Merge changes from upstream Zotero

chrome/content/zotero/bindings/itembox.xml

@@ -3977,10 +3977,21 @@
 						newIndex = index + 1;
 						break;
 					}
-					var a = this.item.getCreator(index);
-					var b = this.item.getCreator(newIndex);
-					this.item.setCreator(newIndex, a);
-					this.item.setCreator(index, b);
+					let creator = this.item.getCreator(index);
+					// When moving to top, increment index of all other creators
+					if (dir == 'top') {
+						let otherCreators = this.item.getCreators();
+						this.item.setCreator(newIndex, creator);
+						for (let i = 0; i < index; i++) {
+							this.item.setCreator(i + 1, otherCreators[i]);
+						}
+					}
+					// When moving up or down, swap places with next creator
+					else {
+						let otherCreator = this.item.getCreator(newIndex);
+						this.item.setCreator(newIndex, creator);
+						this.item.setCreator(index, otherCreator);
+					}
 					if (this.saveOnEdit) {
 						// See note in transformText()
 						yield this.blurOpenField();

chrome/content/zotero/containers/tagSelector.jsx

@@ -68,26 +68,28 @@ Zotero.TagSelector = class TagSelectorContainer extends React.Component {
 				default:
 					return;
 			}
+			return this.setState({tags: await this.getTags()});
 		}
 
-		// Ignore item events other than 'trash'
-		if (type == 'item' && (event == 'trash')) {
+		if (type == 'item' || type == 'item-tag') {
 			return this.setState({tags: await this.getTags()});
 		}
-						
+
 		// If a selected tag no longer exists, deselect it
-		if (type == 'item-tag') {
-			if (event == 'delete' || event == 'trash' || event == 'modify') {
-				for (let tag of this.selectedTags) {
-					if (tag == extraData[ids[0]].old.tag) {
-						this.selectedTags.delete(tag);
-					}
+		if (type == 'tag' && (event == 'modify' || event == 'delete')) {
+			let changed = false;
+			for (let id of ids) {
+				let tag = extraData[id].old.tag;
+				if (this.selectedTags.has(tag)) {
+					this.selectedTags.delete(tag);
+					changed = true;
 				}
 			}
-			return this.setState({tags: await this.getTags()});
+			if (changed && typeof(this.props.onSelection) === 'function') {
+				this.props.onSelection(this.selectedTags);
+			}
+			return;
 		}
-
-		this.setState({tags: await this.getTags()});
 	}
 
 	async getTags(tagsInScope, tagColors) {
@@ -157,7 +159,7 @@ Zotero.TagSelector = class TagSelectorContainer extends React.Component {
 			onSelect={this.state.viewOnly ? () => {} : this.handleTagSelected}
 			onTagContext={this.handleTagContext}
 			onSearch={this.handleSearch}
-			onSettings={this.handleSettings}
+			onSettings={this.handleSettings.bind(this)}
 			loaded={this.state.loaded}
 		/>;
 	}
@@ -387,6 +389,43 @@ Zotero.TagSelector = class TagSelectorContainer extends React.Component {
 			this.props.onSelection(this.selectedTags);
 		}
 	}
+
+	async deleteAutomatic() {
+		var num = (await Zotero.Tags.getAutomaticInLibrary(this.libraryID)).length;
+		if (!num) {
+			return;
+		}
+
+		var ps = Components.classes["@mozilla.org/embedcomp/prompt-service;1"]
+			.getService(Components.interfaces.nsIPromptService);
+		var confirmed = ps.confirm(
+			window,
+			Zotero.getString('pane.tagSelector.deleteAutomatic.title'),
+			Zotero.getString(
+					'pane.tagSelector.deleteAutomatic.message',
+					new Intl.NumberFormat().format(num),
+					num
+				)
+				+ "\n\n"
+				+ Zotero.getString('general.actionCannotBeUndone')
+		);
+		if (confirmed) {
+			Zotero.showZoteroPaneProgressMeter(null, true);
+			try {
+				await Zotero.Tags.removeAutomaticFromLibrary(
+					this.libraryID,
+					(progress, progressMax) => {
+						Zotero.updateZoteroPaneProgressMeter(
+							Math.round(progress / progressMax * 100)
+						);
+					}
+				);
+			}
+			finally {
+				Zotero.hideZoteroPaneOverlays();
+			}
+		}
+	}
 
 	get label() {
 		let count = this.selectedTags.size;

chrome/content/zotero/containers/tagSelector.xul

@@ -41,7 +41,18 @@
 		onpopupshowing="
 			document.getElementById('show-automatic').setAttribute('checked', ZoteroPane.tagSelector.showAutomatic);
 			document.getElementById('display-all-tags').setAttribute('checked', ZoteroPane.tagSelector.displayAllTags);
-			document.getElementById('num-selected').label = ZoteroPane.tagSelector.label">
+			document.getElementById('num-selected').label = ZoteroPane.tagSelector.label;
+			(async function () {
+				var libraryID = ZoteroPane.tagSelector.libraryID;
+				var library = Zotero.Libraries.get(libraryID);
+				var enabled = false;
+				if (library.editable) {
+					if ((await Zotero.Tags.getAutomaticInLibrary(libraryID)).length) {
+						enabled = true;
+					}
+				}
+				document.getElementById('delete-automatic-tags').disabled = !enabled;
+			})();">
 		<menuitem id="num-selected" disabled="true"/>
 		<menuitem id="deselect-all" label="&zotero.tagSelector.clearAll;"
 			oncommand="ZoteroPane.tagSelector.deselectAll(); event.stopPropagation();"/>
@@ -54,5 +65,9 @@
 			type="checkbox"
 			oncommand="ZoteroPane.tagSelector.toggleDisplayAllTags(); event.stopPropagation();"
 		/>
+		<menuitem id="delete-automatic-tags" label="&zotero.tagSelector.deleteAutomaticInLibrary;" type="checkbox"
+									oncommand="ZoteroPane.tagSelector.deleteAutomatic();
+										this.setAttribute('checked', false);
+										event.stopPropagation();"/>
 	</menupopup>
 </overlay>

chrome/content/zotero/overlay.js

@@ -83,7 +83,8 @@ var ZoteroOverlay = new function()
 			if (Zotero.skipLoading) {
 				throw new Error("Skipping loading");
 			}
-
+
+			ZoteroPane.Containers.init();
 			ZoteroPane.init();
 
 			// Clear old Zotero icon pref

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

@@ -4214,7 +4214,7 @@ Zotero.Item.prototype.getImageSrc = function() {
 	if (itemType == 'attachment') {
 		var linkMode = this.attachmentLinkMode;
 
-		if (this.attachmentContentType == 'application/pdf') {
+		if (this.attachmentContentType == 'application/pdf' && this.isFileAttachment()) {
 			if (linkMode == Zotero.Attachments.LINK_MODE_LINKED_FILE) {
 				itemType += '-pdf-link';
 			}

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

@@ -281,105 +281,101 @@ Zotero.Tags = new function() {
 
 
 	/**
+	 * @param {Integer} libraryID
+	 * @param {Integer[]} tagIDs
+	 * @param {Function} [onProgress]
+	 * @param {Integer[]} [types]
 	 * @return {Promise}
 	 */
-	this.removeFromLibrary = Zotero.Promise.coroutine(function* (libraryID, tagIDs, onProgress) {
+	this.removeFromLibrary = Zotero.Promise.coroutine(function* (libraryID, tagIDs, onProgress, types) {
 		var d = new Date();
 
-		tagIDs = Zotero.flattenArguments(tagIDs);
+		if (!Array.isArray(tagIDs)) {
+			tagIDs = [tagIDs];
+		}
+		if (types && !Array.isArray(types)) {
+			types = [types];
+		}
 
-		var deletedNames = [];
+		var colors = this.getColors(libraryID);
 		var done = 0;
 
 		yield Zotero.Utilities.Internal.forEachChunkAsync(
 			tagIDs,
 			100,
 			async function (chunk) {
 				await Zotero.DB.executeTransaction(function* () {
-					var oldItemIDs = [];
-
-					var notifierPairs = [];
+					var rowIDs = [];
+					var itemIDs = [];
+					var uniqueTags = new Set();
+					var notifierIDs = [];
 					var notifierData = {};
-					var a = new Date();
 
-					var sql = 'SELECT tagID, itemID FROM itemTags JOIN items USING (itemID) '
+					var sql = 'SELECT IT.ROWID AS rowID, tagID, itemID, type FROM itemTags IT '
+						+ 'JOIN items USING (itemID) '
 						+ 'WHERE libraryID=? AND tagID IN ('
 						+ Array(chunk.length).fill('?').join(', ')
-						+ ') ORDER BY tagID';
-					var chunkTagItems = yield Zotero.DB.queryAsync(sql, [libraryID, ...chunk]);
-					var i = 0;
-
-					chunk.sort((a, b) => a - b);
-
-					for (let tagID of chunk) {
+						+ ') ';
+					if (types) {
+						sql += 'AND type IN (' + types.join(', ') + ') ';
+					}
+					sql += 'ORDER BY tagID, type';
+					var rows = yield Zotero.DB.queryAsync(sql, [libraryID, ...chunk]);
+					for (let { rowID, tagID, itemID, type } of rows) {
+						uniqueTags.add(tagID);
+
 						let name = this.getName(tagID);
 						if (name === false) {
 							continue;
 						}
-						deletedNames.push(name);
 
-						// Since we're performing the DELETE query directly,
-						// get the list of items that will need their tags reloaded,
-						// and generate data for item-tag notifications
-						let itemIDs = []
-						while (i < chunkTagItems.length && chunkTagItems[i].tagID == tagID) {
-							itemIDs.push(chunkTagItems[i].itemID);
-							i++;
-						}
-						for (let itemID of itemIDs) {
-							let pair = itemID + "-" + tagID;
-							notifierPairs.push(pair);
-							notifierData[pair] = {
-								libraryID: libraryID,
-								tag: name
-							};
+						rowIDs.push(rowID);
+						itemIDs.push(itemID);
+
+						let ids = itemID + '-' + tagID;
+						notifierIDs.push(ids);
+						notifierData[ids] = {
+							libraryID: libraryID,
+							tag: name,
+							type
+						};
+
+						// If we're deleting the tag and not just a specific type, also clear any
+						// tag color
+						if (colors.has(name) && !types) {
+							yield this.setColor(libraryID, name, false);
 						}
-						oldItemIDs = oldItemIDs.concat(itemIDs);
 					}
-					if (oldItemIDs.length) {
-						Zotero.Notifier.queue('remove', 'item-tag', notifierPairs, notifierData);
+					if (itemIDs.length) {
+						Zotero.Notifier.queue('remove', 'item-tag', notifierIDs, notifierData);
 					}
 
-					var sql = "DELETE FROM itemTags WHERE tagID IN ("
-						+ Array(chunk.length).fill('?').join(', ') + ") AND itemID IN "
-						+ "(SELECT itemID FROM items WHERE libraryID=?)";
-					yield Zotero.DB.queryAsync(sql, chunk.concat([libraryID]));
+					sql = "DELETE FROM itemTags WHERE ROWID IN (" + rowIDs.join(", ") + ")";
+					yield Zotero.DB.queryAsync(sql);
 
 					yield this.purge(chunk);
 
 					// Update internal timestamps on all items that had these tags
 					yield Zotero.Utilities.Internal.forEachChunkAsync(
-						Zotero.Utilities.arrayUnique(oldItemIDs),
+						Zotero.Utilities.arrayUnique(itemIDs),
 						Zotero.DB.MAX_BOUND_PARAMETERS - 1,
-						Zotero.Promise.coroutine(function* (chunk2) {
-							var placeholders = Array(chunk2.length).fill('?').join(',');
+						async function (chunk) {
+							var sql = 'UPDATE items SET synced=0, clientDateModified=? '
+								+ 'WHERE itemID IN (' + Array(chunk.length).fill('?').join(',') + ')';
+							await Zotero.DB.queryAsync(sql, [Zotero.DB.transactionDateTime].concat(chunk));
 
-							sql = 'UPDATE items SET synced=0, clientDateModified=? '
-								+ 'WHERE itemID IN (' + placeholders + ')'
-							yield Zotero.DB.queryAsync(sql, [Zotero.DB.transactionDateTime].concat(chunk2));
-
-							yield Zotero.Items.reload(oldItemIDs, ['primaryData', 'tags'], true);
-						})
+							await Zotero.Items.reload(itemIDs, ['primaryData', 'tags'], true);
+						}
 					);
 
-					done += chunk.length;
+					if (onProgress) {
+						done += uniqueTags.size;
+						onProgress(done, tagIDs.length);
+					}
 				}.bind(this));
-
-				if (onProgress) {
-					onProgress(done, tagIDs.length);
-				}
 			}.bind(this)
 		);
 
-		// Also delete tag color setting
-		//
-		// Note that this isn't done in purge(), so the setting will not
-		// be removed if the tag is just removed from all items without
-		// being explicitly deleted.
-		for (let i=0; i<deletedNames.length; i++) {
-			yield this.setColor(libraryID, deletedNames[i], false);
-		}
-
 		Zotero.debug(`Removed ${tagIDs.length} ${Zotero.Utilities.pluralize(tagIDs.length, 'tag')} `
 			+ `in ${new Date() - d} ms`);
 	});
@@ -400,11 +396,12 @@ Zotero.Tags = new function() {
 	 * Remove all automatic tags in the given library
 	 */
 	this.removeAutomaticFromLibrary = async function (libraryID, onProgress) {
+		var tagType = 1;
 		var tagIDs = await this.getAutomaticInLibrary(libraryID);
 		if (onProgress) {
 			onProgress(0, tagIDs.length);
 		}
-		return this.removeFromLibrary(libraryID, tagIDs, onProgress);
+		return this.removeFromLibrary(libraryID, tagIDs, onProgress, tagType);
 	};
 
 
@@ -429,6 +426,10 @@ Zotero.Tags = new function() {
 			tagIDs = Zotero.flattenArguments(tagIDs);
 		}
 
+		if (tagIDs && !tagIDs.length) {
+			return;
+		}
+
 		Zotero.DB.requireTransaction();
 
 		var sql;

resource/schema/renamed-styles.json

@@ -280,7 +280,8 @@
     "frontiers-in-vascular-physiology": "frontiers",
     "frontiers-in-virology": "frontiers",
     "frontiers-in-womens-cancer": "frontiers",
-    "future-science": "future-science-journals",
+    "future-science": "future-science-group",
+    "future-science-journals": "future-science-group",
     "geistes-und-kulturwissenschaften-teilmann": "geistes-und-kulturwissenschaften-heilmann",
     "genetic-vaccines-and-therapy": "biomed-central",
     "geological-society-america-bulletin": "geological-society-of-america-bulletin",