Pull changes from upstream master

chrome/content/zotero/preferences/preferences_sync.js

@@ -398,7 +398,6 @@ Zotero_Preferences.Sync = {
 
 	onStorageSettingsKeyPress: Zotero.Promise.coroutine(function* (event) {
 		if (event.keyCode == 13) {
-			yield this.onStorageSettingsChange();
 			yield this.verifyStorageServer();
 		}
 	}),
@@ -480,6 +479,11 @@ Zotero_Preferences.Sync = {
 
 
 	verifyStorageServer: Zotero.Promise.coroutine(function* () {
+		// onchange weirdly isn't triggered when clicking straight from a field to the button,
+		// so we have to trigger this here (and we don't trigger it for Enter in
+		// onStorageSettingsKeyPress()).
+		yield this.onStorageSettingsChange();
+
 		Zotero.debug("Verifying storage");
 
 		var verifyButton = document.getElementById("storage-verify");

chrome/content/zotero/progressMeterWindow.xul

@@ -0,0 +1,14 @@
+<?xml version="1.0"?>
+
+<?xml-stylesheet href="chrome://global/skin/" type="text/css"?>
+<?xml-stylesheet href="chrome://zotero/skin/zotero.css" type="text/css"?>
+
+<window id="zotero-progress-meter-window"
+        xmlns="http://www.mozilla.org/keymaster/gatekeeper/there.is.only.xul"
+        windowtype="alert:alert">
+
+	<vbox id="zotero-progress-text-box" flex="1">
+		<label/>
+		<progressmeter/>
+	</vbox>
+</window>

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

@@ -0,0 +1,5 @@
+"use strict";
+
+Zotero.DataCache = {
+
+};

chrome/content/zotero/xpcom/db.js

@@ -485,7 +485,7 @@ Zotero.DBConnection.prototype.executeTransaction = Zotero.Promise.coroutine(func
 		// Run begin callbacks
 		for (var i=0; i<this._callbacks.begin.length; i++) {
 			if (this._callbacks.begin[i]) {
-				this._callbacks.begin[i]();
+				this._callbacks.begin[i](id);
 			}
 		}
 		var conn = this._getConnection(options) || (yield this._getConnectionAsync(options));
@@ -516,13 +516,13 @@ Zotero.DBConnection.prototype.executeTransaction = Zotero.Promise.coroutine(func
 		// Run temporary commit callbacks
 		var f;
 		while (f = this._callbacks.current.commit.shift()) {
-			yield Zotero.Promise.resolve(f());
+			yield Zotero.Promise.resolve(f(id));
 		}
 
 		// Run commit callbacks
 		for (var i=0; i<this._callbacks.commit.length; i++) {
 			if (this._callbacks.commit[i]) {
-				yield this._callbacks.commit[i]();
+				yield this._callbacks.commit[i](id);
 			}
 		}
 
@@ -549,13 +549,13 @@ Zotero.DBConnection.prototype.executeTransaction = Zotero.Promise.coroutine(func
 		// Run temporary commit callbacks
 		var f;
 		while (f = this._callbacks.current.rollback.shift()) {
-			yield Zotero.Promise.resolve(f());
+			yield Zotero.Promise.resolve(f(id));
 		}
 
 		// Run rollback callbacks
 		for (var i=0; i<this._callbacks.rollback.length; i++) {
 			if (this._callbacks.rollback[i]) {
-				yield Zotero.Promise.resolve(this._callbacks.rollback[i]());
+				yield Zotero.Promise.resolve(this._callbacks.rollback[i](id));
 			}
 		}
 

chrome/content/zotero/xpcom/fulltext.js

@@ -446,7 +446,8 @@ Zotero.Fulltext = Zotero.FullText = new function(){
 			var totalPages = yield getTotalPagesFromFile(itemID);
 		}
 		catch (e) {
-			Zotero.debug("Error running pdfinfo");
+			Zotero.debug("Error running " + _pdfInfo.path, 1);
+			Zotero.logError(e);
 		}
 
 
@@ -468,9 +469,8 @@ Zotero.Fulltext = Zotero.FullText = new function(){
 			yield Zotero.Utilities.Internal.exec(exec, args);
 		}
 		catch (e) {
-			Components.utils.reportError(e);
-			Zotero.debug("Error running pdftotext", 1);
-			Zotero.debug(e, 1);
+			Zotero.debug("Error running " + exec.path, 1);
+			Zotero.logError(e);
 			return false;
 		}
 

chrome/content/zotero/xpcom/http.js

@@ -1024,6 +1024,7 @@ Zotero.HTTP = new function() {
 		}
 
 		let secInfo = channel.securityInfo;
+		let msg;
 		if (secInfo instanceof Ci.nsITransportSecurityInfo) {
 			secInfo.QueryInterface(Ci.nsITransportSecurityInfo);
 			if ((secInfo.securityState & Ci.nsIWebProgressListener.STATE_IS_INSECURE)
@@ -1052,6 +1053,10 @@ Zotero.HTTP = new function() {
 					== Ci.nsIWebProgressListener.STATE_IS_BROKEN) {
 				msg = Zotero.getString('sync.error.sslConnectionError');
 			}
+			else {
+				Zotero.debug(secInfo.securityState, 1);
+				msg = Zotero.getString('sync.error.sslConnectionError');
+			}
 			throw new Zotero.HTTP.SecurityException(
 				msg,
 				{

chrome/content/zotero/xpcom/integration.js

@@ -686,7 +686,7 @@ Zotero.Integration.Interface.prototype.setDocPrefs = Zotero.Promise.coroutine(fu
 				fieldNoteTypes.push(this._session.data.prefs.noteType);
 			}
 		} else if(convertBibliographies
-				&& type === INTEGRATION_TYPE_BIBLIOGRAPHY) {
+				&& field.type === INTEGRATION_TYPE_BIBLIOGRAPHY) {
 			fieldsToConvert.push(fields[i]);
 			fieldNoteTypes.push(0);
 		}
@@ -1001,11 +1001,9 @@ Zotero.Integration.Fields.prototype._updateDocument = async function(forceCitati
 			// If we're not specifically *not* trying to regen text
 			if (forceCitations != FORCE_CITATIONS_FALSE
 					// Or metadata has changed thus changing the formatted citation
-					|| (citation.properties.formattedCitation !== formattedCitation)
-					// Or we shouldn't ignore citation changes and the citation text has changed
-					|| (!ignoreCitationChanges && plainCitation !== citation.properties.plainCitation)) {
+					|| (citation.properties.formattedCitation !== formattedCitation)) {
 
-				if (plainCitation !== citation.properties.plainCitation) {
+				if (!ignoreCitationChanges && plainCitation !== citation.properties.plainCitation) {
 					// Citation manually modified; ask user if they want to save changes
 					Zotero.debug("[_updateDocument] Attempting to update manually modified citation.\n"
 						+ "Original: " + citation.properties.plainCitation + "\n"
@@ -1038,13 +1036,6 @@ Zotero.Integration.Fields.prototype._updateDocument = async function(forceCitati
 		var serializedCitation = citation.serialize();
 		if (serializedCitation != citation.properties.field) {
 			citationField.setCode(serializedCitation);
-			if (this._session.data.prefs.fieldType === "ReferenceMark"
-					&& this._session.data.prefs.noteType != 0 && isRich
-					&& !citation.properties.dontUpdate) {
-				// For ReferenceMarks with formatting, we need to set the text again, because
-				// setting the field code removes formatting from the mark. I don't like this.
-				citationField.setText(formattedCitation, isRich);
-			}
 		}
 		nUpdated++;
 	}
@@ -1158,10 +1149,10 @@ Zotero.Integration.Fields.prototype.addEditCitation = Zotero.Promise.coroutine(f
 	var previewFn = Zotero.Promise.coroutine(function* (citation) {
 		let idx = yield fieldIndexPromise;
 		yield citationsByItemIDPromise;
-		
-		let citations = this._session.getCiteprocLists();
-		let citationsPre = citations.slice(0, idx);
-		let citationsPost = citations.slice(idx+1);
+
+		var [citations, fieldToCitationIdxMapping, citationToFieldIdxMapping] = this._session.getCiteprocLists();
+		let citationsPre = citations.slice(0, fieldToCitationIdxMapping[idx]);
+		let citationsPost = citations.slice(fieldToCitationIdxMapping[idx]+1);
 		try {
 			return this._session.style.previewCitationCluster(citation, citationsPre, citationsPost, "rtf");
 		} catch(e) {
@@ -1565,10 +1556,17 @@ Zotero.Integration.Session.prototype.addCitation = Zotero.Promise.coroutine(func
 
 Zotero.Integration.Session.prototype.getCiteprocLists = function() {
 	var citations = [];
-	for(let i in this.citationsByIndex) {
-		citations.push([this.citationsByIndex[i].citationID, this.citationsByIndex[i].properties.noteIndex]);
-	}
-	return citations;
+	var fieldToCitationIdxMapping = [];
+	var citationToFieldIdxMapping = {};
+	var i = 0;
+	// This relies on the order of citationsByIndex keys being stable and sorted in ascending order
+	// Which it seems to currently be true for every modern JS engine, so we're probably fine
+	for(let idx in this.citationsByIndex) {
+		citations.push([this.citationsByIndex[idx].citationID, this.citationsByIndex[idx].properties.noteIndex]);
+		fieldToCitationIdxMapping[i] = idx;
+		citationToFieldIdxMapping[idx] = i++;
+	}
+	return [citations, fieldToCitationIdxMapping, citationToFieldIdxMapping];
 }
 
 /**
@@ -1580,7 +1578,7 @@ Zotero.Integration.Session.prototype._updateCitations = async function () {
 	Zotero.debug("Integration: Indices of updated citations");
 	Zotero.debug(Object.keys(this.updateIndices));
 
-	var citations = this.getCiteprocLists();
+	var [citations, fieldToCitationIdxMapping, citationToFieldIdxMapping] = this.getCiteprocLists();
 
 	for (let indexList of [this.newIndices, this.updateIndices]) {
 		for (let index in indexList) {
@@ -1592,12 +1590,12 @@ Zotero.Integration.Session.prototype._updateCitations = async function () {
 			if (!citation) continue;
 			citation = citation.toJSON();
 
-			let citationsPre = citations.slice(0, index);
+			let citationsPre = citations.slice(0, citationToFieldIdxMapping[index]);
 			var citationsPost;
 			if (index in this.newIndices) {
 				citationsPost = [];
 			} else {
-				citationsPost = citations.slice(index+1);
+				citationsPost = citations.slice(citationToFieldIdxMapping[index]+1);
 			}
 
 			Zotero.debug("Integration: style.processCitationCluster("+citation.toSource()+", "+citationsPre.toSource()+", "+citationsPost.toSource());
@@ -1606,7 +1604,7 @@ Zotero.Integration.Session.prototype._updateCitations = async function () {
 			this.bibliographyHasChanged |= info.bibchange;
 
 			for (let citationInfo of newCitations) {
-				let idx = citationInfo[0], text = citationInfo[1];
+				let idx = fieldToCitationIdxMapping[citationInfo[0]], text = citationInfo[1];
 				this.updateIndices[idx] = true;
 				this.citationsByIndex[idx].text = text;
 			}
@@ -1656,13 +1654,6 @@ Zotero.Integration.Session.prototype.writeDelayedCitation = Zotero.Promise.corou
 	}
 
 	field.setCode(citation.serialize());
-	if (this.data.prefs.fieldType === "ReferenceMark"
-			&& this.data.prefs.noteType != 0 && isRich
-			&& !citation.properties.dontUpdate) {
-		// For ReferenceMarks with formatting, we need to set the text again, because
-		// setting the field code removes formatting from the mark. I don't like this.
-		field.setText(text, isRich);
-	}
 
 	// Update bibliography with a static string
 	var fields = yield this.fields.get();
@@ -2065,7 +2056,7 @@ Zotero.Integration.Field = class {
 		}
 		// This is not the best solution in terms of performance
 		for (let prop in field) {
-			if (!(prop in this)) {
+			if (prop[0] != '_' && !(prop in this)) {
 				this[prop] = field[prop].bind ? field[prop].bind(field) : field[prop];
 			}
 		}

chrome/content/zotero/xpcom/notifier.js

@@ -32,7 +32,7 @@ Zotero.Notifier = new function(){
 		'collection-item', 'item-tag', 'tag', 'setting', 'group', 'trash',
 		'bucket', 'relation', 'feed', 'feedItem', 'sync', 'api-key'
 	];
-	var _inTransaction;
+	var _transactionID = false;
 	var _queue = {};
 
 
@@ -106,7 +106,7 @@ Zotero.Notifier = new function(){
 	* - New events and types should be added to the order arrays in commit()
 	**/
 	this.trigger = Zotero.Promise.coroutine(function* (event, type, ids, extraData, force) {
-		if (_inTransaction && !force) {
+		if (_transactionID && !force) {
 			return this.queue(event, type, ids, extraData);
 		}
 
@@ -173,7 +173,7 @@ Zotero.Notifier = new function(){
 			queue = queue._queue;
 		}
 		else {
-			if (!_inTransaction) {
+			if (!_transactionID) {
 				throw new Error("Can't queue event outside of a transaction");
 			}
 			queue = _queue;
@@ -278,11 +278,11 @@ Zotero.Notifier = new function(){
 	 *
 	 * Note: Be sure the matching commit() gets called (e.g. in a finally{...} block) or
 	 * notifications will break until Firefox is restarted or commit(true)/reset() is called manually
+	 *
+	 * @param {String} [transactionID]
 	 */
-	this.begin = function () {
-		if (!_inTransaction) {
-			_inTransaction = true;
-		}
+	this.begin = function (transactionID = true) {
+		_transactionID = transactionID;
 	}
 
 
@@ -291,8 +291,9 @@ Zotero.Notifier = new function(){
 	 *
 	 * @param {Zotero.Notifier.Queue|Zotero.Notifier.Queue[]} [queues] - One or more queues to use
 	 *     instead of the internal queue
+	 * @param {String} [transactionID]
 	 */
-	this.commit = Zotero.Promise.coroutine(function* (queues) {
+	this.commit = Zotero.Promise.coroutine(function* (queues, transactionID = true) {
 		if (queues) {
 			if (!Array.isArray(queues)) {
 				queues = [queues];
@@ -308,7 +309,7 @@ Zotero.Notifier = new function(){
 				}
 			}
 		}
-		else if (!_inTransaction) {
+		else if (!_transactionID) {
 			throw new Error("Can't commit outside of transaction");
 		}
 		else {
@@ -375,7 +376,7 @@ Zotero.Notifier = new function(){
 		}
 
 		if (!queues) {
-			this.reset();
+			this.reset(transactionID);
 		}
 
 		if (totals) {
@@ -407,10 +408,13 @@ Zotero.Notifier = new function(){
 	/*
 	 * Reset the event queue
 	 */
-	this.reset = function () {
+	this.reset = function (transactionID = true) {
+		if (transactionID != _transactionID) {
+			return;
+		}
 		//Zotero.debug("Resetting notifier event queue");
 		_queue = {};
-		_inTransaction = false;
+		_transactionID = false;
 	}
 }
 

chrome/content/zotero/xpcom/schema.js

@@ -829,7 +829,7 @@ Zotero.Schema = new function(){
 					index[id].extract = true;
 				}
 
-				let sql = "SELECT fileName, metadataJSON FROM translatorCache";
+				let sql = "SELECT rowid, fileName, metadataJSON FROM translatorCache";
 				let rows = yield Zotero.DB.queryAsync(sql);
 				// If there's anything in the cache, see what we actually need to extract
 				for (let i = 0; i < rows.length; i++) {
@@ -842,10 +842,10 @@ Zotero.Schema = new function(){
 						Zotero.logError(e);
 						Zotero.debug(json, 1);
 
-						// // If JSON is invalid, clear from cache
+						// If JSON is invalid, clear from cache
 						yield Zotero.DB.queryAsync(
-							"DELETE FROM translatorCache WHERE fileName=?",
-							rows[i].fileName
+							"DELETE FROM translatorCache WHERE rowid=?",
+							rows[i].rowid
 						);
 						continue;
 					}