Fix local citations network (#284)

* Fix local citations network for typescript * Enable LCN Needed to change to arrow functions to get a correctly bound `this` * copy LCN files on build * Also copy LCN lib folder * Clone submodules when building on github actions * Fix typo in LCN URL * Fix localisation for % completion in local citation network
diegodlh · Aug 20, 2024 · 7e17159 · 7e17159
1 parent 743b94d
commit 7e17159
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Showing 6 changed files with 85 additions and 52 deletions.
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -9,6 +9,8 @@ jobs:
         steps:
             - name: checkout
               uses: actions/checkout@v2
+              with:
+                submodules: recursive
 
             - name: install node
               uses: actions/setup-node@v1

diff --git a/src/cita/localCitationNetwork.ts b/src/cita/localCitationNetwork.ts
@@ -4,19 +4,34 @@ import Progress from "./progress";
 import SourceItemWrapper from "./sourceItemWrapper";
 import Wikicite from "./wikicite";
 import * as prefs from "../cita/preferences";
-
-declare const Zotero: any;
-declare const ZoteroPane: any;
+import { config } from "../../package.json";
 
 export default class LCN {
-	items: any[];
-	itemMap: Map<any, any>;
+	items: Zotero.Item[];
+	itemMap: Map<
+		string,
+		{
+			id: string | undefined;
+			doi: string | undefined;
+			title: string;
+			authors: {
+				LN: string;
+				FN: string;
+			}[];
+			year: string;
+			journal: string;
+			references: (string | undefined)[];
+			abstract: string;
+			url: string | undefined;
+		}
+	>;
 	inputKeys: string[];
 	libraryID: number;
 	progress: Progress;
 
-	constructor(items) {
-		if (!items.length) return;
+	constructor(items: Zotero.Item[]) {
+		if (!items.length)
+			throw `Can't create a local citation network without any items`;
 		this.items = items;
 		this.itemMap = new Map(); // itemKey/tmpItemKey -> ItemWrapper
 
@@ -89,7 +104,7 @@ export default class LCN {
 						const linkedToItem = Zotero.Items.getByLibraryAndKey(
 							this.libraryID,
 							citation.target.key,
-						);
+						) as Zotero.Item;
 						// Non-linked citation target items are not part of the
 						// LCN "input items" set.
 						// Citations of these non-linked citation target items
@@ -114,10 +129,10 @@ export default class LCN {
 					// collect item's unique identifiers (including name) and clean
 					// them, to make sure the same item always gets the same tmp key
 					const cleanDOI = Zotero.Utilities.cleanDOI(
-						citation.target.doi,
+						citation.target.doi!,
 					);
 					const cleanISBN = Zotero.Utilities.cleanISBN(
-						citation.target.isbn,
+						citation.target.isbn!,
 					);
 					const qid = citation.target.qid;
 					const uids = {
@@ -139,13 +154,13 @@ export default class LCN {
 					// retrieve tmp keys already given to this item,
 					// i.e., the target item of another source item's citation
 					// had one or more of the same uids or title
-					const tmpKeys = new Set();
+					const tmpKeys: Set<string> = new Set();
 					for (const [key, value] of Object.entries(uids)) {
 						const tmpKey = tmpKeyMap.get(`${key}:${value}`);
 						if (tmpKey) tmpKeys.add(tmpKey);
 					}
 
-					let tmpKey;
+					let tmpKey: string;
 					if (tmpKeys.size === 0) {
 						// if no matching temp keys found, create a new one
 						do {
@@ -182,14 +197,14 @@ export default class LCN {
 					);
 				}
 			}
-			this.itemMap.set(wrappedItem.key, parseWrappedItem(wrappedItem));
+			this.itemMap.set(wrappedItem.key!, parseWrappedItem(wrappedItem));
 		}
 		this.progress.updateLine("done");
 	}
 
-	openItem(key) {
+	openItem(key: string) {
 		ZoteroPane.selectItem(
-			Zotero.Items.getIDFromLibraryAndKey(this.libraryID, key),
+			Zotero.Items.getIDFromLibraryAndKey(this.libraryID, key) as number,
 		);
 		window.focus();
 	}
@@ -212,7 +227,7 @@ export default class LCN {
 		await Zotero.Promise.delay(100);
 
 		window.openDialog(
-			"chrome://cita/content/Local-Citation-Network/index.html?API=Cita&listOfKeys=" +
+			`chrome://${config.addonRef}/content/Local-Citation-Network/index.html?API=Cita&listOfKeys=` +
 				this.inputKeys.join(","),
 			"",
 			windowFeatures.join(","),
@@ -232,7 +247,7 @@ export default class LCN {
 /**
  * Get localized string for LCN window
  */
-function getString(name, params) {
+function getString(name: string, params: unknown) {
 	name = "wikicite.lcn.window." + name;
 	let string;
 	if (params) {
@@ -246,21 +261,22 @@ function getString(name, params) {
 /**
  * Get ItemWrapper and return Data Item as understood by Local Citations Network
  */
-function parseWrappedItem(wrappedItem) {
+function parseWrappedItem(wrappedItem: ItemWrapper | SourceItemWrapper) {
 	const authors = wrappedItem.item
 		.getCreators()
 		.map((creator) => ({ LN: creator.lastName, FN: creator.firstName }));
-	if (!authors.length) authors.push({ LN: undefined });
+	if (!authors.length) authors.push({ LN: "", FN: "" });
 	return {
 		id: wrappedItem.key,
 		doi: wrappedItem.doi,
 		title: wrappedItem.title,
 		authors: authors,
 		year: wrappedItem.item.getField("year"),
 		journal: wrappedItem.item.getField("publicationTitle"),
-		references: wrappedItem.citations
-			? wrappedItem.citations.map((citation) => citation.target.key)
-			: [],
+		references:
+			"citations" in wrappedItem
+				? wrappedItem.citations.map((citation) => citation.target.key)
+				: [],
 		abstract: wrappedItem.item.getField("abstractNote"),
 		url: wrappedItem.url,
 	};

diff --git a/src/cita/zoteroOverlay.tsx b/src/cita/zoteroOverlay.tsx
@@ -3,7 +3,7 @@ import Citations from "./citations";
 import CitationsBoxContainer from "../containers/citationsBoxContainer";
 import Crossref from "./crossref";
 import Extraction from "./extract";
-// import LCN from './localCitationNetwork';
+import LCN from "./localCitationNetwork";
 import OCI from "../oci";
 import OpenCitations from "./opencitations";
 import * as React from "react";
@@ -397,7 +397,15 @@ class ZoteroOverlay {
 	 * @param {Boolean} [wrap=true] Whether to return wrapped items or not
 	 * @return {Array} Array of selected regular items
 	 */
-	async getSelectedItems(menuName: MenuSelectionType, wrap = true) {
+	async getSelectedItems(
+		menuName: MenuSelectionType,
+		wrap: false,
+	): Promise<Zotero.Item[]>;
+	async getSelectedItems(
+		menuName: MenuSelectionType,
+		wrap: true,
+	): Promise<SourceItemWrapper[]>;
+	async getSelectedItems(menuName: MenuSelectionType, wrap: boolean = true) {
 		// Fixme: Consider using the Citations class methods instead
 		let items;
 		switch (menuName) {
@@ -435,10 +443,7 @@ class ZoteroOverlay {
 	}
 
 	async fetchQIDs(menuName: MenuSelectionType) {
-		const items = (await this.getSelectedItems(
-			menuName,
-			true,
-		)) as SourceItemWrapper[];
+		const items = await this.getSelectedItems(menuName, true);
 		const qidMap = await Wikidata.reconcile(items);
 		if (qidMap) {
 			for (const item of items) {
@@ -449,10 +454,7 @@ class ZoteroOverlay {
 	}
 
 	async syncWithWikidata(menuName: MenuSelectionType) {
-		const items = (await this.getSelectedItems(
-			menuName,
-			true,
-		)) as SourceItemWrapper[];
+		const items = await this.getSelectedItems(menuName, true);
 		if (items.length) {
 			Citations.syncItemCitationsWithWikidata(items);
 		}
@@ -496,14 +498,12 @@ class ZoteroOverlay {
 	}
 
 	async localCitationNetwork(menuName: MenuSelectionType) {
-		// fix: enable LCN
-		alert("Local Citation Network isn't supported yet");
-		// const items = await this.getSelectedItems(menuName, false);
-		// if (items.length) {
-		// 	const lcn = new LCN(items);
-		// 	await lcn.init();
-		// 	lcn.show();
-		// }
+		const items = await this.getSelectedItems(menuName, false);
+		if (items.length) {
+			const lcn = new LCN(items);
+			await lcn.init();
+			lcn.show();
+		}
 	}
 
 	/******************************************/
@@ -1174,13 +1174,13 @@ class ZoteroOverlay {
 			MenuFunction,
 			(menuName: MenuSelectionType) => void
 		> = new Map([
-			["fetchQIDs", this.fetchQIDs],
-			["syncWithWikidata", this.syncWithWikidata],
-			["getFromCrossref", this.getFromCrossref],
-			["getFromOCC", this.getFromOCC],
-			["getFromAttachments", this.getFromAttachments],
-			["addAsCitations", this.addAsCitations],
-			["localCitationNetwork", this.localCitationNetwork],
+			["fetchQIDs", () => this.fetchQIDs(menuName)],
+			["syncWithWikidata", () => this.syncWithWikidata(menuName)],
+			["getFromCrossref", () => this.getFromCrossref(menuName)],
+			["getFromOCC", () => this.getFromOCC(menuName)],
+			["getFromAttachments", () => this.getFromAttachments(menuName)],
+			["addAsCitations", () => this.addAsCitations(menuName)],
+			["localCitationNetwork", () => this.localCitationNetwork(menuName)],
 		]);
 		for (const [functionName, func] of menuFunctions) {
 			if (

diff --git a/static/chrome/locale/en-US/wikicite.properties b/static/chrome/locale/en-US/wikicite.properties
@@ -83,8 +83,8 @@ wikicite.lcn.window.filter.select.journal = Journal
 wikicite.lcn.window.footer = Adapted from %1$s's %2$s
 wikicite.lcn.window.input-articles.header = Input articles (%s)
 wikicite.lcn.window.input-articles.info.source = Based on local citation data
-wikicite.lcn.window.input-articles.info.completeness = estimated completeness %s%%
-wikicite.lcn.window.input-articles.info.completeness.tooltip = %1$s of %2$s input articles have reference-lists themselves in Cita (%3$s%%).
+wikicite.lcn.window.input-articles.info.completeness = estimated completeness %s%
+wikicite.lcn.window.input-articles.info.completeness.tooltip = %1$s of %2$s input articles have reference-lists themselves in Cita (%3$s%).
 wikicite.lcn.window.input-articles.info.open-external = Open with %s
 wikicite.lcn.window.input-articles.info.open-external.tooltip = Open new graph for %s articles with DOI using citation data retrieved through external APIs
 wikicite.lcn.window.incoming-suggestions.header = Incoming suggestions (%1$s %2$s)

diff --git a/tsconfig.json b/tsconfig.json
@@ -11,5 +11,5 @@
 		"sourceMap": true
 	},
 	"include": ["src/**/*", "typings", "node_modules/zotero-types"],
-	"exclude": ["build", "static", "src/cita/localCitationNetwork.ts"]
+	"exclude": ["build", "static"]
 }
diff --git a/zotero-plugin.config.ts b/zotero-plugin.config.ts
@@ -1,7 +1,6 @@
 import { defineConfig } from "zotero-plugin-scaffold";
 import pkg from "./package.json";
-import { copyFileSync, readdirSync, renameSync } from "fs";
-import path from "path";
+import { copyFileSync, readdirSync, renameSync, mkdirSync, cpSync } from "fs";
 
 import fse from "fs-extra";
 import { replaceInFileSync } from "zotero-plugin-scaffold/tools";
@@ -96,6 +95,22 @@ export default defineConfig({
 					from: /wikicite_prefs_citation-storage-(note|extra)=/g,
 					to: "$&\n    .label=",
 				});
+
+				// Copy local citations network
+				mkdirSync("build/addon/chrome/content/Local-Citation-Network/");
+				copyFileSync(
+					"Local-Citation-Network/index.js",
+					"build/addon/chrome/content/Local-Citation-Network/index.js",
+				);
+				copyFileSync(
+					"Local-Citation-Network/index.html",
+					"build/addon/chrome/content/Local-Citation-Network/index.html",
+				);
+				cpSync(
+					"Local-Citation-Network/lib",
+					"build/addon/chrome/content/Local-Citation-Network/lib",
+					{ recursive: true },
+				);
 			},
 		},
 		// If you want to checkout update.json into the repository, uncomment the following lines: