "Browser is offline");
 			return false;
 		}
 		
@@ -478,43 +476,138 @@ Zotero.Sync.Runner = new function () {
 		Zotero.purgeDataObjects(true);
 		
 		_background = !!background;
-		
-		_queue = [
-			Zotero.Sync.Server.sync,
-			Zotero.Sync.Storage.sync,
-			Zotero.Sync.Server.sync,
-			Zotero.Sync.Storage.sync
-		];
 		_running = true;
-		_lastSyncError = '';
 		this.setSyncIcon('animate');
-		this.next();
+		
-	}
+		var storageSync = function () {
-	
+			var syncNeeded = false;
-	
+			
-	this.next = function () {
+			Zotero.Sync.Storage.sync(
-		if (!_queue.length) {
+				'webdav',
-			this.setSyncIcon();
+				
-			_running = false;
+				{
-			return;
+					// WebDAV success
+					onSuccess: function () {
+						syncNeeded = true;
+						
+						Zotero.Sync.Storage.sync(
+							'zfs',
+							
+							{
+								// ZFS success
+								onSuccess: function () {
+									Zotero.Sync.Server.sync(
+										Zotero.Sync.Runner.stop,
+										Zotero.Sync.Runner.stop,
+										Zotero.Sync.Runner.error
+									)
+								},
+								
+								// ZFS skip
+								onSkip: function () {
+									if (syncNeeded) {
+										Zotero.Sync.Server.sync(
+											Zotero.Sync.Runner.stop,
+											Zotero.Sync.Runner.stop,
+											Zotero.Sync.Runner.error
+										)
+									}
+								},
+								
+								// ZFS cancel
+								onStop: Zotero.Sync.Runner.stop,
+								
+								// ZFS failure
+								onError: Zotero.Sync.Runner.error,
+								
+								onWarning: Zotero.Sync.Runner.warning
+							}
+						)
+					},
+					
+					// WebDAV skip
+					onSkip: function () {
+						Zotero.Sync.Storage.sync(
+							'zfs',
+							
+							{
+								// ZFS success
+								onSuccess: function () {
+									Zotero.Sync.Server.sync({
+										onSuccess: Zotero.Sync.Runner.stop,
+										onSkip: Zotero.Sync.Runner.stop,
+										onStop: Zotero.Sync.Runner.stop,
+										onError: Zotero.Sync.Runner.error
+									})
+								},
+								
+								// ZFS skip
+								onSkip: Zotero.Sync.Runner.stop,
+								
+								// ZFS cancel
+								onStop: Zotero.Sync.Runner.stop,
+								
+								// ZFS failure
+								onError: Zotero.Sync.Runner.error,
+								
+								onWarning: Zotero.Sync.Runner.warning
+							}
+						)
+					},
+					
+					// WebDAV cancel
+					onStop: Zotero.Sync.Runner.stop,
+					
+					// WebDAV failure
+					onError: Zotero.Sync.Runner.error
+				}
+			)
 		}
-		var func = _queue.shift();
+		
-		func();
+		Zotero.Sync.Server.sync({
+			// Sync 1 success
+			onSuccess: storageSync,
+			
+			// Sync 1 skip
+			onSkip: storageSync,
+			
+			// Sync 1 stop
+			onStop: Zotero.Sync.Runner.stop,
+			
+			// Sync 1 error
+			onError: Zotero.Sync.Runner.error
+		});
 	}
 	
 	
-	this.setError = function (msg) {
+	this.stop = function () {
-		this.setSyncIcon('error');
+		if (_warning) {
-		_lastSyncError = msg;
+			Zotero.Sync.Runner.setSyncIcon('warning', _warning);
-	}
+			_warning = null;
-	
+		}
-	
+		else {
-	this.reset = function () {
+			Zotero.Sync.Runner.setSyncIcon();
-		_queue = [];
+		}
 		_running = false;
 	}
 	
 	
+	/**
+	 * Log a warning, but don't throw an error
+	 */
+	this.warning = function (e) {
+		Components.utils.reportError(e);
+		_warning = e;
+	}
+	
+	
+	this.error = function (e) {
+		Zotero.Sync.Runner.setSyncIcon('error', e);
+		_running = false;
+		throw (e);
+	}
+	
+	
 	/**
 	 * @param	{Integer}	[timeout=15]		Timeout in seconds
 	 * @param	{Boolean}	[recurring=false]
@@ -593,12 +686,13 @@ Zotero.Sync.Runner = new function () {
 	}
 	
 	
-	this.setSyncIcon = function (status) {
+	this.setSyncIcon = function (status, e) {
 		status = status ? status : '';
 		
 		switch (status) {
 			case '':
 			case 'animate':
+			case 'warning':
 			case 'error':
 				break;
 			
@@ -610,17 +704,113 @@ Zotero.Sync.Runner = new function () {
 		var wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
 			.getService(Components.interfaces.nsIWindowMediator);
 		var win = wm.getMostRecentWindow('navigator:browser');
-		var icon = win.document.getElementById('zotero-tb-sync');
-		icon.setAttribute('status', status);
 		
-		switch (status) {
+		var warning = win.document.getElementById('zotero-tb-sync-warning');
-			case 'animate':
+		var icon = win.document.getElementById('zotero-tb-sync');
-				icon.setAttribute('disabled', true);
+		
-				break;
+		
+		var message;
+		var buttonText;
+		var buttonCallback;
+		
+		if (e) {
+			if (e.error == Zotero.Error.ERROR_ZFS_OVER_QUOTA) {
+				// TODO: localize
+				message = "You have reached your Zotero File Storage quota. Some files were not synced.\n\n"
+							+ "See your zotero.org account settings for additional storage options.";
+				
+				buttonText = "Open Account Settings";
+				buttonCallback = function () {
+					var url = "https://www.zotero.org/settings/storage";
+					
+					var wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
+								.getService(Components.interfaces.nsIWindowMediator);
+					var win = wm.getMostRecentWindow("navigator:browser");
+					var browser = win.getBrowser();
+					browser.selectedTab = browser.addTab(url);
+				}
+			}
 			
-			default:
+			if (!message) {
-				icon.setAttribute('disabled', false);
+				message = e.message ? e.message : e;
+			}
 		}
+		
+		if (status == 'warning' || status == 'error') {
+			icon.setAttribute('status', '');
+			warning.hidden = false;
+			warning.setAttribute('mode', status);
+			warning.tooltipText = "A sync error occurred. Click to view details.";
+			warning.onclick = function () {
+				var wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
+							.getService(Components.interfaces.nsIWindowMediator);
+				var win = wm.getMostRecentWindow("navigator:browser");
+				
+				var pr = Components.classes["@mozilla.org/network/default-prompt;1"]
+								.createInstance(Components.interfaces.nsIPrompt);
+				// Warning
+				if (status == 'warning') {
+					var title = Zotero.getString('general.warning');
+					
+					// If secondary button not specified, just use an alert
+					if (!buttonText) {
+						prompt.alert(title, message);
+						return;
+					}
+					
+					var buttonFlags = pr.BUTTON_POS_0 * pr.BUTTON_TITLE_OK
+										+ pr.BUTTON_POS_1 * pr.BUTTON_TITLE_IS_STRING;
+					Zotero.debug(buttonFlags);
+					var index = pr.confirmEx(
+						title,
+						message,
+						buttonFlags,
+						"",
+						buttonText,
+						"", null, {}
+					);
+					
+					if (index == 1) {
+						setTimeout(buttonCallback, 1);
+					}
+				}
+				
+				// Error
+				else if (status == 'error') {
+					var errorsLogged = Zotero.getErrors().length > 0;
+					// Probably not necessary, but let's be sure
+					if (!errorsLogged) {
+						Components.utils.reportError(message);
+					}
+					
+					var buttonFlags = pr.BUTTON_POS_0 * pr.BUTTON_TITLE_OK
+										+ pr.BUTTON_POS_1 * pr.BUTTON_TITLE_IS_STRING;
+					var index = pr.confirmEx(
+						Zotero.getString('general.error'),
+						message,
+						buttonFlags,
+						"",
+						// TODO: localize
+						"Report Error...",
+						"", null, {}
+					);
+					
+					if (index == 1) {
+						win.setTimeout(function () {
+							win.ZoteroPane.reportErrors();
+						}, 1);
+					}
+				}
+			}
+		}
+		else {
+			icon.setAttribute('status', status);
+			warning.hidden = true;
+			warning.onclick = null;
+		}
+		
+		// Disable button while spinning
+		icon.disabled = status == 'animate';
 	}
 }
 
@@ -852,7 +1042,22 @@ Zotero.Sync.Server = new function () {
 	var _throttleTimeout;
 	var _canAutoResetClient = true;
 	
-	function login(callback, callbackCallback) {
+	var _callbacks = {
+		onSuccess: function () {
+			Zotero.Sync.Runner.setSyncIcon();
+		},
+		onSkip: function () {
+			Zotero.Sync.Runner.setSyncIcon();
+		},
+		onStop: function () {
+			Zotero.Sync.Runner.setSyncIcon();
+		},
+		onError: function (msg) {
+			Zotero.Sync.Runner.error(msg);
+		}
+	};
+	
+	function login(callback) {
 		var url = _serverURL + "login";
 		
 		var username = Zotero.Sync.Server.username;
@@ -906,18 +1111,26 @@ Zotero.Sync.Server = new function () {
 			//Zotero.debug('Got session ID ' + _sessionID + ' from server');
 			
 			if (callback) {
-				callback(callbackCallback);
+				callback();
 			}
 		});
 	}
 	
 	
-	function sync(callback) {
+	function sync(callbacks) {
+		for (var func in callbacks) {
+			_callbacks[func] = callbacks[func];
+		}
+		
+		var self = this;
+		
 		Zotero.Sync.Runner.setSyncIcon('animate');
 		
 		if (!_sessionID) {
 			Zotero.debug("Session ID not available -- logging in");
-			Zotero.Sync.Server.login(Zotero.Sync.Server.sync, callback);
+			Zotero.Sync.Server.login(function () {
+				Zotero.Sync.Server.sync(_callbacks);
+			});
 			return;
 		}
 		
@@ -955,7 +1168,9 @@ Zotero.Sync.Server = new function () {
 				Zotero.debug("Invalid session ID -- logging in");
 				_sessionID = false;
 				_syncInProgress = false;
-				Zotero.Sync.Server.login(Zotero.Sync.Server.sync, callback);
+				Zotero.Sync.Server.login(function () {
+					Zotero.Sync.Server.sync(_callbacks);
+				});
 				return;
 			}
 			
@@ -976,32 +1191,36 @@ Zotero.Sync.Server = new function () {
 			// Strip XML declaration and convert to E4X
 			var xml = new XML(xmlhttp.responseText.replace(/<\?xml.*\?>/, ''));
 			
-			Zotero.DB.beginTransaction();
-			
 			try {
+				// If no earliest date is provided by the server, the server
+				// account is empty
+				var earliestRemoteDate = parseInt(xml.@earliest) ?
+					new Date((xml.@earliest + 43200) * 1000) : false;
+				var noServerData = !!earliestRemoteDate;
+				
+				// Check to see if we're syncing with a different user
 				var userID = parseInt(xml.@userID);
 				var libraryID = parseInt(xml.@defaultLibraryID);
-				if (!_checkSyncUser(userID, libraryID)) {
+				var c = _checkSyncUser(userID, libraryID, noServerData);
+				if (c == 0) {
+					// Groups were deleted, so restart sync
+					Zotero.debug("Restarting sync");
+					_syncInProgress = false;
+					Zotero.Sync.Server.sync(_callbacks);
+					return;
+				}
+				else if (c == -1) {
 					Zotero.debug("Sync cancelled");
-					Zotero.DB.rollbackTransaction();
 					Zotero.Sync.Server.unlock(function () {
-						if (callback) {
+						_callbacks.onStop();
-							Zotero.Sync.Runner.setSyncIcon();
-							callback();
-						}
-						else {
-							Zotero.Sync.Runner.reset();
-							Zotero.Sync.Runner.next();
-						}
 					});
 					_syncInProgress = false;
 					return;
 				}
 				
-				Zotero.UnresponsiveScriptIndicator.disable();
+				Zotero.DB.beginTransaction();
 				
-				var earliestRemoteDate = parseInt(xml.@earliest) ?
+				Zotero.UnresponsiveScriptIndicator.disable();
-					new Date((xml.@earliest + 43200) * 1000) : false;
 				
 				var lastLocalSyncTime = Zotero.Sync.Server.lastLocalSyncTime;
 				var lastLocalSyncDate = lastLocalSyncTime ?
@@ -1039,14 +1258,7 @@ Zotero.Sync.Server = new function () {
 					Zotero.debug("Sync cancelled");
 					Zotero.DB.rollbackTransaction();
 					Zotero.Sync.Server.unlock(function () {
-						if (callback) {
+						_callbacks.onSkip();
-							Zotero.Sync.Runner.setSyncIcon();
-							callback();
-						}
-						else { 
-							Zotero.Sync.Runner.reset();
-							Zotero.Sync.Runner.next();
-						}
 					});
 					Zotero.reloadDataObjects();
 					Zotero.Sync.EventListener.resetIgnored();
@@ -1067,13 +1279,7 @@ Zotero.Sync.Server = new function () {
 					Zotero.DB.commitTransaction();
 					Zotero.Sync.Server.unlock(function () {
 						_syncInProgress = false;
-						if (callback) {
+						_callbacks.onSuccess();
-							Zotero.Sync.Runner.setSyncIcon();
-							callback();
-						}
-						else {
-							Zotero.Sync.Runner.next();
-						}
 					});
 					return;
 				}
@@ -1114,13 +1320,7 @@ Zotero.Sync.Server = new function () {
 					Zotero.DB.commitTransaction();
 					Zotero.Sync.Server.unlock(function () {
 						_syncInProgress = false;
-						if (callback) {
+						_callbacks.onSuccess();
-							Zotero.Sync.Runner.setSyncIcon();
-							callback();
-						}
-						else {
-							Zotero.Sync.Runner.next();
-						}
 					});
 				}
 				
@@ -1203,7 +1403,7 @@ Zotero.Sync.Server = new function () {
 	}
 	
 	
-	function lock(callback, callbackCallback) {
+	function lock(callback) {
 		Zotero.debug("Getting session lock");
 		
 		if (!_sessionID) {
@@ -1234,11 +1434,7 @@ Zotero.Sync.Server = new function () {
 			
 			if (response.firstChild.tagName == 'error') {
 				if (_checkServerSessionLock(response.firstChild)) {
-					Zotero.Sync.Server.lock(function () {
+					Zotero.Sync.Server.lock(callback ? function () { callback(); } : null);
-						if (callback) {
-							callback(callbackCallback);
-						}
-					});
 					return;
 				}
 				
@@ -1252,7 +1448,7 @@ Zotero.Sync.Server = new function () {
 			_sessionLock = true;
 			
 			if (callback) {
-				callback(callbackCallback);
+				callback();
 			}
 		});
 	}
@@ -1300,7 +1496,9 @@ Zotero.Sync.Server = new function () {
 	function clear(callback) {
 		if (!_sessionID) {
 			Zotero.debug("Session ID not available -- logging in");
-			Zotero.Sync.Server.login(Zotero.Sync.Server.clear, callback);
+			Zotero.Sync.Server.login(function () {
+				Zotero.Sync.Server.clear();
+			});
 			return;
 		}
 		
@@ -1312,7 +1510,9 @@ Zotero.Sync.Server = new function () {
 			if (_invalidSession(xmlhttp)) {
 				Zotero.debug("Invalid session ID -- logging in");
 				_sessionID = false;
-				Zotero.Sync.Server.login(Zotero.Sync.Server.clear, callback);
+				Zotero.Sync.Server.login(function () {
+					Zotero.Sync.Server.clear(callback);
+				});
 				return;
 			}
 			
@@ -1343,7 +1543,9 @@ Zotero.Sync.Server = new function () {
 	function resetServer(callback) {
 		if (!_sessionID) {
 			Zotero.debug("Session ID not available -- logging in");
-			Zotero.Sync.Server.login(Zotero.Sync.Server.resetServer, callback);
+			Zotero.Sync.Server.login(function () {
+				Zotero.Sync.Server.resetServer(callback);
+			});
 			return;
 		}
 		
@@ -1355,7 +1557,9 @@ Zotero.Sync.Server = new function () {
 			if (_invalidSession(xmlhttp)) {
 				Zotero.debug("Invalid session ID -- logging in");
 				_sessionID = false;
-				Zotero.Sync.Server.login(Zotero.Sync.Server.reset, callback);
+				Zotero.Sync.Server.login(function () {
+					Zotero.Sync.Server.reset();
+				});
 				return;
 			}
 			
@@ -1391,11 +1595,12 @@ Zotero.Sync.Server = new function () {
 			+ "('lastlocalsync', 'lastremotesync', 'syncdeletelog')";
 		Zotero.DB.query(sql);
 		
+		var sql = "DELETE FROM version WHERE schema IN "
+			+ "('lastlocalsync', 'lastremotesync', 'syncdeletelog')";
+		Zotero.DB.query(sql);
+		
 		Zotero.DB.query("DELETE FROM syncDeleteLog");
 		Zotero.DB.query("DELETE FROM storageDeleteLog");
-		sql = "DELETE FROM settings WHERE setting='account' AND "
-				+ "key IN ('userID', 'username')";
-		Zotero.DB.query(sql);
 		
 		sql = "INSERT INTO version VALUES ('syncdeletelog', ?)";
 		Zotero.DB.query(sql, Zotero.Date.getUnixTimestamp());
@@ -1545,6 +1750,41 @@ Zotero.Sync.Server = new function () {
 					}, 1);
 					break;
 				
+				case 'LIBRARY_ACCESS_DENIED':
+					var background = Zotero.Sync.Runner.background;
+					setTimeout(function () {
+						var libraryID = parseInt(firstChild.getAttribute('libraryID'));
+						var group = Zotero.Groups.getByLibraryID(libraryID);
+						
+						var pr = Components.classes["@mozilla.org/network/default-prompt;1"]
+									.createInstance(Components.interfaces.nsIPrompt);
+						var buttonFlags = (pr.BUTTON_POS_0) * (pr.BUTTON_TITLE_IS_STRING)
+										+ (pr.BUTTON_POS_1) * (pr.BUTTON_TITLE_CANCEL)
+										+ pr.BUTTON_DELAY_ENABLE;
+						var index = pr.confirmEx(
+							Zotero.getString('general.warning'),
+							// TODO: localize
+							"You no longer have write access to the Zotero group '" + group.name + "', "
+								+ "and changes you've made cannot be synced to the server.\n\n"
+								+ "If you continue, your copy of the group will be reset to its state "
+								+ "on the server, and your local modifications will be lost.\n\n"
+								+ "If you would like a chance to copy your changes elsewhere or to request "
+								+ "write access from a group administrator, cancel the sync now.",
+							buttonFlags,
+							"Reset Group and Sync",
+							null, null, null, {}
+							);
+						
+						if (index == 0) {
+							group.erase();
+							Zotero.Sync.Server.resetClient();
+							Zotero.Sync.Storage.resetAllSyncStates();
+							Zotero.Sync.Runner.sync();
+							return;
+						}
+					}, 1);
+					break;
+				
 				case 'TAG_TOO_LONG':
 					if (!Zotero.Sync.Runner.background) {
 						var tag = xmlhttp.responseXML.firstChild.getElementsByTagName('tag');
@@ -1626,9 +1866,19 @@ Zotero.Sync.Server = new function () {
 	/**
 	 * Make sure we're syncing with the same account we used last time
 	 *
-	 * @return 	TRUE if sync should continue, FALSE if cancelled
+	 * @param	{Integer}	userID			New userID
+	 * @param	{Integer}	libraryID		New libraryID
+	 * @param	{Integer}	noServerData	The server account is empty — this is
+	 * 											the account after a server clear
+	 * @return 	1 if sync should continue, 0 if sync should restart, -1 if sync should cancel
 	 */
-	function _checkSyncUser(userID, libraryID) {
+	function _checkSyncUser(userID, libraryID, noServerData) {
+		if (Zotero.DB.transactionInProgress()) {
+			throw ("Transaction in progress in Zotero.Sync.Server._checkSyncUser");
+		}
+		
+		Zotero.DB.beginTransaction();
+		
 		var sql = "SELECT value FROM settings WHERE "
 					+ "setting='account' AND key='username'";
 		var lastUsername = Zotero.DB.valueQuery(sql);
@@ -1636,7 +1886,11 @@ Zotero.Sync.Server = new function () {
 		var lastUserID = Zotero.userID;
 		var lastLibraryID = Zotero.libraryID;
 		
+		var restartSync = false;
+		
 		if (lastUserID && lastUserID != userID) {
+			var groups = Zotero.Groups.getAll();
+			
 			var pr = Components.classes["@mozilla.org/network/default-prompt;1"]
 						.createInstance(Components.interfaces.nsIPrompt);
 			var buttonFlags = (pr.BUTTON_POS_0) * (pr.BUTTON_TITLE_IS_STRING)
@@ -1644,54 +1898,106 @@ Zotero.Sync.Server = new function () {
 			+ (pr.BUTTON_POS_2) * (pr.BUTTON_TITLE_IS_STRING)
 			+ pr.BUTTON_POS_1_DEFAULT
 			+ pr.BUTTON_DELAY_ENABLE;
-			var index = pr.confirmEx(
-				Zotero.getString('general.warning'),
-				// TODO: localize
-				"This Zotero database was last synced with a different "
-					+ "zotero.org account ('" + lastUsername + "') from the "
-					+ "current one ('" + username + "'). "
-					+ "If you continue, local Zotero data will be "
-					+ "combined with data from the '" + username + "' account "
-					+ "stored on the server.\n\n"
-					+ "To avoid combining data, revert to the '"
-					+ lastUsername + "' account or use the Reset options "
-					+ "in the Sync pane of the Zotero preferences.",
-				buttonFlags,
-				"Sync",
-				null,
-				"Open Sync Preferences",
-				null, {}
-			);
 			
-			if (index > 0) {
+			var msg = "This Zotero database was last synced with a different "
-				if (index == 1) {
+					+ "zotero.org account ('" + lastUsername + "') from the "
-					// Cancel
+					+ "current one ('" + username + "'). ";
+			
+			if (!noServerData) {
+				// TODO: localize
+				msg += "If you continue, local Zotero data will be "
+						+ "combined with data from the '" + username + "' account "
+						+ "stored on the server.";
+				// If there are local groups belonging to the previous user,
+				// we need to remove them
+				if (groups.length) {
+					msg += "Local groups, including any with changed items, will also "
+							+ "be removed.";
 				}
-				else if (index == 2) {
+				msg += "\n\n"
-					var wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
+						+ "To avoid combining or losing data, revert to the '"
-							   .getService(Components.interfaces.nsIWindowMediator);
+						+ lastUsername + "' account or use the Reset options "
-					var lastWin = wm.getMostRecentWindow("navigator:browser");
+						+ "in the Sync pane of the Zotero preferences.";
-					lastWin.ZoteroPane.openPreferences('zotero-prefpane-sync');
+				
+				var syncButtonText = "Sync";
+			}
+			else if (groups.length) {
+				msg += "If you continue, local groups, including any with changed items, "
+						+ "will be removed and replaced with groups linked to the '"
+						+ username + "' account."
+						+ "\n\n"
+						+ "To avoid losing local changes to groups, be sure you "
+						+ "have synced with the '" + lastUsername + "' account before "
+						+ "syncing with the '" + username + "' account.";
+				
+				var syncButtonText = "Remove Groups and Sync";
+			}
+			// If there are no local groups and the server is empty,
+			// don't bother prompting
+			else {
+				var noPrompt = true;
+			}
+			
+			if (!noPrompt) {
+				var index = pr.confirmEx(
+					Zotero.getString('general.warning'),
+					msg,
+					buttonFlags,
+					syncButtonText,
+					null,
+					"Open Sync Preferences",
+					null, {}
+				);
+				
+				if (index > 0) {
+					if (index == 1) {
+						// Cancel
+					}
+					else if (index == 2) {
+						var wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
+								   .getService(Components.interfaces.nsIWindowMediator);
+						var lastWin = wm.getMostRecentWindow("navigator:browser");
+						lastWin.ZoteroPane.openPreferences('zotero-prefpane-sync');
+					}
+					
+					return -1;
 				}
 				
-				return false;
+				// Delete all local groups
+				for each(var group in groups) {
+					group.erase();
+				}
+				
+				restartSync = true;
 			}
 		}
 		
 		if (lastUserID != userID || lastLibraryID != libraryID) {
 			Zotero.userID = userID;
 			Zotero.libraryID = libraryID;
+			
+			// Update userID in relations
+			if (lastUserID && lastLibraryID) {
+				Zotero.Relations.updateUser(lastUserID, lastLibraryID, userID, libraryID);
+			}
+			
+			Zotero.Sync.Server.resetClient();
+			Zotero.Sync.Storage.resetAllSyncStates();
 		}
 		
 		if (lastUsername != username) {
-			var sql = "REPLACE INTO settings VALUES ('account', 'username', ?)";
+			Zotero.username = username;
-			Zotero.DB.query(sql, username);
 		}
 		
-		return true;
+		Zotero.DB.commitTransaction();
+		
+		return restartSync ? 0 : 1;
 	}
 	
 	
+	
+	
+	
 	function _invalidSession(xmlhttp) {
 		if (xmlhttp.responseXML.childNodes[0].firstChild.tagName != 'error') {
 			return false;
@@ -1783,8 +2089,7 @@ Zotero.Sync.Server = new function () {
 			Zotero.Sync.Server.unlock()
 		}
 		
-		Zotero.Sync.Runner.setError(e.message ? e.message : e);
+		_callbacks.onError(e);
-		Zotero.Sync.Runner.reset();
 		
 		throw (e);
 	}
@@ -1970,6 +2275,7 @@ Zotero.Sync.Server.Data = new function() {
 		var itemStorageModTimes = {};
 		var childItemStore = [];
 		
+		// Remotely changed groups
 		if (xml.groups.length()) {
 			Zotero.debug("Processing remotely changed groups");
 			for each(var xmlNode in xml.groups.group) {
@@ -1978,6 +2284,7 @@ Zotero.Sync.Server.Data = new function() {
 			}
 		}
 		
+		// Remotely deleted groups
 		if (xml.deleted.groups.toString()) {
 			Zotero.debug("Processing remotely deleted groups");
 			var groupIDs = xml.deleted.groups.toString().split(' ');
@@ -1988,21 +2295,14 @@ Zotero.Sync.Server.Data = new function() {
 				if (!group) {
 					continue;
 				}
-				// TODO: prompt to save
 				
-				Zotero.Notifier.disable();
+				// TODO: prompt to save data to local library?
 				
-				// TODO: figure out a better way to do this
-				var notifierData = {};
-				notifierData[groupID] = group.serialize();
 				group.erase();
-				
-				Zotero.Notifier.enable();
-				
-				Zotero.Notifier.trigger('delete', 'group', groupID, notifierData);
 			}
 		}
 		
+		// Other objects
 		for each(var syncObject in Zotero.Sync.syncObjects) {
 			var Type = syncObject.singular; // 'Item'
 			var Types = syncObject.plural; // 'Items'
@@ -2271,11 +2571,7 @@ Zotero.Sync.Server.Data = new function() {
 							syncSession.removeFromDeleted(creator.ref);
 						}
 					}
-					else if (obj.isAttachment() &&
+					else if (obj.isImportedAttachment()) {
-							(obj.attachmentLinkMode ==
-								Zotero.Attachments.LINK_MODE_IMPORTED_FILE ||
-							 obj.attachmentLinkMode ==
-								Zotero.Attachments.LINK_MODE_IMPORTED_URL)) {
 						// Mark new attachments for download
 						if (isNewObject) {
 							obj.attachmentSyncState =
@@ -2285,7 +2581,8 @@ Zotero.Sync.Server.Data = new function() {
 						else {
 							var mtime = xmlNode.@storageModTime.toString();
 							if (mtime) {
-								itemStorageModTimes[obj.key] = parseInt(mtime);
+								var lk = Zotero.Items.getLibraryKeyHash(obj)
+								itemStorageModTimes[lk] = parseInt(mtime);
 							}
 						}
 					}
@@ -2504,15 +2801,16 @@ Zotero.Sync.Server.Data = new function() {
 				}
 			}
 			
-			// Check mod times of updated items against stored time to see
+			// Check mod times and hashes of updated items against stored values to see
 			// if they've been updated elsewhere and mark for download if so
 			if (type == 'item') {
 				var ids = [];
 				var modTimes = {};
-				for (var key in itemStorageModTimes) {
+				for (var libraryKeyHash in itemStorageModTimes) {
-					var item = Zotero.Items.getByLibraryAndKey(null, key);
+					var lk = Zotero.Items.parseLibraryKeyHash(libraryKeyHash);
+					var item = Zotero.Items.getByLibraryAndKey(lk.libraryID, lk.key);
 					ids.push(item.id);
-					modTimes[item.id] = itemStorageModTimes[key];
+					modTimes[item.id] = itemStorageModTimes[libraryKeyHash];
 				}
 				if (ids.length > 0) {
 					Zotero.Sync.Storage.checkForUpdatedFiles(ids, modTimes);
@@ -3003,15 +3301,23 @@ Zotero.Sync.Server.Data = new function() {
 				xml.@charset = charset;
 			}
 			
-			// Include storage sync time and paths for non-links
 			if (item.attachment.linkMode != Zotero.Attachments.LINK_MODE_LINKED_URL) {
-				var mtime = Zotero.Sync.Storage.getSyncedModificationTime(item.primary.itemID);
+				// Include paths for non-links
-				if (mtime) {
-					xml.@storageModTime = mtime;
-				}
-				
 				var path = <path>{item.attachment.path}</path>;
 				xml.path += path;
+				
+				// Include storage sync time and hash for imported files
+				if (item.attachment.linkMode != Zotero.Attachments.LINK_MODE_LINKED_FILE) {
+					var mtime = Zotero.Sync.Storage.getSyncedModificationTime(item.primary.itemID);
+					if (mtime) {
+						xml.@storageModTime = mtime;
+					}
+					
+					var hash = Zotero.Sync.Storage.getSyncedHash(item.primary.itemID);
+					if (hash) {
+						xml.@storageHash = hash;
+					}
+				}
 			}
 			
 			if (item.note) {

chrome/content/zotero/xpcom/uri.js

@@ -1,5 +1,6 @@
 Zotero.URI = new function () {
 	var _baseURI = ZOTERO_CONFIG.BASE_URI;
+	var _apiURI = ZOTERO_CONFIG.API_URI;
 	
 	
 	/**
@@ -22,8 +23,11 @@ Zotero.URI = new function () {
 	 *
 	 * @return	{String}
 	 */
-	this.getCurrentUserURI = function () {
+	this.getCurrentUserURI = function (noLocal) {
 		var userID = Zotero.userID;
+		if (!userID && noLocal) {
+			throw new Exception("Local userID not available and noLocal set in Zotero.URI.getCurrentUserURI()");
+		}
 		if (userID) {
 			return _baseURI + "users/" + userID;
 		}
@@ -42,22 +46,44 @@ Zotero.URI = new function () {
 	
 	
 	this.getLibraryURI = function (libraryID) {
-		var libraryType = Zotero.Libraries.getType(libraryID);
+		var path = this.getLibraryPath(libraryID);
+		return _baseURI + path;
+	}
+	
+	
+	/**
+	 * Get path portion of library URI (e.g., users/6 or groups/1)
+	 */
+	this.getLibraryPath = function (libraryID) {
+		if (libraryID) {
+			var libraryType = Zotero.Libraries.getType(libraryID);
+		}
+		else {
+			libraryType = 'user';
+		}
 		switch (libraryType) {
+			case 'user':
+				var id = Zotero.userID;
+				if (!id) {
+					throw new Exception("User id not available in Zotero.URI.getLibraryPath()");
+				}
+				break;
+			
 			case 'group':
 				var id = Zotero.Groups.getGroupIDFromLibraryID(libraryID);
 				break;
 			
-			case 'user':
-				throw ("User library ids are not supported in Zotero.URI.getLibraryURI");
-			
 			default:
-				throw ("Unsupported library type '" + libraryType + "' in Zotero.URI.getLibraryURI()");
+				throw ("Unsupported library type '" + libraryType + "' in Zotero.URI.getLibraryPath()");
 		}
-		return _baseURI + libraryType + "s/" + id;
+		
+		return libraryType + "s/" + id;
 	}
 	
 	
+	/**
+	 * Return URI of item, which might be a local URI if user hasn't synced
+	 */
 	this.getItemURI = function (item) {
 		if (item.libraryID) {
 			var baseURI = this.getLibraryURI(item.libraryID);
@@ -69,6 +95,14 @@ Zotero.URI = new function () {
 	}
 	
 	
+	/**
+	 * Get path portion of item URI (e.g., users/6/items/ABCD1234 or groups/1/items/ABCD1234)
+	 */
+	this.getItemPath = function (item) {
+		return this.getLibraryPath(item.libraryID) + "/items/" + item.key;
+	}
+	
+	
 	this.getGroupsURL = function () {
 		return ZOTERO_CONFIG.WWW_BASE_URL + "groups";
 	}

chrome/content/zotero/xpcom/utilities.js

@@ -396,19 +396,51 @@ Zotero.Utilities.prototype.getSQLDataType = function(value) {
 
 
 /*
- * From http://developer.mozilla.org/en/docs/nsICryptoHash#Computing_the_Hash_of_a_String
+ * Adapted from http://developer.mozilla.org/en/docs/nsICryptoHash
+ *
+ * @param	{String|nsIFile}	strOrFile
+ * @param	{Boolean}			[base64=false]	Return as base-64-encoded string rather than hex string
+ * @return	{String}
  */
-Zotero.Utilities.prototype.md5 = function(str) {
+Zotero.Utilities.prototype.md5 = function(strOrFile, base64) {
-	var converter = Components.classes["@mozilla.org/intl/scriptableunicodeconverter"].
+	if (typeof strOrFile == 'string') {
-		createInstance(Components.interfaces.nsIScriptableUnicodeConverter);
+		var converter = Components.classes["@mozilla.org/intl/scriptableunicodeconverter"].
-	converter.charset = "UTF-8";
+			createInstance(Components.interfaces.nsIScriptableUnicodeConverter);
-	var result = {};
+		converter.charset = "UTF-8";
-	var data = converter.convertToByteArray(str, result);
+		var result = {};
-	var ch = Components.classes["@mozilla.org/security/hash;1"]
+		var data = converter.convertToByteArray(strOrFile, result);
-		.createInstance(Components.interfaces.nsICryptoHash);
+		var ch = Components.classes["@mozilla.org/security/hash;1"]
-	ch.init(ch.MD5);
+			.createInstance(Components.interfaces.nsICryptoHash);
-	ch.update(data, data.length);
+		ch.init(ch.MD5);
-	var hash = ch.finish(false);
+		ch.update(data, data.length);
+	}
+	else if (strOrFile instanceof Components.interfaces.nsIFile) {
+		var istream = Components.classes["@mozilla.org/network/file-input-stream;1"]
+						.createInstance(Components.interfaces.nsIFileInputStream);
+		// open for reading
+		istream.init(strOrFile, 0x01, 0444, 0);
+		var ch = Components.classes["@mozilla.org/security/hash;1"]
+					   .createInstance(Components.interfaces.nsICryptoHash);
+		// we want to use the MD5 algorithm
+		ch.init(ch.MD5);
+		// this tells updateFromStream to read the entire file
+		const PR_UINT32_MAX = 0xffffffff;
+		ch.updateFromStream(istream, PR_UINT32_MAX);
+	}
+	
+	// pass false here to get binary data back
+	var hash = ch.finish(base64);
+	
+	if (istream) {
+		istream.close();
+	}
+	
+	if (base64) {
+		return hash;
+	}
+	
+	/*
+	// This created 36-character hashes
 	
 	// return the two-digit hexadecimal code for a byte
 	function toHexString(charCode) {
@@ -417,6 +449,17 @@ Zotero.Utilities.prototype.md5 = function(str) {
 	
 	// convert the binary hash data to a hex string.
 	return [toHexString(hash.charCodeAt(i)) for (i in hash)].join("");
+	*/
+	
+	// From http://rcrowley.org/2007/11/15/md5-in-xulrunner-or-firefox-extensions/
+	var ascii = []; ii = hash.length;
+	for (var i = 0; i < ii; ++i) {
+		var c = hash.charCodeAt(i);
+		var ones = c % 16;
+		var tens = c >> 4;
+		ascii.push(String.fromCharCode(tens + (tens > 9 ? 87 : 48)) + String.fromCharCode(ones + (ones > 9 ? 87 : 48)));
+	}
+	return ascii.join('');
 }
 
 
@@ -795,17 +838,18 @@ Zotero.Utilities.Translate.prototype.retrieveDocument = function(url) {
  * @param {String} 		url					URL to load
  * @param {String}		[body=null]			Request body to POST to the URL; a GET request is
  *											executed if no body is present
- * @param {String}		[requestContentType=application/x-www-form-urlencoded]
+ * @param {Object}		[headers]			HTTP headers to include in request;
- *											Request content type for POST; ignored if no body
+ *											Content-Type defaults to application/x-www-form-urlencoded
+ *											for POST; ignored if no body
  * @param {String} 		[responseCharset] 	Character set to force on the response
  * @return {String} 						Request body
  */
-Zotero.Utilities.Translate.prototype.retrieveSource = function(url, body, requestContentType, responseCharset) {
+Zotero.Utilities.Translate.prototype.retrieveSource = function(url, body, headers, responseCharset) {
 	/* Apparently, a synchronous XMLHttpRequest would have the behavior of this routine in FF3, but
 	 * in FF3.5, synchronous XHR blocks all JavaScript on the thread. See 
 	 * http://hacks.mozilla.org/2009/07/synchronous-xhr/. */
 	if(this.translate.locationIsProxied) url = this._convertURL(url);
-	if(!requestContentType) requestContentType = null;
+	if(!headers) headers = null;
 	if(!responseCharset) responseCharset = null;
 	
 	var mainThread = Zotero.mainThread;
@@ -813,7 +857,7 @@ Zotero.Utilities.Translate.prototype.retrieveSource = function(url, body, reques
 	var listener = function(aXmlhttp) { xmlhttp = aXmlhttp };
 	
 	if(body) {
-		Zotero.Utilities.HTTP.doPost(url, body, listener, requestContentType, responseCharset);
+		Zotero.Utilities.HTTP.doPost(url, body, listener, headers, responseCharset);
 	} else {
 		Zotero.Utilities.HTTP.doGet(url, listener, responseCharset);
 	}
@@ -870,7 +914,7 @@ Zotero.Utilities.Translate.prototype.doGet = function(urls, processor, done, res
  * Already documented in Zotero.Utilities.HTTP
  * @ignore
  */
-Zotero.Utilities.Translate.prototype.doPost = function(url, body, onDone, requestContentType, responseCharset) {
+Zotero.Utilities.Translate.prototype.doPost = function(url, body, onDone, headers, responseCharset) {
 	url = this._convertURL(url);
 	
 	var translate = this.translate;
@@ -880,7 +924,7 @@ Zotero.Utilities.Translate.prototype.doPost = function(url, body, onDone, reques
 		} catch(e) {
 			translate.error(false, e);
 		}
-	}, requestContentType, responseCharset);
+	}, headers, responseCharset);
 }
 
 /**
@@ -936,7 +980,6 @@ Zotero.Utilities.HTTP = new function() {
 		}
 		else {
 			Zotero.debug("HTTP GET " + url);
-		
 		}
 		if (this.browserIsOffline()){
 			return false;
@@ -981,12 +1024,20 @@ Zotero.Utilities.HTTP = new function() {
 	* @param {String} url URL to request
 	* @param {String} body Request body
 	* @param {Function} onDone Callback to be executed upon request completion
-	* @param {String} requestContentType Request content type (usually
+	* @param {String} headers Request HTTP headers
-	*	application/x-www-form-urlencoded)
 	* @param {String} responseCharset Character set to force on the response
 	* @return {Boolean} True if the request was sent, or false if the browser is offline
 	*/
-	this.doPost = function(url, body, onDone, requestContentType, responseCharset) {
+	this.doPost = function(url, body, onDone, headers, responseCharset) {
+		if (url instanceof Components.interfaces.nsIURI) {
+			// Don't display password in console
+			var disp = url.clone();
+			if (disp.password) {
+				disp.password = "********";
+			}
+			url = url.spec;
+		}
+		
 		var bodyStart = body.substr(0, 1024);
 		// Don't display sync password or session id in console
 		bodyStart = bodyStart.replace(/password=[^&]+/, 'password=********');
@@ -995,7 +1046,7 @@ Zotero.Utilities.HTTP = new function() {
 		Zotero.debug("HTTP POST "
 			+ (body.length > 1024 ?
 				bodyStart + '... (' + body.length + ' chars)' : bodyStart)
-			+ " to " + url);
+			+ " to " + (disp ? disp.spec : url));
 		
 		
 		if (this.browserIsOffline()){
@@ -1025,7 +1076,27 @@ Zotero.Utilities.HTTP = new function() {
 		xmlhttp.channel.loadGroup = ds.getInterface(Ci.nsILoadGroup);
 		xmlhttp.channel.loadFlags |= Ci.nsIChannel.LOAD_DOCUMENT_URI;
 		
-		xmlhttp.setRequestHeader("Content-Type", (requestContentType ? requestContentType : "application/x-www-form-urlencoded" ));
+		if (headers) {
+			if (typeof headers == 'string') {
+				var msg = "doPost() now takes a headers object rather than a requestContentType -- update your code";
+				Zotero.debug(msg, 2);
+				Components.utils.reportError(msg);
+				headers = {
+					"Content-Type": headers
+				};
+			}
+		}
+		else {
+			headers = {};
+		}
+		
+		if (!headers["Content-Type"]) {
+			headers["Content-Type"] = "application/x-www-form-urlencoded";
+		}
+		
+		for (var header in headers) {
+			xmlhttp.setRequestHeader(header, headers[header]);
+		}
 		
 		/** @ignore */
 		xmlhttp.onreadystatechange = function(){
@@ -1042,10 +1113,24 @@ Zotero.Utilities.HTTP = new function() {
 	*
 	* @param {String} url URL to request
 	* @param {Function} onDone Callback to be executed upon request completion
+	* @param {Object} requestHeaders HTTP headers to include with request
 	* @return {Boolean} True if the request was sent, or false if the browser is offline
 	*/
-	this.doHead = function(url, onDone) {
+	this.doHead = function(url, onDone, requestHeaders) {
-		Zotero.debug("HTTP HEAD "+url);
+		if (url instanceof Components.interfaces.nsIURI) {
+			// Don't display password in console
+			var disp = url.clone();
+			if (disp.password) {
+				disp.password = "********";
+			}
+			Zotero.debug("HTTP HEAD " + disp.spec);
+			url = url.spec;
+		}
+		else {
+			Zotero.debug("HTTP HEAD " + url);
+		
+		}
+		
 		if (this.browserIsOffline()){
 			return false;
 		}
@@ -1068,10 +1153,20 @@ Zotero.Utilities.HTTP = new function() {
 		ds.itemType = Ci.nsIDocShellTreeItem.typeContent;
 		var xmlhttp = Cc["@mozilla.org/xmlextras/xmlhttprequest;1"].
 						createInstance(Ci.nsIXMLHttpRequest);
+		// Prevent certificate/authentication dialogs from popping up
+		xmlhttp.mozBackgroundRequest = true;
 		xmlhttp.open("HEAD", url, true);
+		if (requestHeaders) {
+			for (var header in requestHeaders) {
+				xmlhttp.setRequestHeader(header, requestHeaders[header]);
+			}
+		}
 		xmlhttp.channel.loadGroup = ds.getInterface(Ci.nsILoadGroup);
 		xmlhttp.channel.loadFlags |= Ci.nsIChannel.LOAD_DOCUMENT_URI;
 		
+		// Don't cache HEAD requests
+		xmlhttp.channel.loadFlags |= Ci.nsIRequest.LOAD_BYPASS_CACHE;
+		
 		/** @ignore */
 		xmlhttp.onreadystatechange = function(){
 			_stateChange(xmlhttp, onDone);

chrome/content/zotero/xpcom/zotero.js

@@ -28,7 +28,8 @@ const ZOTERO_CONFIG = {
 	REPOSITORY_RETRY_INTERVAL: 3600, // 1 hour
 	BASE_URI: 'http://zotero.org/',
 	WWW_BASE_URL: 'http://www.zotero.org/',
-	SYNC_URL: 'https://sync.zotero.org/'
+	SYNC_URL: 'https://sync.zotero.org/',
+	API_URL: 'https://api.zotero.org/'
 };
 
 /*
@@ -100,6 +101,17 @@ var Zotero = new function(){
 		Zotero.DB.query(sql, parseInt(val));
 	});
 	
+	this.__defineGetter__('username', function () {
+		var sql = "SELECT value FROM settings WHERE "
+					+ "setting='account' AND key='username'";
+		return Zotero.DB.valueQuery(sql);
+	});
+	
+	this.__defineSetter__('username', function (val) {
+		var sql = "REPLACE INTO settings VALUES ('account', 'username', ?)";
+		Zotero.DB.query(sql, val);
+	});
+	
 	this.getLocalUserKey = function (generate) {
 		if (_localUserKey) {
 			return _localUserKey;
@@ -1160,8 +1172,9 @@ var Zotero = new function(){
 		Zotero.Fulltext.purgeUnusedWords();
 		Zotero.Items.purge();
 		
-		if (!skipStoragePurge && Zotero.Sync.Storage.active && Zotero.Utilities.prototype.probability(10)) {
+		if (!skipStoragePurge && Zotero.Utilities.prototype.probability(10)) {
-			Zotero.Sync.Storage.purgeDeletedStorageFiles();
+			Zotero.Sync.Storage.purgeDeletedStorageFiles('zfs');
+			Zotero.Sync.Storage.purgeDeletedStorageFiles('webdav');
 		}
 	}
 	

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

@@ -1,5 +1,6 @@
 extensions.zotero@chnm.gmu.edu.description	= The Next-Generation Research Tool
 
+general.success						= Success
 general.error						= Error
 general.warning						= Warning
 general.dontShowWarningAgain			= Don't show this warning again.

chrome/skin/default/zotero/overlay.css

@@ -205,9 +205,15 @@
 	font-weight: bold;
 }
 
-#zotero-tb-storage-sync
+#zotero-tb-sync-warning
 {
-	list-style-image: url(chrome://zotero/skin/drive_network.png);
+	list-style-image: url(chrome://zotero/skin/error.png);
+	margin-right: -5px;
+}
+
+#zotero-tb-sync-warning[error=true]
+{
+	list-style-image: url(chrome://zotero/skin/exclamation.png);
 }
 
 #zotero-tb-sync {
@@ -220,10 +226,6 @@
 	list-style-image: url(chrome://zotero/skin/arrow_rotate_animated.png);
 }
 
-#zotero-tb-sync[status=error] {
-	list-style-image: url(chrome://zotero/skin/arrow_rotate_error.png);
-}
-
 #zotero-tb-sync #zotero-last-sync-time
 {
 	color: gray;

components/zotero-service.js

@@ -64,6 +64,9 @@ var xpcomFiles = [
 	'style',
 	'sync',
 	'storage',
+	'storage/session',
+	'storage/zfs',
+	'storage/webdav',
 	'timeline',
 	'translate',
 	'uri',

defaults/preferences/zotero.js

@@ -37,6 +37,10 @@ pref("extensions.zotero.sortAttachmentsChronologically", false);
 pref("extensions.zotero.showTrashWhenEmpty", true);
 pref("extensions.zotero.viewOnDoubleClick", true);
 
+pref("extensions.zotero.groups.copyChildLinks", true);
+pref("extensions.zotero.groups.copyChildFileAttachments", true);
+pref("extensions.zotero.groups.copyChildNotes", true);
+
 pref("extensions.zotero.backup.numBackups", 2);
 pref("extensions.zotero.backup.interval", 1440);
 
@@ -113,14 +117,16 @@ pref("extensions.zotero.annotations.warnOnClose", true);
 pref("extensions.zotero.sync.autoSync", true);
 pref("extensions.zotero.sync.server.username", '');
 pref("extensions.zotero.sync.server.compressData", true);
-pref("extensions.zotero.sync.storage.protocol", "webdavs");
+pref("extensions.zotero.sync.storage.enabled", true);
-pref("extensions.zotero.sync.storage.enabled", false);
+pref("extensions.zotero.sync.storage.protocol", "zotero");
 pref("extensions.zotero.sync.storage.verified", false);
+pref("extensions.zotero.sync.storage.scheme", 'https');
 pref("extensions.zotero.sync.storage.url", '');
 pref("extensions.zotero.sync.storage.username", '');
 pref("extensions.zotero.sync.storage.maxDownloads", 4);
 pref("extensions.zotero.sync.storage.maxUploads", 4);
 pref("extensions.zotero.sync.storage.deleteDelayDays", 30);
+pref("extensions.zotero.sync.storage.groups.enabled", true);
 
 // Proxy
 pref("extensions.zotero.proxies.transparent", true);

userdata.sql

@@ -1,4 +1,4 @@
--- 62
+-- 63
 
 -- This file creates tables containing user-specific data for new users --
 -- any changes made here must be mirrored in transition steps in schema.js::_migrateSchema()
@@ -70,6 +70,7 @@ CREATE TABLE itemAttachments (
     originalPath TEXT,
     syncState INT DEFAULT 0,
     storageModTime INT,
+    storageHash TEXT,
     FOREIGN KEY (itemID) REFERENCES items(itemID),
     FOREIGN KEY (sourceItemID) REFERENCES items(itemID)
 );