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https://github.com/zotero/zotero.git
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Merge pull request #2693 from tnajdek/mendeley-import-improve-feedback
Multiple improvements to Mendeley importer
This commit is contained in:
Dan Stillman
GitHub
commit
c5dbf0169f
7 changed files with 124 additions and 88 deletions
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@ -57,7 +57,12 @@ var Zotero_Import_Wizard = {
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Zotero.Translators.init(); // async
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},
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onCancel: function () {
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if (this._translation && this._translation.interrupt) {
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this._translation.interrupt();
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}
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},
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onModeChosen: async function () {
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var wizard = this._wizard;
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@ -10,6 +10,7 @@
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xmlns="http://www.mozilla.org/keymaster/gatekeeper/there.is.only.xul"
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xmlns:html="http://www.w3.org/1999/xhtml"
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title="&zotero.import;"
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onwizardcancel="Zotero_Import_Wizard.onCancel()"
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onload="Zotero_Import_Wizard.init()">
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<script src="../include.js"/>
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@ -64,16 +64,18 @@ const get = async (tokens, endPoint, params = {}, headers = {}, options = {}) =>
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return JSON.parse(response.responseText);
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};
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const getAll = async (tokens, endPoint, params = {}, headers = {}, options = {}) => {
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const getAll = async (tokens, endPoint, params = {}, headers = {}, options = {}, interruptChecker = () => {}) => {
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const PER_PAGE = endPoint === 'annotations' ? 200 : 500;
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const response = await apiFetch(tokens, endPoint, { ...params, limit: PER_PAGE }, headers, options);
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var next = getNextLinkFromResponse(response);
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var data = JSON.parse(response.responseText);
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interruptChecker();
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while (next) {
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const response = await apiFetchUrl(tokens, next, headers, options); //eslint-disable-line no-await-in-loop
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data = [...data, ...JSON.parse(response.responseText)];
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next = getNextLinkFromResponse(response);
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interruptChecker();
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}
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return data;
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@ -1,11 +1,13 @@
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/* global map:false, mendeleyOnlineMappings:false, mendeleyAPIUtils:false */
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var EXPORTED_SYMBOLS = ["Zotero_Import_Mendeley"];
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/* eslint-disable no-await-in-loop, camelcase */
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/* global mendeleyDBMaps:false, mendeleyOnlineMappings:false, mendeleyAPIUtils:false */
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var EXPORTED_SYMBOLS = ["Zotero_Import_Mendeley"]; //eslint-disable-line no-unused-vars
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Components.utils.import("resource://gre/modules/Services.jsm");
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Components.utils.import("resource://gre/modules/osfile.jsm");
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Services.scriptloader.loadSubScript("chrome://zotero/content/include.js");
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Services.scriptloader.loadSubScript("chrome://zotero/content/import/mendeley/mendeleyOnlineMappings.js");
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Services.scriptloader.loadSubScript("chrome://zotero/content/import/mendeley/mendeleyAPIUtils.js");
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Services.scriptloader.loadSubScript("chrome://zotero/content/import/mendeley/mendeleySchemaMap.js");
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const { apiTypeToDBType, apiFieldToDBField } = mendeleyOnlineMappings;
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const { apiFetch, get, getAll, getTokens } = mendeleyAPIUtils;
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@ -17,13 +19,32 @@ var Zotero_Import_Mendeley = function () {
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this.mendeleyCode = null;
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this._tokens = null;
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this._db;
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this._file;
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this._db = null;
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this._file = null;
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this._saveOptions = null;
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this._itemDone;
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this._itemDone = () => {};
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this._progress = 0;
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this._progressMax;
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this._progressMax = 0;
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this._tmpFilesToDelete = [];
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this._caller = null;
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this._interrupted = false;
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this._totalSize = 0;
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this._started = Date.now();
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this._interruptChecker = (tickProgress = false) => {
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if (this._interrupted) {
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throw new Error(`Mendeley import interrupted!
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Started: ${this._started} (${Math.round((Date.now() - this._started) / 1000)}s ago)
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Progress: ${this._progress} / ${this._progressMax}
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New items created: ${this.newItems.length}
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Total size of files to download: ${Math.round(this._totalSize / 1024)}KB
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`);
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}
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if (tickProgress) {
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this._progress++;
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this._itemDone();
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}
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};
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};
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Zotero_Import_Mendeley.prototype.setLocation = function (file) {
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@ -32,9 +53,9 @@ Zotero_Import_Mendeley.prototype.setLocation = function (file) {
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Zotero_Import_Mendeley.prototype.setHandler = function (name, handler) {
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switch (name) {
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case 'itemDone':
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this._itemDone = handler;
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break;
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case 'itemDone':
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this._itemDone = handler;
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break;
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}
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};
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@ -57,34 +78,16 @@ Zotero_Import_Mendeley.prototype.translate = async function (options = {}) {
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...(options.saveOptions || {})
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};
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if (true) {
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Services.scriptloader.loadSubScript("chrome://zotero/content/import/mendeley/mendeleySchemaMap.js");
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}
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// TEMP: Load uncached from ~/zotero-client for development
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else {
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Components.utils.import("resource://gre/modules/FileUtils.jsm");
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let file = FileUtils.getDir("Home", []);
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file = OS.Path.join(file.path, 'zotero-client', 'chrome', 'content', 'zotero', 'import', 'mendeley', 'mendeleySchemaMap.js');
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let fileURI = OS.Path.toFileURI(file);
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let xmlhttp = await Zotero.HTTP.request(
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'GET',
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fileURI,
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{
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noCache: true,
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responseType: 'text'
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}
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);
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eval(xmlhttp.response);
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}
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const libraryID = options.libraryID || Zotero.Libraries.userLibraryID;
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const { key: rootCollectionKey } = options.collections
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? Zotero.Collections.getLibraryAndKeyFromID(options.collections[0])
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: {};
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Zotero.debug(`Begining Mendeley import at ${this._started}. libraryID: ${libraryID}, linkFiles: ${this.linkFiles}, rootCollectionKey: ${rootCollectionKey}`);
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// TODO: Get appropriate version based on schema version
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const mapVersion = 83;
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map = map[mapVersion];
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const map = mendeleyDBMaps[mapVersion];
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const mendeleyGroupID = 0;
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@ -94,7 +97,7 @@ Zotero_Import_Mendeley.prototype.translate = async function (options = {}) {
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if (this._file) {
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this._db = new Zotero.DBConnection(this._file);
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}
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try {
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if (this._file && !await this._isValidDatabase()) {
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throw new Error("Not a valid Mendeley database");
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@ -108,14 +111,22 @@ Zotero_Import_Mendeley.prototype.translate = async function (options = {}) {
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throw new Error("Missing import token");
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}
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// we don't know how long the import will be but want to show progress to give
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// feedback that import has started so we arbitrary set progress at 2%
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this._progress = 1;
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this._progressMax = 50;
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this._itemDone();
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const folders = this._tokens
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? await this._getFoldersAPI(mendeleyGroupID)
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: await this._getFoldersDB(mendeleyGroupID);
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const collectionJSON = this._foldersToAPIJSON(folders, rootCollectionKey);
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const folderKeys = this._getFolderKeys(collectionJSON);
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await this._saveCollections(libraryID, collectionJSON, folderKeys);
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this._interruptChecker(true);
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//
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// Items
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//
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@ -123,40 +134,59 @@ Zotero_Import_Mendeley.prototype.translate = async function (options = {}) {
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? await this._getDocumentsAPI(mendeleyGroupID)
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: await this._getDocumentsDB(mendeleyGroupID);
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this._progressMax = documents.length;
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// Update progress to reflect items to import and remaining meta data stages
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// We arbitrary set progress at approx 4%. We then add 8, one "tick" for each remaining meta data download.
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this._progress = Math.max(Math.floor(0.04 * documents.length), 2);
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this._progressMax = documents.length + this._progress + 8;
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// Get various attributes mapped to document ids
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let urls = this._tokens
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? await this._getDocumentURLsAPI(documents)
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: await this._getDocumentURLsDB(mendeleyGroupID);
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this._interruptChecker(true);
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let creators = this._tokens
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? await this._getDocumentCreatorsAPI(documents)
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: await this._getDocumentCreatorsDB(mendeleyGroupID, map.creatorTypes);
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this._interruptChecker(true);
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let tags = this._tokens
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? await this._getDocumentTagsAPI(documents)
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: await this._getDocumentTagsDB(mendeleyGroupID);
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this._interruptChecker(true);
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let collections = this._tokens
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? await this._getDocumentCollectionsAPI(documents, rootCollectionKey, folderKeys)
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: await this._getDocumentCollectionsDB(mendeleyGroupID, documents, rootCollectionKey, folderKeys);
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this._interruptChecker(true);
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let files = this._tokens
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? await this._getDocumentFilesAPI(documents)
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: await this._getDocumentFilesDB(mendeleyGroupID);
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this._interruptChecker(true);
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let annotations = this._tokens
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? await this._getDocumentAnnotationsAPI(mendeleyGroupID)
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: await this._getDocumentAnnotationsDB(mendeleyGroupID);
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this._interruptChecker(true);
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let profile = this._tokens
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? await this._getProfileAPI()
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: await this._getProfileDB();
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this._interruptChecker(true);
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let groups = this._tokens
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? await this._getGroupsAPI()
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: await this._getGroupsDB();
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this._interruptChecker(true);
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const fileHashLookup = new Map();
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for (let [documentID, fileEntries] of files) {
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@ -165,7 +195,6 @@ Zotero_Import_Mendeley.prototype.translate = async function (options = {}) {
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}
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}
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for (let group of groups) {
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let groupAnnotations = this._tokens
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? await this._getDocumentAnnotationsAPI(group.id, profile.id)
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@ -263,11 +292,12 @@ Zotero_Import_Mendeley.prototype.translate = async function (options = {}) {
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);
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}
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this.newItems.push(Zotero.Items.get(documentIDMap.get(document.id)));
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this._progress++;
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if (this._itemDone) {
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this._itemDone();
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}
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this._interruptChecker(true);
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}
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Zotero.debug(`Completed Mendeley import in ${Math.round((Date.now() - this._started) / 1000)}s. (Started: ${this._started})`);
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}
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catch (e) {
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Zotero.logError(e);
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}
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finally {
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try {
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@ -275,6 +305,7 @@ Zotero_Import_Mendeley.prototype.translate = async function (options = {}) {
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await this._db.closeDatabase();
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}
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if (this._tokens) {
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Zotero.debug(`Clearing ${this._tmpFilesToDelete.length} temporary files after Mendeley import`);
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await Promise.all(
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this._tmpFilesToDelete.map(f => this._removeTemporaryFile(f))
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);
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@ -288,14 +319,20 @@ Zotero_Import_Mendeley.prototype.translate = async function (options = {}) {
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}
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};
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Zotero_Import_Mendeley.prototype.interrupt = function () {
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this._interrupted = true;
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if (this._caller) {
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this._caller.stop();
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}
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};
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Zotero_Import_Mendeley.prototype._removeTemporaryFile = async function (file) {
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const containingDir = OS.Path.dirname(file);
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try {
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await Zotero.File.removeIfExists(file);
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await OS.File.removeEmptyDir(containingDir);
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}
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catch (e) {
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Zotero.logError(e);
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Zotero.logError("Error while removing temporary file " + file + ": " + e);
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}
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};
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@ -345,7 +382,7 @@ Zotero_Import_Mendeley.prototype._getFoldersAPI = async function (groupID) {
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if (groupID && groupID !== 0) {
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params.group_id = groupID; //eslint-disable-line camelcase
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}
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return (await getAll(this._tokens, 'folders', params, headers)).map(f => ({
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return (await getAll(this._tokens, 'folders', params, headers, {}, this._interruptChecker)).map(f => ({
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id: f.id,
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uuid: f.id,
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name: f.name,
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@ -365,11 +402,11 @@ Zotero_Import_Mendeley.prototype._foldersToAPIJSON = function (folderRows, paren
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};
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Zotero_Import_Mendeley.prototype._getFolderDescendents = function (folderID, folderKey, folderRows, maxDepth) {
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if (maxDepth == 0) return []
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if (maxDepth == 0) return [];
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var descendents = [];
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var children = folderRows
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.filter(f => f.parentId == folderID)
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.map(f => {
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.map((f) => {
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let c = {
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folderID: f.id,
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remoteUUID: f.remoteUuid,
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@ -492,7 +529,7 @@ Zotero_Import_Mendeley.prototype._getDocumentsAPI = async function (groupID) {
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}
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return (await getAll(this._tokens, 'documents', params, headers)).map(d => ({
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return (await getAll(this._tokens, 'documents', params, headers, {}, this._interruptChecker)).map(d => ({
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...d,
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uuid: d.id,
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remoteUuid: d.id
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@ -693,12 +730,13 @@ Zotero_Import_Mendeley.prototype._fetchFile = async function (fileID, filePath)
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Zotero_Import_Mendeley.prototype._getDocumentFilesAPI = async function (documents) {
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const map = new Map();
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let totalSize = 0;
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this._totalSize = 0;
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Components.utils.import("resource://zotero/concurrentCaller.js");
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var caller = new ConcurrentCaller({
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this._caller = new ConcurrentCaller({
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numConcurrent: 6,
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onError: e => Zotero.logError(e),
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logger: Zotero.debug,
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Promise: Zotero.Promise
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});
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@ -712,7 +750,7 @@ Zotero_Import_Mendeley.prototype._getDocumentFilesAPI = async function (document
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let tmpFile = OS.Path.join(Zotero.getTempDirectory().path, `m-api-${file.id}.${ext}`);
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this._tmpFilesToDelete.push(tmpFile);
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caller.add(this._fetchFile.bind(this, file.id, tmpFile));
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this._caller.add(this._fetchFile.bind(this, file.id, tmpFile));
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files.push({
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fileURL: OS.Path.toFileURI(tmpFile),
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title: file.file_name || '',
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@ -720,13 +758,14 @@ Zotero_Import_Mendeley.prototype._getDocumentFilesAPI = async function (document
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hash: file.filehash,
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fileBaseName
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});
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totalSize += file.size;
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this._totalSize += file.size;
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this._progressMax += 1;
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}
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map.set(doc.id, files);
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}
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// TODO: check if enough space available totalSize
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await caller.runAll();
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await this._caller.runAll();
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this._caller = null;
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return map;
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};
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@ -823,7 +862,7 @@ Zotero_Import_Mendeley.prototype._getDocumentAnnotationsAPI = async function (gr
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}
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const map = new Map();
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(await getAll(this._tokens, 'annotations', params, { Accept: 'application/vnd.mendeley-annotation.1+json' }))
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(await getAll(this._tokens, 'annotations', params, { Accept: 'application/vnd.mendeley-annotation.1+json' }, {}, this._interruptChecker))
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.forEach((a) => {
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if (profileID !== null && a.profile_id !== profileID) {
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// optionally filter annotations by profile id
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@ -885,7 +924,7 @@ Zotero_Import_Mendeley.prototype._getGroupsAPI = async function () {
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const params = { type: 'all' };
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const headers = { Accept: 'application/vnd.mendeley-group-list+json' };
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return getAll(this._tokens, 'groups/v2', params, headers);
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return getAll(this._tokens, 'groups/v2', params, headers, {}, this._interruptChecker);
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};
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Zotero_Import_Mendeley.prototype._getGroupsDB = async function () {
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@ -985,14 +1024,14 @@ Zotero_Import_Mendeley.prototype._documentToAPIJSON = async function (map, docum
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for (let field in parent) {
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switch (field) {
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case 'itemType':
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case 'key':
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case 'parentItem':
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case 'note':
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case 'creators':
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case 'dateAdded':
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case 'dateModified':
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continue;
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case 'itemType':
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case 'key':
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case 'parentItem':
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case 'note':
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case 'creators':
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case 'dateAdded':
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case 'dateModified':
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continue;
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}
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// Move unknown/invalid fields to Extra
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@ -1035,7 +1074,7 @@ Zotero_Import_Mendeley.prototype._documentToAPIJSON = async function (map, docum
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// seriesEditor isn't valid on some item types (e.g., book)
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if (creator.creatorType == 'seriesEditor'
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&& !Zotero.CreatorTypes.isValidForItemType(
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Zotero.CreatorTypes.getID('seriesEditor'), itemTypeID)) {
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Zotero.CreatorTypes.getID('seriesEditor'), itemTypeID)) {
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creator.creatorType = 'editor';
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}
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}
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@ -1160,7 +1199,6 @@ Zotero_Import_Mendeley.prototype._processField = function (parent, children, zFi
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}
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else {
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Zotero.warn(`Unknown function subfield: ${subfield}`);
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return;
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||||
}
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||||
}
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||||
else {
|
||||
|
|
@ -1191,20 +1229,21 @@ Zotero_Import_Mendeley.prototype._makeCreator = function (creatorType, firstName
|
|||
Zotero_Import_Mendeley.prototype._addExtraField = function (extra, field, val) {
|
||||
// Strip the field if it appears at the beginning of the value (to avoid "DOI: DOI: 10...")
|
||||
if (typeof val == 'string') {
|
||||
val = val.replace(new RegExp(`^${field}:\s*`, 'i'), "");
|
||||
val = val.replace(new RegExp(`^${field}:\\s*`, 'i'), "");
|
||||
}
|
||||
extra = extra ? extra + '\n' : '';
|
||||
if (field != 'arXiv') {
|
||||
field = field[0].toUpperCase() + field.substr(1);
|
||||
field = field.replace(/([a-z])([A-Z][a-z])/, "$1 $2");
|
||||
}
|
||||
|
||||
return extra + `${field}: ${val}`;
|
||||
};
|
||||
|
||||
Zotero_Import_Mendeley.prototype._convertNote = function (note) {
|
||||
return note
|
||||
// Add newlines after <br>
|
||||
.replace(/<br\s*\/>/g, '<br\/>\n')
|
||||
.replace(/<br\s*\/>/g, '<br/>\n')
|
||||
//
|
||||
// Legacy pre-HTML stuff
|
||||
//
|
||||
|
|
@ -1360,7 +1399,7 @@ Zotero_Import_Mendeley.prototype._findExistingItem = async function (libraryID,
|
|||
Zotero.debug(`Found existing item ${existingItem.libraryKey} for `
|
||||
+ `${predicate} ${itemJSON.relations[predicate]}`);
|
||||
return existingItem;
|
||||
}
|
||||
};
|
||||
|
||||
|
||||
Zotero_Import_Mendeley.prototype._getItemByRelation = async function (libraryID, predicate, object) {
|
||||
|
|
@ -1443,7 +1482,7 @@ Zotero_Import_Mendeley.prototype._saveFilesAndAnnotations = async function (file
|
|||
Zotero.logError(e);
|
||||
}
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
|
||||
Zotero_Import_Mendeley.prototype._findExistingFile = function (parentItemID, file) {
|
||||
|
|
@ -1460,7 +1499,7 @@ Zotero_Import_Mendeley.prototype._findExistingFile = function (parentItemID, fil
|
|||
}
|
||||
}
|
||||
return false;
|
||||
}
|
||||
};
|
||||
|
||||
Zotero_Import_Mendeley.prototype._isDownloadedFile = function (path) {
|
||||
var parentDir = OS.Path.dirname(path);
|
||||
|
|
@ -1468,7 +1507,7 @@ Zotero_Import_Mendeley.prototype._isDownloadedFile = function (path) {
|
|||
|| parentDir.endsWith(OS.Path.join('Local', 'Mendeley Ltd', 'Mendeley Desktop', 'Downloaded'))
|
||||
|| parentDir.endsWith(OS.Path.join('Local', 'Mendeley Ltd.', 'Mendeley Desktop', 'Downloaded'))
|
||||
|| parentDir.endsWith(OS.Path.join('data', 'Mendeley Ltd.', 'Mendeley Desktop', 'Downloaded'));
|
||||
}
|
||||
};
|
||||
|
||||
Zotero_Import_Mendeley.prototype._isTempDownloadedFile = function (path) {
|
||||
return path.startsWith(OS.Path.join(Zotero.getTempDirectory().path, 'm-api'));
|
||||
|
|
@ -1498,7 +1537,7 @@ Zotero_Import_Mendeley.prototype._getRealFilePath = async function (path) {
|
|||
return altPath;
|
||||
}
|
||||
return false;
|
||||
}
|
||||
};
|
||||
|
||||
Zotero_Import_Mendeley.prototype._saveAnnotations = async function (annotations, parentItemID, attachmentItemID, fileHash) {
|
||||
if (!annotations.length) return;
|
||||
|
|
@ -1507,7 +1546,6 @@ Zotero_Import_Mendeley.prototype._saveAnnotations = async function (annotations,
|
|||
var libraryID = parentItem.libraryID;
|
||||
if (attachmentItemID) {
|
||||
var attachmentItem = Zotero.Items.get(attachmentItemID);
|
||||
var attachmentURIPath = Zotero.API.getLibraryPrefix(libraryID) + '/items/' + attachmentItem.key;
|
||||
|
||||
if (attachmentItem) {
|
||||
let file = await attachmentItem.getFilePathAsync();
|
||||
|
|
@ -1616,7 +1654,7 @@ Zotero_Import_Mendeley.prototype._saveAnnotations = async function (annotations,
|
|||
});
|
||||
}
|
||||
note.setNote('<h1>' + Zotero.getString('extractedAnnotations') + '</h1>\n' + noteStrings.join('\n'));
|
||||
return note.saveTx(this._saveOptions);
|
||||
await note.saveTx(this._saveOptions);
|
||||
};
|
||||
|
||||
|
||||
|
|
@ -1633,17 +1671,7 @@ Zotero_Import_Mendeley.prototype._updateParentKeys = function (objectType, json,
|
|||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
Zotero_Import_Mendeley.prototype._updateItemCollectionKeys = function (json, oldKey, newKey) {
|
||||
for (; i < json.length; i++) {
|
||||
let x = json[i];
|
||||
if (x[prop] == oldKey) {
|
||||
x[prop] = newKey;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
};
|
||||
|
||||
//
|
||||
// Clean up extra files created <5.0.51
|
||||
|
|
|
|||
|
|
@ -1,4 +1,5 @@
|
|||
var map = {
|
||||
// eslint-disable-next-line no-unused-vars
|
||||
var mendeleyDBMaps = {
|
||||
83: {
|
||||
itemTypes: {
|
||||
Bill: "bill",
|
||||
|
|
|
|||
|
|
@ -14,7 +14,7 @@
|
|||
"identifiers":
|
||||
{
|
||||
"doi": "10.1111",
|
||||
"pmid": "11111111",
|
||||
"pmid": "PMID: 11111111",
|
||||
"arxiv": "1111.2222"
|
||||
},
|
||||
"starred": false,
|
||||
|
|
|
|||
|
|
@ -174,8 +174,7 @@ describe('Zotero_Import_Mendeley', function () {
|
|||
|
||||
// identifiers
|
||||
assert.equal(journal.getField('DOI'), '10.1111');
|
||||
assert.include(journal.getField('extra'), 'PMID: 11111111');
|
||||
assert.include(journal.getField('extra'), 'arXiv: 1111.2222');
|
||||
assert.sameMembers(journal.getField('extra').split('\n'), ['PMID: 11111111', 'arXiv: 1111.2222']);
|
||||
|
||||
// attachment & annotations
|
||||
assert.lengthOf(withpdf.getAttachments(), 1);
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue