Bringing Crossref, Semantic Scholar, Open Citations and Open Alex loo…

…kup + auto-import + redesign to Cita for Zotero 7 (#300)

Huge commit that includes:
* Getting citations from Crossref, Semantic Scholar, Open Alex, and Open Citations
* Storing arXiv ID, Open Citations OMID, Open Alex ID, and Semantic Scholar CorpusID for each item
* Restyle the citations pane to match the Zotero 7 item pane style
* Split the bottom of the Citations tab into an Identifiers tab to keep track of all an item's identifiers
* Allow drag and drop reordering of citation order
* Significant code refactoring, with the indexer and pid classes
* much more...

package.json

@@ -36,16 +36,22 @@
 	},
 	"homepage": "https://github.com/diegodlh/zotero-cita",
 	"dependencies": {
+		"@react-hook/resize-observer": "^2.0.2",
+		"openalex-sdk": "^1.1.6",
 		"prop-types": "^15.7.2",
 		"quickstatements-to-wikibase-edit": "^1.2.1",
 		"react": "^18.3.1",
 		"react-dom": "^18.3.1",
+		"react-error-boundary": "^4.1.1",
+		"react-intersection-observer": "^9.13.1",
+		"semver-parser": "^4.1.6",
 		"wikibase-edit": "^7.0.4",
 		"wikibase-sdk": "^10.0.2",
-		"zotero-plugin-toolkit": "^2.3.37"
+		"zotero-plugin-toolkit": "^4.0.6"
 	},
 	"devDependencies": {
 		"@types/language-tags": "^1.0.4",
+		"@types/lodash": "^4.17.9",
 		"@types/node": "^20.10.4",
 		"@types/react-dom": "^18.3.0",
 		"eslint": "^8.55.0",
@@ -58,7 +64,7 @@
 		"typescript": "^5.3.3",
 		"typescript-eslint": "^7.14.1",
 		"zotero-plugin-scaffold": "^0.0.34",
-		"zotero-types": "^2.1.0"
+		"zotero-types": "^3.0.1"
 	},
 	"engines": {
 		"npm": ">=8.1"

patches/openalex-sdk+1.1.6.patch

@@ -0,0 +1,91 @@
+diff --git a/node_modules/openalex-sdk/dist/src/index.js b/node_modules/openalex-sdk/dist/src/index.js
+index 70b2df5..518d455 100644
+--- a/node_modules/openalex-sdk/dist/src/index.js
++++ b/node_modules/openalex-sdk/dist/src/index.js
+@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
+     return (mod && mod.__esModule) ? mod : { "default": mod };
+ };
+ Object.defineProperty(exports, "__esModule", { value: true });
+-const fs_1 = __importDefault(require("fs"));
++//const fs_1 = __importDefault(require("fs"));
+ const authors_1 = require("./utils/authors");
+ const exportCSV_1 = require("./utils/exportCSV");
+ const helpers_1 = require("./utils/helpers");
+diff --git a/node_modules/openalex-sdk/dist/src/utils/authors.js b/node_modules/openalex-sdk/dist/src/utils/authors.js
+index 0b1cbc5..f824766 100644
+--- a/node_modules/openalex-sdk/dist/src/utils/authors.js
++++ b/node_modules/openalex-sdk/dist/src/utils/authors.js
+@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
+ };
+ Object.defineProperty(exports, "__esModule", { value: true });
+ exports.handleAllAuthorsPages = exports.handleMultipleAuthorsPages = exports.validateAuthorParameters = void 0;
+-const fs_1 = __importDefault(require("fs"));
++//const fs_1 = __importDefault(require("fs"));
+ const exportCSV_1 = require("./exportCSV");
+ const helpers_1 = require("./helpers");
+ const http_1 = require("./http");
+diff --git a/node_modules/openalex-sdk/dist/src/utils/exportCSV.js b/node_modules/openalex-sdk/dist/src/utils/exportCSV.js
+index 7f4d748..9c01df5 100644
+--- a/node_modules/openalex-sdk/dist/src/utils/exportCSV.js
++++ b/node_modules/openalex-sdk/dist/src/utils/exportCSV.js
+@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
+ };
+ Object.defineProperty(exports, "__esModule", { value: true });
+ exports.convertToCSV = void 0;
+-const fs_1 = __importDefault(require("fs"));
++//const fs_1 = __importDefault(require("fs"));
+ function flattenObject(obj, parentKey = '', depth = 0) {
+     const flattened = {};
+     for (const [key, value] of Object.entries(obj)) {
+diff --git a/node_modules/openalex-sdk/dist/src/utils/institutions.js b/node_modules/openalex-sdk/dist/src/utils/institutions.js
+index 1082435..099275a 100644
+--- a/node_modules/openalex-sdk/dist/src/utils/institutions.js
++++ b/node_modules/openalex-sdk/dist/src/utils/institutions.js
+@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
+ };
+ Object.defineProperty(exports, "__esModule", { value: true });
+ exports.handleAllInstitutionsPages = exports.handleMultipleInstitutionsPages = exports.validateInstitutionsParameters = void 0;
+-const fs_1 = __importDefault(require("fs"));
++//const fs_1 = __importDefault(require("fs"));
+ const exportCSV_1 = require("./exportCSV");
+ const helpers_1 = require("./helpers");
+ const http_1 = require("./http");
+diff --git a/node_modules/openalex-sdk/dist/src/utils/sources.js b/node_modules/openalex-sdk/dist/src/utils/sources.js
+index 699da8d..38c68b8 100644
+--- a/node_modules/openalex-sdk/dist/src/utils/sources.js
++++ b/node_modules/openalex-sdk/dist/src/utils/sources.js
+@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
+ };
+ Object.defineProperty(exports, "__esModule", { value: true });
+ exports.handleAllSourcesPages = exports.handleMultipleSourcesPages = exports.validateSourcesParameters = void 0;
+-const fs_1 = __importDefault(require("fs"));
++//const fs_1 = __importDefault(require("fs"));
+ const exportCSV_1 = require("./exportCSV");
+ const helpers_1 = require("./helpers");
+ const http_1 = require("./http");
+diff --git a/node_modules/openalex-sdk/dist/src/utils/topics.js b/node_modules/openalex-sdk/dist/src/utils/topics.js
+index b2946cc..b9fd0ed 100644
+--- a/node_modules/openalex-sdk/dist/src/utils/topics.js
++++ b/node_modules/openalex-sdk/dist/src/utils/topics.js
+@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
+ };
+ Object.defineProperty(exports, "__esModule", { value: true });
+ exports.handleAllTopicsPages = exports.handleMultipleTopicsPages = exports.validateTopicsParameters = void 0;
+-const fs_1 = __importDefault(require("fs"));
++//const fs_1 = __importDefault(require("fs"));
+ const exportCSV_1 = require("./exportCSV");
+ const helpers_1 = require("./helpers");
+ const http_1 = require("./http");
+diff --git a/node_modules/openalex-sdk/dist/src/utils/works.js b/node_modules/openalex-sdk/dist/src/utils/works.js
+index 46d5d38..2a5591c 100644
+--- a/node_modules/openalex-sdk/dist/src/utils/works.js
++++ b/node_modules/openalex-sdk/dist/src/utils/works.js
+@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
+ };
+ Object.defineProperty(exports, "__esModule", { value: true });
+ exports.formatNumber = exports.handleAllPagesInChunks = exports.handleMultiplePages = exports.handleAllPages = exports.validateParameters = void 0;
+-const fs_1 = __importDefault(require("fs"));
++//const fs_1 = __importDefault(require("fs"));
+ const exportCSV_1 = require("./exportCSV");
+ const helpers_1 = require("./helpers");
+ const http_1 = require("./http");

patches/zotero-types+3.0.1.patch

@@ -0,0 +1,23 @@
+diff --git a/node_modules/zotero-types/types/xpcom/db.d.ts b/node_modules/zotero-types/types/xpcom/db.d.ts
+index 8a2aeb1..8f9bf2d 100644
+--- a/node_modules/zotero-types/types/xpcom/db.d.ts
++++ b/node_modules/zotero-types/types/xpcom/db.d.ts
+@@ -70,12 +70,12 @@ declare namespace _ZoteroTypes {
+     executeTransaction<T>(
+       func: () => T | Promise<T>,
+       options?: {
+-        disbledForeignKeys: boolean;
+-        timeout: number;
+-        vacuumOnCommit: boolean;
+-        inBackup: boolean;
+-        onCommit: (id: string) => void;
+-        onRollback: (id: string) => void;
++        disbledForeignKeys?: boolean;
++        timeout?: number;
++        vacuumOnCommit?: boolean;
++        inBackup?: boolean;
++        onCommit?: (id: string) => void;
++        onRollback?: (id: string) => void;
+       },
+     ): Promise<T>;
+

src/cita/PID.ts

@@ -0,0 +1,164 @@
+export default class PID {
+	type: PIDType;
+	id: string;
+
+	constructor(type: PIDType, id: string) {
+		this.type = type;
+		this.id = id;
+	}
+
+	get url(): string | null {
+		const cleanPID = this.cleanID;
+		if (cleanPID) {
+			switch (this.type) {
+				case "DOI": {
+					const url =
+						"https://doi.org/" +
+						// From Zotero's itembox.xml:
+						// Encode some characters that are technically valid in DOIs,
+						// though generally not used. '/' doesn't need to be encoded.
+						cleanPID
+							.replace(/#/g, "%23")
+							.replace(/\?/g, "%3f")
+							.replace(/%/g, "%25")
+							.replace(/"/g, "%22");
+					return url;
+				}
+				case "OMID":
+					return "https://opencitations.net/meta/" + cleanPID;
+				case "OpenAlex":
+					return "https://openalex.org/works/" + cleanPID;
+				case "arXiv":
+					return "https://arxiv.org/abs/" + cleanPID;
+				case "QID":
+					return "https://www.wikidata.org/wiki/" + cleanPID;
+				case "CorpusID":
+					return (
+						"https://api.semanticscholar.org/CorpusID:" + cleanPID
+					);
+			}
+		}
+		return null;
+	}
+
+	/** Get the cleaned ID
+	 * @returns The cleaned ID or null if it couldn't be cleaned
+	 */
+	get cleanID(): string | null {
+		switch (this.type) {
+			case "DOI":
+				return Zotero.Utilities.cleanDOI(this.id);
+			case "ISBN":
+				return Zotero.Utilities.cleanISBN(this.id) || null;
+			case "QID": {
+				let qid = this.id.toUpperCase().trim();
+				if (qid[0] !== "Q") qid = "Q" + qid;
+				if (!qid.match(/^Q\d+$/)) return null;
+				return qid;
+			}
+			case "OMID": {
+				let omid = this.id.toLowerCase().trim();
+				if (/^https?:/.test(omid))
+					omid = omid.match(/br\/\d+/)?.[0] ?? "";
+				if (omid.substring(0, 3) !== "br/") omid = "br/" + omid;
+				if (!omid.match(/^br\/06[1-9]*0\d+$/)) return null;
+				return omid;
+			}
+			case "arXiv": {
+				const arXiv_RE =
+					/\b(([-A-Za-z.]+\/\d{7}|\d{4}\.\d{4,5})(?:v(\d+))?)(?!\d)/g; // 1: full ID, 2: ID without version, 3: version #
+				const m = arXiv_RE.exec(this.id);
+				if (m) {
+					const cleanArXiv = m[2];
+					return cleanArXiv;
+				}
+
+				return null;
+			}
+			case "OpenAlex": {
+				let openAlex = this.id.trim();
+				if (/^https?:/.test(openAlex))
+					openAlex = openAlex.match(/[Ww]\d+/)?.[0] ?? "";
+				openAlex = openAlex.toUpperCase();
+				if (openAlex[0] !== "W") openAlex = "W" + openAlex;
+				if (!openAlex.match(/^W\d+$/)) return null;
+				return openAlex;
+			}
+			case "CorpusID": {
+				const _semantic = parseInt(this.id.trim(), 10);
+				const semantic = `${_semantic}`;
+				if (!semantic) return null;
+				return semantic;
+			}
+			default:
+				return this.id;
+		}
+	}
+
+	/**
+	 * Clean the ID if possible
+	 * @returns The cleaned ID or null if it couldn't be cleaned
+	 */
+	cleaned(): this | null {
+		if (this.cleanID) {
+			this.id = this.cleanID;
+			return this;
+		} else {
+			return null;
+		}
+	}
+
+	get zoteroIdentifier():
+		| { DOI: string }
+		| { ISBN: string }
+		| { arXiv: string }
+		| { adsBibcode: string }
+		| { PMID: string }
+		| null {
+		return Zotero.Utilities.extractIdentifiers(this.id)[0] ?? null;
+	}
+
+	get comparable(): string | undefined {
+		const rawID = this.cleanID?.toLowerCase();
+		return rawID ? `${this.type}:${rawID}` : undefined;
+	}
+
+	static readonly allTypes: PIDType[] = [
+		"DOI",
+		"ISBN",
+		"QID",
+		"OMID",
+		"arXiv",
+		"OpenAlex",
+		"MAG",
+		"CorpusID",
+		"PMID",
+		"PMCID",
+	];
+
+	static readonly showable: PIDType[] = [
+		"DOI",
+		"ISBN",
+		"QID",
+		"OMID",
+		"arXiv",
+		"OpenAlex",
+		"CorpusID",
+		// Don't show PMID or PMCID because we can't fetch citations from them
+	];
+
+	static readonly fetchable: PIDType[] = [
+		"QID",
+		"OMID",
+		"OpenAlex",
+		"DOI",
+		"CorpusID",
+	];
+
+	static isEqual(a: PID, b: PID): boolean {
+		if (a.type !== b.type) return false;
+		const aComp = a.comparable;
+		const bComp = b.comparable;
+		return aComp !== null && aComp === bComp;
+	}
+}

src/cita/citation.ts

@@ -4,7 +4,7 @@ import Wikidata, { CitesWorkClaim } from "./wikidata";
 import ItemWrapper from "./itemWrapper";
 import SourceItemWrapper from "./sourceItemWrapper";
 import Matcher from "./matcher";
-import OCI from "../oci";
+import OCI, { OCIPIDType } from "../oci";
 import Progress from "./progress";
 import { EntityId } from "wikibase-sdk";
 
@@ -15,11 +15,12 @@ class Citation {
 	ocis: {
 		citingId: string;
 		citedId: string;
-		idType: "qid" | "doi" | "occ";
+		idType: OCIPIDType;
 		oci: string;
 		supplierName: string;
 		valid: boolean;
 	}[];
+	readonly uuid: string;
 
 	/**
 	 * Create a citation.
@@ -92,6 +93,9 @@ class Citation {
 		// this.series_ordinal;
 		// // crosref does provide a citation key which seems to have some ordinal information
 		// // but I say to leave this out for now
+
+		// generate a unique identifier for this citation
+		this.uuid = crypto.randomUUID();
 	}
 
 	addCreator(creatorType: any, creatorName: string) {
@@ -114,8 +118,8 @@ class Citation {
 		try {
 			newOci = OCI.getOci(
 				supplier,
-				this.source[idType]!,
-				this.target[idType]!,
+				this.source.getPID(idType)!.id,
+				this.target.getPID(idType)!.id,
 			);
 		} catch {
 			//
@@ -330,7 +334,7 @@ class Citation {
 			return;
 		}
 
-		if (item.libraryID !== this.source.item.libraryID) {
+		if (item.libraryID && item.libraryID !== this.source.item.libraryID) {
 			Services.prompt.alert(
 				window as mozIDOMWindowProxy,
 				"",