- closes #921: Revise handling of deleted citations. Upon encountering a deleted citation, the plug-in now highlights the citation and allows the user to reselect the item (which applies to all places the item is cited), to delete all citations of the item from the document, or to cancel the update

- adds syntax checking to build script
- only display the last 5 lines of the python error/traceback

chrome/content/zotero/selectItemsDialog.js

@@ -36,6 +36,9 @@ function doLoad()
 	Zotero.setFontSize(sbc);
 	
 	io = window.arguments[0];
+	if(io.wrappedJSObject) io = io.wrappedJSObject;
+	if(io.addBorder) document.getElementsByTagName("dialog")[0].style.border = "1px solid black";
+	if(io.singleSelection) document.getElementById("zotero-items-tree").setAttribute("seltype", "single");
 	
 	collectionsView = new Zotero.CollectionTreeView();
 	document.getElementById('zotero-collections-tree').view = collectionsView;

chrome/content/zotero/xpcom/integration.js

@@ -20,7 +20,7 @@
     ***** END LICENSE BLOCK *****
 */
 
-const API_VERSION = 1;
+const API_VERSION = 2;
 const COMPAT_API_VERSION = 5;
 
 Zotero.Integration = new function() {
@@ -415,6 +415,12 @@ Zotero.Integration.Request = function(xml) {
 		if(this.needPrefs) {
 			this.setDocPrefs();
 		}
+		if(this.body.reselectItem.length()) {
+			this.reselectItem();
+		} else {
+			// if no more reselections, clear the reselectItem map
+			this._session.reselectItem = new Object();
+		}
 		if(this.body.updateCitations.length() || this.body.updateBibliography.length()) {
 			this.processCitations();
 		}
@@ -431,8 +437,7 @@ Zotero.Integration.Request = function(xml) {
 		try {
 			var text = Zotero.getString("integration.error."+e, Zotero.version);
 			code = e;
-		} catch(e) {
+		} catch(e) {}
-		}
 		
 		this.responseXML = <SOAP-ENV:Envelope xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/">
 			<SOAP-ENV:Body>
@@ -494,7 +499,7 @@ Zotero.Integration.Request.prototype.setDocPrefs = function() {
 	
 	var io = new function() {
 		this.wrappedJSObject = this;
-	}
+	};
 	
 	io.openOffice = this.header.client.@agent == "OpenOffice.org"
 	
@@ -502,7 +507,7 @@ Zotero.Integration.Request.prototype.setDocPrefs = function() {
 	io.useEndnotes = this._session.prefs.useEndnotes;
 	io.useBookmarks = this._session.prefs.fieldType;
 	
-	this.watcher = Components.classes["@mozilla.org/embedcomp/window-watcher;1"]
+	Components.classes["@mozilla.org/embedcomp/window-watcher;1"]
 		.getService(Components.interfaces.nsIWindowWatcher)
 		.openWindow(null, 'chrome://zotero/content/integrationDocPrefs.xul', '',
 		'chrome,modal,centerscreen' + (Zotero.isWin ? ',popup' : ''), io, true);
@@ -528,6 +533,28 @@ Zotero.Integration.Request.prototype.setDocPrefs = function() {
 	this.responseBody.appendChild(<setDocPrefsResponse/>);
 }
 
+/**
+ * Reselects an item to replace a deleted item
+ **/
+Zotero.Integration.Request.prototype.reselectItem = function() {
+	default xml namespace = Zotero.Integration.ns; with({});
+	
+	var io = new function() {
+		this.wrappedJSObject = this;
+	};
+	io.addBorder = Zotero.isWin;
+	io.singleSelection = true;
+	
+	Components.classes["@mozilla.org/embedcomp/window-watcher;1"]
+		.getService(Components.interfaces.nsIWindowWatcher)
+		.openWindow(null,'chrome://zotero/content/selectItemsDialog.xul', '',
+		'chrome,modal,centerscreen,resizable=yes' + (Zotero.isWin ? ',popup' : ''), io, true);
+	
+	if(io.dataOut && io.dataOut.length) {
+		this._session.reselectItem[this.body.reselectItem.@id] = io.dataOut[0];
+	}
+}
+
 /**
  * Updates citations
  **/
@@ -552,44 +579,48 @@ Zotero.Integration.Request.prototype.processCitations = function() {
 		}
 	}
 	
-	// load bibliography data here
+	if(!this._session.haveMissing) {
-	if(this.header.bibliography.length()) {
+		// load bibliography data here
-		this._session.loadBibliographyData(Zotero.Utilities.prototype.trim(this.header.bibliography.toString()));
+		if(this.header.bibliography.length()) {
-	}
+			this._session.loadBibliographyData(Zotero.Utilities.prototype.trim(this.header.bibliography.toString()));
-	
-	this._session.updateItemSet();
-	
-	// create new citation
-	if(editCitationIndex) { 
-		this._session.updateCitations(editCitationIndex-1);
-		var added = this._session.editCitation(editCitationIndex, editCitation);
-		if(!added) {
-			if(editCitation) {
-				this._session.addCitation(editCitationIndex, editCitation);
-			} else {
-				this._session.deleteCitation(editCitationIndex);
-			}
 		}
+		
 		this._session.updateItemSet();
 	}
-	this._session.updateCitations();
 	
-	// edit bibliography
+	if(!this._session.haveMissing) {
-	if(this.body.updateBibliography.@edit.toString()) {
+		// create new citation
-		this._session.editBibliography();
+		if(editCitationIndex) { 
-	}
+			this._session.updateCitations(editCitationIndex-1);
-	
+			var added = this._session.editCitation(editCitationIndex, editCitation);
-	// update
+			if(!added) {
-	var output = new Array();
+				if(editCitation) {
-	if(this.body.updateBibliography.length()	 					// if we want updated bib
+					this._session.addCitation(editCitationIndex, editCitation);
-			&& (this._session.bibliographyHasChanged					// and bibliography changed
+				} else {
-			|| this.body.updateBibliography.@force.toString())) {	// or if we should generate regardless of changes
+					this._session.deleteCitation(editCitationIndex);
-		if(this._session.bibliographyDataHasChanged) {
+				}
-			this.responseBody.updateBibliographyResponse.code = this._session.getBibliographyData();
+			}
+			this._session.updateItemSet();
+		}
+		this._session.updateCitations();
+		
+		// edit bibliography
+		if(this.body.updateBibliography.@edit.toString()) {
+			this._session.editBibliography();
+		}
+		
+		// update
+		var output = new Array();
+		if(this.body.updateBibliography.length()	 					// if we want updated bib
+				&& (this._session.bibliographyHasChanged				// and bibliography changed
+				|| this.body.updateBibliography.@force.toString())) {	// or if we should generate regardless of changes
+			if(this._session.bibliographyDataHasChanged) {
+				this.responseBody.updateBibliographyResponse.code = this._session.getBibliographyData();
+			}
+			this.responseBody.updateBibliographyResponse.text = this._session.getBibliography(true);
 		}
-		this.responseBody.updateBibliographyResponse.text = this._session.getBibliography(true);
 	}
-	
+		
 	// get citations
 	if(this.body.updateCitations.length()) {
 		this.responseBody.updateCitationsResponse.citations = this._session.getCitations(!!this.body.updateCitations.@force.toString() || this._session.regenerateAll, true);
@@ -797,6 +828,7 @@ Zotero.Integration.Session = function() {
 	// holds items not in document that should be in bibliography
 	this.uncitedItems = new Object();
 	this.prefs = new Object();
+	this.reselectItem = new Object();
 	
 	this.resetRequest();
 }
@@ -832,11 +864,12 @@ Zotero.Integration.Session.prototype.resetRequest = function() {
 	this.citationsByItemID = new Object();
 	this.citationsByIndex = new Array();
 	
+	this.haveMissing = false;
 	this.regenerateAll = false;
 	this.bibliographyHasChanged = false;
 	this.bibliographyDataHasChanged = false;
 	this.updateItemIDs = new Object();
-	this.updateIndices = new Object()
+	this.updateIndices = new Object();
 }
 
 /*
@@ -900,28 +933,28 @@ Zotero.Integration.Session.prototype.addCitation = function(index, arg) {
 	}
 	
 	var completed = this.completeCitation(citation);
-	if(!completed) {
-		// doesn't exist
-		this.deleteCitation(index);
-		return;
-	}
 	
 	// add to citationsByItemID and citationsByIndex
-	for(var i=0; i<citation.citationItems.length; i++) {
+	if(completed) {
-		var citationItem = citation.citationItems[i];
+		for(var i=0; i<citation.citationItems.length; i++) {
-		if(!this.citationsByItemID[citationItem.itemID]) {
+			var citationItem = citation.citationItems[i];
-			this.citationsByItemID[citationItem.itemID] = [citation];
+			if(!this.citationsByItemID[citationItem.itemID]) {
-		} else {
+				this.citationsByItemID[citationItem.itemID] = [citation];
-			var byItemID = this.citationsByItemID[citationItem.itemID];
-			if(byItemID[byItemID.length-1].properties.index < index) {
-				// if index is greater than the last index, add to end
-				byItemID.push(citation);
 			} else {
-				// otherwise, splice in at appropriate location
+				var byItemID = this.citationsByItemID[citationItem.itemID];
-				for(var j=0; byItemID[j].properties.index < index && j<byItemID.length-1; j++) {}
+				if(byItemID[byItemID.length-1].properties.index < index) {
-				byItemID.splice(j, 0, citation);
+					// if index is greater than the last index, add to end
+					byItemID.push(citation);
+				} else {
+					// otherwise, splice in at appropriate location
+					for(var j=0; byItemID[j].properties.index < index && j<byItemID.length-1; j++) {}
+					byItemID.splice(j, 0, citation);
+				}
 			}
 		}
+	} else {
+		this.updateIndices[index] = true;
+		this.haveMissing = true;
 	}
 	
 	citation.properties.index = index;
@@ -933,11 +966,21 @@ Zotero.Integration.Session.prototype.addCitation = function(index, arg) {
  */
 Zotero.Integration.Session.prototype.completeCitation = function(object) {
 	// replace item IDs with real items
+	var missing = [];
+	var missingItems = [];
 	for(var i=0; i<object.citationItems.length; i++) {
 		var citationItem = object.citationItems[i];
 		
-		var zoteroItem;
+		// deal with a reselected item
-		if(citationItem.key) {
+		if(citationItem.key && this.reselectItem[citationItem.key]) {
+			citationItem.itemID = this.reselectItem[citationItem.key];
+			citationItem.key = undefined;
+		} else if(citationItem.itemID && this.reselectItem[citationItem.itemID]) {
+			citationItem.itemID = this.reselectItem[citationItem.itemID];
+			citationItem.key = undefined;
+		}
+		
+		if(citationItem.key !== undefined) {
 			var item = this.itemSet.getItemsByKeys([citationItem.key])[0];
 		} else {
 			this.updateItemIDs[citationItem.itemID] = true;
@@ -946,12 +989,18 @@ Zotero.Integration.Session.prototype.completeCitation = function(object) {
 		
 		// loop through items not in itemSet
 		if(item == false) {
+			var zoteroItem = null;
 			if(citationItem.key) {
 				zoteroItem = Zotero.Items.getByKey(citationItem.key);
 			} else {
 				zoteroItem = Zotero.Items.get(citationItem.itemID);
 			}
-			if(!zoteroItem) return false;
+			if(!zoteroItem) {
+				// item does not exist
+				missing.push(i);
+				missingItems.push(citationItem.key ? citationItem.key : citationItem.itemID);
+				continue;
+			}
 			item = this.itemSet.add([zoteroItem])[0];
 			
 			this.dateModified[citationItem.itemID] = item.zoteroItem.getField("dateModified", true, true);
@@ -962,6 +1011,11 @@ Zotero.Integration.Session.prototype.completeCitation = function(object) {
 		citationItem.item = item;
 		if(!citationItem.itemID) citationItem.itemID = item.id;
 	}
+	if(missing.length) {
+		object.properties.missing = missing;
+		object.properties.missingItems = missingItems;
+		return false;
+	}
 	return true;
 }
 
@@ -1045,8 +1099,9 @@ Zotero.Integration.Session.prototype.unserializeCitation = function(arg, index)
 /*
  * marks a citation for removal
  */
-Zotero.Integration.Session.prototype.deleteCitation = function(index) {
+Zotero.Integration.Session.prototype.deleteCitation = function(index, key) {
 	this.citationsByIndex[index] = {properties:{"delete":true}};
+	if(key) this.citationsByIndex[index].properties.key = key;
 	this.updateIndices[index] = true;
 }
 
@@ -1133,7 +1188,7 @@ Zotero.Integration.Session.prototype.getCitationPositions = function(citation, u
 	for(var previousIndex = citation.properties.index-1;
 		previousIndex != -1
 			&& (!this.citationsByIndex[previousIndex]
-			|| this.citationsByIndex[previousIndex].properties.delete); 
+			|| this.citationsByIndex[previousIndex].properties["delete"]); 
 		previousIndex--) {}
 	var previousCitation = (previousIndex == -1 ? false : this.citationsByIndex[previousIndex]);
 	
@@ -1182,7 +1237,7 @@ Zotero.Integration.Session.prototype.updateCitations = function(toIndex) {
 	for(var i=0; i<=toIndex; i++) {
 		var citation = this.citationsByIndex[i];
 		// get position, updating if necesary
-		if(citation && !citation.properties.delete && !citation.properties.custom) {
+		if(citation && !citation.properties["delete"] && !citation.properties.custom) {
 			this.getCitationPositions(citation, true);
 		}
 	}
@@ -1193,20 +1248,14 @@ Zotero.Integration.Session.prototype.updateCitations = function(toIndex) {
  * then re-sorting
  */
 Zotero.Integration.Session.prototype.updateItemSet = function() {
-	var addItems = [];
 	var deleteItems = [];
+	var missingItems = [];
 	
+	// see if items were deleted from Zotero
 	for(var i in this.citationsByItemID) {
-		// see if items were deleted from Zotero
 		if (!Zotero.Items.get(i)) {
-			deleteItems.push(itemID);
+			deleteItems.push(i);
-			if(this.citationsByItemID[i].length) {
+			missingItems.push(i);
-				for(var j=0; j<this.citationsByItemID[i].length; j++) {
-					var citation = this.citationsByItemID[i][j];
-					this.updateIndices[citation.properties.index] = true;
-					citation.properties.delete = true;
-				}
-			}
 		}
 	}
 	
@@ -1228,12 +1277,26 @@ Zotero.Integration.Session.prototype.updateItemSet = function() {
 		}
 	}
 	
+	// delete items from item set
 	if(deleteItems.length) {
 		this.itemSet.remove(deleteItems);
 		this.bibliographyHasChanged = true;
 	}
 	
-	this.sortItemSet();
+	// add missing attribute to citations of missing items
+	if(missingItems.length) {
+		for each(var i in missingItems) {
+			if(this.citationsByItemID[i].length) {
+				for(var j=0; j<this.citationsByItemID[i].length; j++) {
+					this.updateIndices[this.citationsByItemID[i][j].properties.index] = true;
+					this.completeCitation(this.citationsByItemID[i][j]);
+				}
+			}
+		}
+		this.haveMissing = true;
+	} else {
+		this.sortItemSet();
+	}
 }
 
 /*
@@ -1326,15 +1389,28 @@ Zotero.Integration.Session.prototype.getCitations = function(regenerateAll, useX
 			output.push(i);
 		}
 		
-		if(citation.properties["delete"]) {
+		if(citation.properties["delete"] || citation.properties.missing) {
-			// delete citation
+			// delete citation, or flag as missing
 			if(useXML) {
-				citationXML.@delete = "1";
+				if(citation.properties.missing) {
+					if(citation.citationItems.length > 1) {
+						// use n tags if there are multiple items in the citation
+						for(var j=0; j<citation.properties.missing.length; j++) {
+							citationXML.missing += <missing n={citation.properties.missing[j]+1} 
+								id={citation.properties.missingItems[j]}/>;
+						}
+					} else {
+						citationXML.missing = <missing id={citation.properties.missingItems[0]}/>;
+					}
+				} else {
+					citationXML["@delete"] = "1";
+				}
+				output.appendChild(citationXML);
 			} else {
 				output.push("!");
 				output.push("!");
 			}
-		} else {
+		} else if(!useXML || !this.haveMissing) {
 			var field = this.getCitationField(citation);
 
 			if(useXML) {
@@ -1365,9 +1441,9 @@ Zotero.Integration.Session.prototype.getCitations = function(regenerateAll, useX
 			} else {
 				output.push(citationText == "" ? " " : citationText);
 			}
+			
+			if(useXML) output.appendChild(citationXML);
 		}
-		
-		if(useXML) output.appendChild(citationXML);
 	}
 	
 	return output;
@@ -1533,7 +1609,7 @@ Zotero.Integration.Session.BibliographyEditInterface.prototype.remove = function
 		for(var j=0; j<this.session.citationsByItemID[itemID].length; j++) {
 			var citation = this.session.citationsByItemID[itemID][j];
 			this.session.updateIndices[citation.properties.index] = true;
-			citation.properties.delete = true;
+			citation.properties["delete"] = true;
 		}
 	}