From f0f22009c49790c38d5ea72a3cffc2af11eca0bd Mon Sep 17 00:00:00 2001
From: Simon Kornblith <simon@simonster.com>
Date: Sat, 5 Jun 2010 17:49:04 +0000
Subject: [PATCH] - fix (most) unnecessary citation update issues - switch
 Zotero.JSON to native Firefox JSON support - update to citeproc-js 1.0.21

From Frank's announcement:
In this release:

- Tighten up internal "NUMERIC" update_mode to mean styles that render
citation-number in citations (renderings in the bibliography are now
ignored for purposes of setting this flag).

- The numeric styles fix introduced at version 1.0.17 broke with
styles that sort the bibliography on anything other than citation-
number (i.e. document first-reference order).  With this release,
arbitrary sorts of the bibliography work with numeric styles.

- Position evaluation code is now invoked only in styles that make use
of position testing (to save a few cycles).

- Numeric styles now perform targetted citation updates correctly.
---
 chrome/content/zotero/xpcom/citeproc.js    |  25 ++--
 chrome/content/zotero/xpcom/integration.js |  76 +++++------
 chrome/content/zotero/xpcom/zotero.js      | 140 +--------------------
 3 files changed, 62 insertions(+), 179 deletions(-)

diff --git a/chrome/content/zotero/xpcom/citeproc.js b/chrome/content/zotero/xpcom/citeproc.js
index 4c617b164..59f5a238c 100644
--- a/chrome/content/zotero/xpcom/citeproc.js
+++ b/chrome/content/zotero/xpcom/citeproc.js
@@ -1432,7 +1432,7 @@ CSL.dateParser = function (txt) {
 };
 CSL.Engine = function (sys, style, lang, xmlmode) {
 	var attrs, langspec, localexml, locale;
-	this.processor_version = "1.0.20";
+	this.processor_version = "1.0.21";
 	this.csl_version = "1.0";
 	this.sys = sys;
 	this.sys.xml = new CSL.System.Xml.Parsing();
@@ -2224,7 +2224,7 @@ CSL.Engine.prototype.processCitationCluster = function (citation, citationsPre,
 		sortedItems.push(newitem);
 		citation.citationItems[pos].item = Item;
 	}
-	if (!this[this.tmp.area].opt["citation-number-sort"] && sortedItems && sortedItems.length > 1 && this.citation_sort.tokens.length > 0) {
+	if (!this.citation.opt["citation-number-sort"] && sortedItems && sortedItems.length > 1 && this.citation_sort.tokens.length > 0) {
 		len = sortedItems.length;
 		for (pos = 0; pos < len; pos += 1) {
 			sortedItems[pos][1].sortkeys = CSL.getSortKeys.call(this, sortedItems[pos][0], "citation_sort");
@@ -2248,7 +2248,7 @@ CSL.Engine.prototype.processCitationCluster = function (citation, citationsPre,
 	}
 	this.registry.citationreg.citationByIndex = citationByIndex;
 	this.registry.citationreg.citationsByItemId = {};
-	if (this.opt.update_mode === CSL.POSITION || true) {
+	if (this.opt.update_mode === CSL.POSITION) {
 		textCitations = [];
 		noteCitations = [];
 	}
@@ -2267,7 +2267,7 @@ CSL.Engine.prototype.processCitationCluster = function (citation, citationsPre,
 				this.registry.citationreg.citationsByItemId[item[1].id].push(citationByIndex[pos]);
 			}
 		}
-		if (this.opt.update_mode === CSL.POSITION || true) {
+		if (this.opt.update_mode === CSL.POSITION) {
 			if (citationByIndex[pos].properties.noteIndex) {
 				noteCitations.push(citationByIndex[pos]);
 			} else {
@@ -2278,7 +2278,7 @@ CSL.Engine.prototype.processCitationCluster = function (citation, citationsPre,
 	if (!has_bibliography) {
 		this.updateItems(update_items);
 	}
-	if (this.opt.update_mode === CSL.POSITION || true) {
+	if (this.opt.update_mode === CSL.POSITION) {
 		for (pos = 0; pos < 2; pos += 1) {
 			citations = [textCitations, noteCitations][pos];
 			first_ref = {};
@@ -2385,7 +2385,7 @@ CSL.Engine.prototype.processCitationCluster = function (citation, citationsPre,
 			}
 		}
 	}
-	if (this[this.tmp.area].opt["citation-number-sort"] && sortedItems && sortedItems.length > 1 && this.citation_sort.tokens.length > 0) {
+	if (this.citation.opt["citation-number-sort"] && sortedItems && sortedItems.length > 1 && this.citation_sort.tokens.length > 0) {
 		len = sortedItems.length;
 		for (pos = 0; pos < len; pos += 1) {
 			sortedItems[pos][1].sortkeys = CSL.getSortKeys.call(this, sortedItems[pos][0], "citation_sort");
@@ -4188,7 +4188,9 @@ CSL.Node.text = {
 			}
 			if ("citation-number" === variable || "year-suffix" === variable || "citation-label" === variable) {
 				if (variable === "citation-number") {
-					state.opt.update_mode = CSL.NUMERIC;
+					if (state.build.area === "citation") {
+						state.opt.update_mode = CSL.NUMERIC;
+					}
 					if ("citation-number" === state[state.tmp.area].opt.collapse) {
 						this.range_prefix = "-";
 					}
@@ -7032,6 +7034,7 @@ CSL.Registry = function (state) {
 	this.uncited = [];
 	this.refreshes = {};
 	this.akeys = {};
+	this.oldseq = {};
 	this.ambigcites = {};
 	this.sorter = new CSL.Registry.Comparifier(state, "bibliography_sort");
 	this.modes = CSL.getModes.call(this.state);
@@ -7047,6 +7050,7 @@ CSL.Registry = function (state) {
 };
 CSL.Registry.prototype.init = function (myitems, uncited_flag) {
 	var len, pos;
+	this.oldseq = {};
 	if (uncited_flag && this.mylist && this.mylist.length) {
 		this.uncited = myitems;
 		for (pos = 0, len = myitems.length; pos < len; pos += 1) {
@@ -7139,6 +7143,7 @@ CSL.Registry.prototype.rebuildlist = function () {
 	for (pos = 0; pos < len; pos += 1) {
 		item = this.mylist[pos];
 		this.reflist.push(this.registry[item]);
+		this.oldseq[item] = this.registry[item].seq;
 		this.registry[item].seq = (pos + 1);
 	}
 };
@@ -7200,10 +7205,10 @@ CSL.Registry.prototype.renumber = function () {
 	len = this.reflist.length;
 	for (pos = 0; pos < len; pos += 1) {
 		item = this.reflist[pos];
-		if (this.state.opt.update_mode === CSL.NUMERIC && this.state.tmp.taintedItemIDs && item.seq !== (pos + 1)) {
+		item.seq = (pos + 1);
+		if (this.state.opt.update_mode === CSL.NUMERIC && this.state.tmp.taintedItemIDs && item.seq !== this.oldseq[item.id]) {
 			this.state.tmp.taintedItemIDs[item.id] = true;
 		}
-		item.seq = (pos + 1);
 	}
 };
 CSL.Registry.prototype.yearsuffix = function () {
@@ -7893,4 +7898,4 @@ CSL.getModes = function () {
 CSL.Registry.CitationReg = function (state) {
 	this.citationById = {};
 	this.citationByIndex = [];
-};
\ No newline at end of file
+};
diff --git a/chrome/content/zotero/xpcom/integration.js b/chrome/content/zotero/xpcom/integration.js
index dfe37b353..22cb32531 100644
--- a/chrome/content/zotero/xpcom/integration.js
+++ b/chrome/content/zotero/xpcom/integration.js
@@ -557,12 +557,6 @@ Zotero.Integration.Document.prototype._updateSession = function(newField, editFi
 	}
 	var endTime = (new Date()).getTime();
 	Zotero.debug("Collected "+this._fields.length+" fields in "+(endTime-collectFieldsTime)/1000+"; "+1000/((endTime-collectFieldsTime)/this._fields.length)+" fields/second");
-	
-	// if we are reloading this session, assume no item IDs to be updated except for edited items
-	if(this._reloadSession) {
-		this._session.updateItemIDs = {};
-		this._session.bibliographyHasChanged = false;
-	}
 
 	// load uncited items from bibliography
 	if(bibliographyData && !this._session.bibliographyData) {
@@ -588,7 +582,13 @@ Zotero.Integration.Document.prototype._updateSession = function(newField, editFi
 		}
 	}
 	
-	this._session.updateCitations(true);
+	// if we are reloading this session, assume no item IDs to be updated except for edited items
+	if(this._reloadSession) {
+		this._session.updateCitations();
+		this._session.updateIndices = {};
+		this._session.updateItemIDs = {};
+		this._session.bibliographyHasChanged = false;
+	}
 	
 	// create new citation or edit existing citation
 	if(editFieldIndex) { 
@@ -886,7 +886,6 @@ Zotero.Integration.Session.prototype.setData = function(data) {
 	this.data = data;
 	if(data.style.styleID && oldStyleID != data.style.styleID) {
 		this.styleID = data.style.styleID;
-		Zotero.debug("style is "+data.style.styleID);
 		try {
 			var getStyle = Zotero.Styles.get(data.style.styleID);
 			data.style.hasBibliography = getStyle.hasBibliography;
@@ -990,12 +989,15 @@ Zotero.Integration.Session.prototype.getCitationField = function(citation) {
 	var type;
 	var field = [];
 	
-	field.push('"citationID":'+Zotero.JSON.serialize(citation.citationID));
+	field.push('"citationID":'+uneval(citation.citationID));
 	var properties = [];
 	for(var j=0; j<Zotero.Integration.Session._saveProperties.length; j++) {
 		var property = Zotero.Integration.Session._saveProperties[j];
 		if(citation.properties[property] || citation.properties[property] === false) {
-			properties.push('"'+property+'":'+Zotero.JSON.serialize(citation.properties[property]));
+			let propval = typeof citation.properties[property] == "object" ? 
+					Zotero.JSON.serialize(citation.properties[property]) :
+					uneval(citation.properties[property]);
+			properties.push('"'+property+'":'+propval);
 		}
 	}
 	if(properties.length) field.push('"properties":{'+properties.join(",")+"}");
@@ -1009,7 +1011,10 @@ Zotero.Integration.Session.prototype.getCitationField = function(citation) {
 			type = typeof(citation.citationItems[j][k]);
 			if(citation.citationItems[j][k] && Zotero.Integration.Session._saveItems.indexOf(k) !== -1
 			    && Zotero.Integration.Session._acceptableTypes.indexOf(type) !== -1) {
-				citationItem.push('"'+k+'":'+Zotero.JSON.serialize(citation.citationItems[j][k]));
+			    let propval = typeof citation.citationItems[j][k] == "object" ?
+			    		Zotero.JSON.serialize(citation.citationItems[j][k]) :
+			    		uneval(citation.citationItems[j][k]);
+				citationItem.push('"'+k+'":'+propval);
 			}
 		}
 		
@@ -1125,13 +1130,16 @@ Zotero.Integration.Session.prototype.addCitation = function(index, noteIndex, ar
 		}
 	}
 	
-	if(!citation.citationID) {
-		this.newIndices[index] = true;
-		this.updateIndices[index] = true;
-	} else if(!this.oldCitationIDs[citation.citationID]) {
+	var needNewID = !citation.citationID || this.citationIDs[citation.citationID];
+	if(needNewID || !this.oldCitationIDs[citation.citationID]) {
+		if(needNewID) {
+			Zotero.debug("Zotero.Integration: "+citation.citationID+" ("+index+") needs new citationID");
+			citation.citationID = Zotero.randomString();
+		}
 		this.newIndices[index] = true;
 		this.updateIndices[index] = true;
 	}
+	Zotero.debug("Zotero.Integration: adding citationID "+citation.citationID);
 	this.citationIDs[citation.citationID] = true;
 }
 /**
@@ -1251,9 +1259,9 @@ Zotero.Integration.Session.prototype.deleteCitation = function(index) {
 				}
 			}
 		}
-		
-		if(oldCitation.citationID) delete this.citationIDs[oldCitation.citationID];
 	}
+	Zotero.debug("Zotero.Integration: deleting old citationID "+oldCitation.citationID);
+	if(oldCitation.citationID) delete this.citationIDs[oldCitation.citationID];
 	
 	this.updateIndices[index] = true;
 }
@@ -1319,7 +1327,9 @@ Zotero.Integration.Session.prototype.formatCitation = function(index, citation)
 		//Zotero.debug("style.processCitationCluster("+citation.toSource()+", "+citationsPre.toSource()+", "+citationsPost.toSource());
 		var newCitations = this.style.processCitationCluster(citation, citationsPre, citationsPost);
 		for each(var newCitation in newCitations) {
+			Zotero.debug("Zotero.Integration: Citation "+citationIndices[newCitation[0]]+" needs to be updated");
 			this.citationText[citationIndices[newCitation[0]]] = newCitation[1];
+			this.updateIndices[citationIndices[newCitation[0]]] = true;
 		}
 		// this is a heuristic: if other citations get updated, then we should update the
 		// bibliography. it would be nice if citeproc-js gave us a better hint about this
@@ -1330,8 +1340,8 @@ Zotero.Integration.Session.prototype.formatCitation = function(index, citation)
 /**
  * Updates the list of citations to be serialized to the document
  */
-Zotero.Integration.Session.prototype.updateCitations = function(force) {
-	var allUpdatesForced = false;
+Zotero.Integration.Session.prototype.updateCitations = function() {
+	/*var allUpdatesForced = false;
 	var forcedUpdates = {};
 	if(force) {
 		allUpdatesForced = true;
@@ -1353,23 +1363,21 @@ Zotero.Integration.Session.prototype.updateCitations = function(force) {
 				}
 			}
 		}
-	}
+	}*/
 	
 	Zotero.debug("Zotero.Integration: indices of new citations");
 	Zotero.debug([key for(key in this.newIndices)]);
 	Zotero.debug("Zotero.Integration: indices of updated citations");
 	Zotero.debug([key for(key in this.updateIndices)]);
-	Zotero.debug("Zotero.Integration: indices of forcedUpdates");
-	Zotero.debug([key for(key in forcedUpdates)]);
 	
 	var deleteCitations = [];
-	for each(var indexList in [this.newIndices, this.updateIndices, forcedUpdates]) {
+	for each(var indexList in [this.newIndices, this.updateIndices]) {
 		for(var index in indexList) {
 			index = parseInt(index);
 			
 			var citation = this.citationsByIndex[index];
 			if(citation.properties.delete) {
-				deleteCitations.push(index);
+				if(deleteCitations.indexOf(index) == -1) deleteCitations.push(index);
 				continue;
 			}
 			if(this.formatCitation(index, citation)) {
@@ -1382,10 +1390,10 @@ Zotero.Integration.Session.prototype.updateCitations = function(force) {
 		}
 	}
 	
-	if(allUpdatesForced) {
+	/*if(allUpdatesForced) {
 		this.newIndices = {};
 		this.updateIndices = {};
-	}
+	}*/
 	
 	return deleteCitations;
 }
@@ -1489,18 +1497,20 @@ Zotero.Integration.Session.prototype.getBibliographyData = function() {
  * and position)
  */
 Zotero.Integration.Session.prototype.previewCitation = function(citation) {
+	// remove cached citation text
+	this.citationText = {};
+	this.addCitation(citation.properties.index, citation.properties.noteIndex, citation);
+
 	// add citation items
 	try {
-		this.addCitation(citation.properties.index, citation.properties.noteIndex, citation);
 		this.formatCitation(citation.properties.index, citation);
-		this.deleteCitation(citation.properties.index);
 	} catch(e) {
 		Zotero.debug(e);
+		this.deleteCitation(citation.properties.index);
 		throw e;
 	}
+	this.deleteCitation(citation.properties.index);
 	
-	// we don't delete the citationText only because the add citation dialog always calls
-	// previewCitation before returning
 	return this.citationText[citation.properties.index];
 } 
 
@@ -1542,10 +1552,6 @@ Zotero.Integration.Session.prototype.editCitation = function(index, noteIndex, c
 		.openWindow(null, 'chrome://zotero/content/integration/addCitationDialog.xul', '',
 			'chrome,centerscreen,resizable', io);
 	while(!window.closed) Zotero.mainThread.processNextEvent(true);
-		
-	if(citation && !io.citation.citationItems.length) {
-		io.citation = citation;
-	}
 	
 	if(io.citation.citationItems.length) {		// we have an item
 		this.addCitation(index, noteIndex, io.citation);
@@ -1625,7 +1631,7 @@ Zotero.Integration.Session.BibliographyEditInterface.prototype.remove = function
 			citation.properties["delete"] = true;
 		}
 		delete this.session.citationsByItemID[itemID];
-		this.session.updateCitations(true);
+		this.session.updateCitations();
 	}
 	
 	// delete uncited if neceessary
diff --git a/chrome/content/zotero/xpcom/zotero.js b/chrome/content/zotero/xpcom/zotero.js
index cedec20ea..24c14586d 100644
--- a/chrome/content/zotero/xpcom/zotero.js
+++ b/chrome/content/zotero/xpcom/zotero.js
@@ -2552,144 +2552,16 @@ Zotero.WebProgressFinishListener = function(onFinish) {
 }
 
 /*
- * Saves or loads JSON objects. Based on public domain code from
- * http://www.json.org/json.js
+ * Saves or loads JSON objects.
  */
 Zotero.JSON = new function() {
-	this.serialize = serialize;
-	this.unserialize = unserialize;
+	var nativeJSON = Components.classes["@mozilla.org/dom/json;1"].createInstance(Components.interfaces.nsIJSON);
 	
-	// m is a table of character substitutions.
-	var m = {
-		'\b': '\\b',
-		'\t': '\\t',
-		'\n': '\\n',
-		'\f': '\\f',
-		'\r': '\\r',
-		'"' : '\\"',
-		'\\': '\\\\'
-	};
-
-	// Format integers to have at least two digits.
-	function f(n) {
-		return n < 10 ? '0' + n : n;
+	this.serialize = function(arg) {
+		return nativeJSON.encode(arg);
 	}
 	
-	function replaceFunction(a) {
-		var c = m[a];
-		if (c) {
-			return c;
-		}
-		c = a.charCodeAt();
-		return '\\u00' +
-			Math.floor(c / 16).toString(16) +
-			(c % 16).toString(16);
-	}
-	
-	function serialize(arg) {
-		if(arg === null) {
-			return "null";
-		} else if(arg instanceof Array) {
-			var a = [],	 // The array holding the partial texts.
-				i,		  // Loop counter.
-				l = arg.length,
-				v;		  // The value to be stringified.
-	
-	
-			// For each value in arg array...
-	
-			for (i = 0; i < l; i += 1) {
-				var out = serialize(arg[i]);
-				if(out !== undefined) {
-					a.push(out);
-				}
-			}
-	
-			// Join all of the member texts together and wrap them in brackets.
-	
-			return '[' + a.join(',') + ']';
-		} else if(typeof(arg) == "boolean") {
-			return String(arg);
-		} else if(arg instanceof Date) {
-			// Eventually, this method will be based on the date.toISOString method.
-	
-			return '"' + arg.getUTCFullYear() + '-' +
-					f(arg.getUTCMonth() + 1) + '-' +
-					f(arg.getUTCDate()) + 'T' +
-					f(arg.getUTCHours()) + ':' +
-					f(arg.getUTCMinutes()) + ':' +
-					f(arg.getUTCSeconds()) + 'Z"';
-		} else if(typeof(arg) == "number") {
-			// JSON numbers must be finite. Encode non-finite numbers as null.
-
-			return isFinite(arg) ? String(arg) : 'null';
-		} else if(typeof(arg) == "string") {
-			if (/["\\\x00-\x1f]/.test(arg)) {
-				return '"' + arg.replace(/[\x00-\x1f\\"]/g, replaceFunction) + '"';
-			}
-			return '"' + arg + '"';
-		} else if(arg instanceof Object) {
-			var a = [],	 // The array holding the partial texts.
-				k,		  // The current key.
-				v;		  // The current value.
-	
-			// Iterate through all of the keys in the object, ignoring the proto chain
-			// and keys that are not strings.
-	
-			for (k in arg) {
-				if (typeof k === 'string' &&
-						Object.prototype.hasOwnProperty.apply(arg, [k])) {
-					var out = serialize(arg[k]);
-					if(out !== undefined) {
-						a.push(serialize(k) + ':' + out);
-					}
-				}
-			}
-			
-			// Join all of the member texts together and wrap them in braces.
-			
-			return '{' + a.join(',') + '}';
-		}
-		
-		return undefined;
-	}
-
-
-	function unserialize(arg) {
-		var j;
-
-		// Parsing happens in three stages. In the first stage, we run the text against
-		// a regular expression which looks for non-JSON characters. We are especially
-		// concerned with '()' and 'new' because they can cause invocation, and '='
-		// because it can cause mutation. But just to be safe, we will reject all
-		// unexpected characters.
-		
-		// We split the first stage into 3 regexp operations in order to work around
-		// crippling deficiencies in Safari's regexp engine. First we replace all
-		// backslash pairs with '@' (a non-JSON character). Second we delete all of
-		// the string literals. Third, we look to see if only JSON characters
-		// remain. If so, then the text is safe for eval.
-
-		if (/^[,:{}\[\]0-9.\-+Eaeflnr-u \n\r\t]*$/.test(arg.
-				replace(/\\./g, '@').
-				replace(/"[^"\\\n\r]*"/g, ''))) {
-
-			// In the second stage we use the eval function to compile the text into a
-			// JavaScript structure. The '{' operator is subject to a syntactic ambiguity
-			// in JavaScript: it can begin a block or an object literal. We wrap the text
-			// in parens to eliminate the ambiguity.
-			
-			// Friendly AMO reviewer: This is the official json.org library and is safe.
-			j = eval('(' + arg + ')');
-			
-			// In the optional third stage, we recursively walk the new structure, passing
-			// each name/value pair to a filter function for possible transformation.
-
-			return j;
-		}
-
-		// If the text is not JSON parseable, then a SyntaxError is thrown.
-
-		throw new SyntaxError('parseJSON');
+	this.unserialize = function(arg) {
+		return nativeJSON.decode(arg);
 	}
 }
\ No newline at end of file