Merge branch 'master' of https://github.com/zotero/zotero into jurism…

…-5.0-dev

COPYING

@@ -1,8 +1,11 @@
-Zotero is Copyright © 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017
+Zotero is Copyright © 2018 Corporation for Digital Scholarship, 
+Vienna, Virginia, USA http://digitalscholar.org
+
+Copyright © 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017
 Roy Rosenzweig Center for History and New Media, George Mason University,
 Fairfax, Virginia, USA  http://zotero.org
 
-The Roy Rosenzweig Center for History and New Media distributes the Zotero source code
+The Corporation for Digital Scholarship distributes the Zotero source code
 under the GNU Affero General Public License, version 3 (AGPLv3). The full text
 of this license is given below.
 

chrome/content/zotero/bindings/relatedbox.xml

@@ -152,28 +152,7 @@
 							let id = relatedItem.id;
 							let icon = document.createElement("image");
 							icon.className = "zotero-box-icon";
-							let type = Zotero.ItemTypes.getName(relatedItem.itemTypeID);
-							if (type=='attachment')
-							{
-								switch (relatedItem.attaachmentLinkMode) {
-									case Zotero.Attachments.LINK_MODE_LINKED_URL:
-										type += '-web-link';
-										break;
-									
-									case Zotero.Attachments.LINK_MODE_IMPORTED_URL:
-										type += '-snapshot';
-										break;
-									
-									case Zotero.Attachments.LINK_MODE_LINKED_FILE:
-										type += '-link';
-										break;
-									
-									case Zotero.Attachments.LINK_MODE_IMPORTED_FILE:
-										type += '-file';
-										break;
-								}
-							}
-							icon.setAttribute('src','chrome://zotero/skin/treeitem-' + type + '.png');
+							icon.setAttribute('src', relatedItem.getImageSrc());
 					
 							var label = document.createElement("label");
 							label.className = "zotero-box-label";

chrome/content/zotero/preferences/preferences_search.xul

@@ -49,6 +49,14 @@
 				<textbox size="10" preference="pref-fulltext-textMaxLength"/>
 				<label value="(&zotero.preferences.default; 500000)"/>
 			</hbox>
+
+			<separator class="thin"/>
+
+			<hbox align="center">
+				<label value="&zotero.preferences.fulltext.pdfMaxPages;"/>
+				<textbox size="5" preference="pref-fulltext-pdfmaxpages"/>
+				<label value="(&zotero.preferences.default; 100)"/>
+			</hbox>
 		</groupbox>
 
 		<groupbox id="fulltext-stats">

chrome/content/zotero/xpcom/integration.js

@@ -565,7 +565,7 @@ Zotero.Integration.Interface.prototype.editBibliography = Zotero.Promise.corouti
 		throw new Zotero.Exception.Alert("integration.error.mustInsertBibliography",
 			[], "integration.error.title");
 	}
-	let bibliography = new Zotero.Integration.Bibliography(bibliographyField);
+	let bibliography = new Zotero.Integration.Bibliography(bibliographyField, bibliographyField.unserialize());
 	var citationsMode = FORCE_CITATIONS_FALSE;
 	if(this._session.data.prefs.delayCitationUpdates) {
 		// Refreshes citeproc state before proceeding
@@ -604,7 +604,7 @@ Zotero.Integration.Interface.prototype.addEditBibliography = Zotero.Promise.coro
 		bibliographyField.clearCode();
 	}
 
-	let bibliography = new Zotero.Integration.Bibliography(bibliographyField);
+	let bibliography = new Zotero.Integration.Bibliography(bibliographyField, bibliographyField.unserialize());
 	var citationsMode = FORCE_CITATIONS_FALSE;
 	if(this._session.data.prefs.delayCitationUpdates) {
 		// Refreshes citeproc state before proceeding
@@ -893,7 +893,8 @@ Zotero.Integration.Fields.prototype._processFields = Zotero.Promise.coroutine(fu
 		let field = Zotero.Integration.Field.loadExisting(this._fields[i]);
 		if (field.type === INTEGRATION_TYPE_ITEM) {
 			var noteIndex = field.getNoteIndex(),
-				citation = new Zotero.Integration.Citation(field, noteIndex);
+				data = field.unserialize(),
+				citation = new Zotero.Integration.Citation(field, noteIndex, data);
 
 			yield this._session.addCitation(i, noteIndex, citation);
 		} else if (field.type === INTEGRATION_TYPE_BIBLIOGRAPHY) {
@@ -905,7 +906,8 @@ Zotero.Integration.Fields.prototype._processFields = Zotero.Promise.coroutine(fu
 		}
 	}
 	if (this._bibliographyFields.length) {
-		this._session.bibliography = new Zotero.Integration.Bibliography(this._bibliographyFields[0]);
+		var data = this._bibliographyFields[0].unserialize()
+		this._session.bibliography = new Zotero.Integration.Bibliography(this._bibliographyFields[0], data);
 		yield this._session.bibliography.loadItemData();
 	} else {
 		delete this._session.bibliography;
@@ -1118,20 +1120,21 @@ Zotero.Integration.Fields.prototype._updateDocument = async function(forceCitati
  */
 Zotero.Integration.Fields.prototype.addEditCitation = Zotero.Promise.coroutine(function* (field) {
 	var newField;
+	var citation;
 
 	if (field) {
 		field = Zotero.Integration.Field.loadExisting(field);
 
 		if (field.type != INTEGRATION_TYPE_ITEM) {
 			throw new Zotero.Exception.Alert("integration.error.notInCitation");
 		}
+		citation = new Zotero.Integration.Citation(field, field.getNoteIndex(), field.unserialize());
 	} else {
 		newField = true;
 		field = new Zotero.Integration.CitationField(yield this.addField(true));
-		field.clearCode();
+		citation = new Zotero.Integration.Citation(field);
 	}
 
-	var citation = new Zotero.Integration.Citation(field);
 	yield citation.prepareForEditing();
 
 	// -------------------
@@ -1158,19 +1161,31 @@ Zotero.Integration.Fields.prototype.addEditCitation = Zotero.Promise.coroutine(f
 		}.bind(this));
 	}
 
-	var previewFn = Zotero.Promise.coroutine(function* (citation) {
-		let idx = yield fieldIndexPromise;
-		yield citationsByItemIDPromise;
+	var previewFn = async function (citation) {
+		let idx = await fieldIndexPromise;
+		await citationsByItemIDPromise;
+		var fields = await this.get();
 
-		var [citations, fieldToCitationIdxMapping, citationToFieldIdxMapping] = this._session.getCiteprocLists();
-		let citationsPre = citations.slice(0, fieldToCitationIdxMapping[idx]);
-		let citationsPost = citations.slice(fieldToCitationIdxMapping[idx]+1);
+		var [citations, fieldToCitationIdxMapping, citationToFieldIdxMapping] = this._session.getCiteprocLists(true);
+		for (var prevIdx = idx-1; prevIdx >= 0; prevIdx--) {
+			if (prevIdx in fieldToCitationIdxMapping) break;
+		}
+		for (var nextIdx = idx+1; nextIdx < fields.length; nextIdx++) {
+			if (nextIdx in fieldToCitationIdxMapping) break;
+		}
+		let citationsPre = citations.slice(0, fieldToCitationIdxMapping[prevIdx]+1);
+		let citationsPost = citations.slice(fieldToCitationIdxMapping[nextIdx]);
 		try {
-			return this._session.style.previewCitationCluster(citation, citationsPre, citationsPost, "rtf");
+			var result = this._session.style.previewCitationCluster(citation, citationsPre, citationsPost, "rtf");
 		} catch(e) {
 			throw e;
+		} finally {
+			// CSL.previewCitationCluster() sets citationID, which means that we do not mark it
+			// as a new citation in Session.addCitation() if the ID is still present
+			delete citation.citationID;
 		}
-	}.bind(this));
+		return result;
+	}.bind(this);
 
 	var io = new Zotero.Integration.CitationEditInterface(
 		citation, this._session.style.opt.sort_citations,
@@ -1571,26 +1586,37 @@ Zotero.Integration.Session.prototype.addCitation = Zotero.Promise.coroutine(func
 	}
 
 	// We need a new ID if there's another citation with the same citation ID in this document
-	var needNewID = !citation.citationID || this.documentCitationIDs[citation.citationID];
+	var duplicateIndex = this.documentCitationIDs[citation.citationID];
+	var needNewID = !citation.citationID || duplicateIndex != undefined;
 	if(needNewID || this.regenAll) {
+		if (duplicateIndex != undefined) {
+			// If this is a duplicate, we need to mark both citations as "new"
+			// since we do not know which one was the "original" one
+			// and either one may need to be updated
+			this.newIndices[duplicateIndex] = true;
+		}
 		if(needNewID) {
 			Zotero.debug("Integration: "+citation.citationID+" ("+index+") needs new citationID");
 			citation.citationID = Zotero.randomString();
 		}
 		this.newIndices[index] = true;
 	}
 	Zotero.debug("Integration: Adding citationID "+citation.citationID);
-	this.documentCitationIDs[citation.citationID] = citation.citationID;
+	this.documentCitationIDs[citation.citationID] = index;
 });
 
-Zotero.Integration.Session.prototype.getCiteprocLists = function() {
+Zotero.Integration.Session.prototype.getCiteprocLists = function(excludeNew) {
 	var citations = [];
-	var fieldToCitationIdxMapping = [];
+	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) {
+		if (excludeNew && this.newIndices[idx]) {
+			i++;
+			continue;
+		}
 		citations.push([this.citationsByIndex[idx].citationID, this.citationsByIndex[idx].properties.noteIndex]);
 		fieldToCitationIdxMapping[i] = idx;
 		citationToFieldIdxMapping[idx] = i++;
@@ -2360,8 +2386,10 @@ Zotero.Integration.BibliographyField = class extends Zotero.Integration.Field {
 };
 
 Zotero.Integration.Citation = class {
-	constructor(citationField, noteIndex) {
-		let data = citationField.unserialize();
+	constructor(citationField, noteIndex, data) {
+		if (!data) {
+			data = {citationItems: [], properties: {}};
+		}
 		this.citationID = data.citationID;
 		this.citationItems = data.citationItems;
 		this.properties = data.properties;
@@ -2605,9 +2633,9 @@ Zotero.Integration.Citation = class {
 };
 
 Zotero.Integration.Bibliography = class {
-	constructor(bibliographyField) {
+	constructor(bibliographyField, data) {
 		this._field = bibliographyField;
-		this.data = bibliographyField.unserialize();
+		this.data = data;
 
 		this.uncitedItemIDs = new Set();
 		this.omittedItemIDs = new Set();

chrome/content/zotero/xpcom/proxy.js

@@ -321,7 +321,11 @@ Zotero.Proxy.prototype.compileRegexp = function() {
 	})
 
 	// now replace with regexp fragment in reverse order
-	var re = "^"+Zotero.Utilities.quotemeta(this.scheme)+"$";
+	if (this.scheme.includes('://')) {
+		re = "^"+Zotero.Utilities.quotemeta(this.scheme)+"$";
+	} else {
+		re = "^https?"+Zotero.Utilities.quotemeta('://'+this.scheme)+"$";
+	}
 	for(var i=this.parameters.length-1; i>=0; i--) {
 		var param = this.parameters[i];
 		re = re.replace(Zotero_Proxy_schemeParameterRegexps[param], "$1"+parametersToCheck[param]);

chrome/content/zotero/xpcom/schema.js

@@ -2615,6 +2615,23 @@ Zotero.Schema = new function(){
 				yield Zotero.DB.queryAsync("DELETE FROM relationPredicates WHERE predicate='dc:isReplacedBy'");
 			}
 
+			else if (i == 100) {
+				let userID = yield Zotero.DB.valueQueryAsync("SELECT value FROM settings WHERE setting='account' AND key='userID'");
+				let predicateID = yield Zotero.DB.valueQueryAsync("SELECT predicateID FROM relationPredicates WHERE predicate='dc:relation'");
+				if (userID && predicateID) {
+					let rows = yield Zotero.DB.queryAsync("SELECT itemID, object FROM items JOIN itemRelations IR USING (itemID) WHERE libraryID=? AND predicateID=?", [1, predicateID]);
+					for (let row of rows) {
+						let matches = row.object.match(/^http:\/\/zotero.org\/users\/(\d+)\/items\/([A-Z0-9]+)$/);
+						if (matches) {
+							// Wrong libraryID
+							if (matches[1] != userID) {
+								yield Zotero.DB.queryAsync(`UPDATE itemRelations SET object='http://zotero.org/users/${userID}/items/${matches[2]}' WHERE itemID=? AND predicateID=?`, [row.itemID, predicateID]);
+							}
+						}
+					}
+				}
+			}
+
 			// If breaking compatibility or doing anything dangerous, clear minorUpdateFrom
 		}
 

chrome/content/zotero/xpcom/server.js

@@ -28,6 +28,7 @@ Zotero.Server = new function() {
 	this.responseCodes = {
 		200:"OK",
 		201:"Created",
+		204:"No Content",
 		300:"Multiple Choices",
 		400:"Bad Request",
 		404:"Not Found",

chrome/content/zotero/xpcom/server_connector.js

@@ -799,6 +799,17 @@ Zotero.Server.Connector.UpdateSession.prototype = {
 	}
 };
 
+Zotero.Server.Connector.DelaySync = function () {};
+Zotero.Server.Endpoints["/connector/delaySync"] = Zotero.Server.Connector.DelaySync;
+Zotero.Server.Connector.DelaySync.prototype = {
+	supportedMethods: ["POST"],
+
+	init: async function (options) {
+		Zotero.Sync.Runner.delaySync(10000);
+		return [204];
+	}
+};
+
 /**
  * Gets progress for an attachment that is currently being saved
  *

chrome/content/zotero/xpcom/sync/syncRunner.js

@@ -69,6 +69,7 @@ Zotero.Sync.Runner_Module = function (options = {}) {
 
 	var _enabled = false;
 	var _autoSyncTimer;
+	var _delaySyncUntil;
 	var _firstInSession = true;
 	var _syncInProgress = false;
 	var _stopping = false;
@@ -139,6 +140,14 @@ Zotero.Sync.Runner_Module = function (options = {}) {
 
 			this.updateIcons('animate');
 
+			// If a delay is set (e.g., from the connector target selector), wait to sync
+			while (_delaySyncUntil && new Date() < _delaySyncUntil) {
+				this.setSyncStatus(Zotero.getString('sync.status.waiting'));
+				let delay = _delaySyncUntil - new Date();
+				Zotero.debug(`Waiting ${delay} ms to sync`);
+				yield Zotero.Promise.delay(delay);
+			}
+
 			// purgeDataObjects() starts a transaction, so if there's an active one then show a
 			// nice message and wait until there's not. Another transaction could still start
 			// before purgeDataObjects() and result in a wait timeout, but this should reduce the
@@ -884,11 +893,20 @@ Zotero.Sync.Runner_Module = function (options = {}) {
 
 		// Implements nsITimerCallback
 		var callback = {
-			notify: function (timer) {
+			notify: async function (timer) {
 				if (!_getAPIKey()) {
 					return;
 				}
 
+				// If a delay is set (e.g., from the connector target selector), wait to sync.
+				// We do this in sync() too for manual syncs, but no need to start spinning if
+				// it's just an auto-sync.
+				while (_delaySyncUntil && new Date() < _delaySyncUntil) {
+					let delay = _delaySyncUntil - new Date();
+					Zotero.debug(`Waiting ${delay} ms to start auto-sync`);
+					await Zotero.Promise.delay(delay);
+				}
+
 				if (Zotero.locked) {
 					Zotero.debug('Zotero is locked -- skipping auto-sync', 4);
 					return;
@@ -935,6 +953,11 @@ Zotero.Sync.Runner_Module = function (options = {}) {
 	}
 
 
+	this.delaySync = function (ms) {
+		_delaySyncUntil = new Date(Date.now() + ms);
+	};
+
+
 	/**
 	 * Trigger updating of the main sync icon, the sync error icon, and
 	 * library-specific sync error icons across all windows

resource/schema/userdata.sql

@@ -1,4 +1,4 @@
--- 99
+-- 100
 
 -- Copyright (c) 2009 Center for History and New Media
 --                    George Mason University, Fairfax, Virginia, USA