Mendeley import: Import highlight and note annotations
Using new PDF worker functionality If you've previously imported, you should be able to import again to get annotations in the new PDF reader. Details: - Text highlights will be processed to extract text - Rectangle highlights will turn into image annotations - Any extracted-annotation notes created by previous improts won't be removed, but they're no longer created as long as the file exists.
This commit is contained in:
Dan Stillman
parent
c16432b217
commit
5cdc088c49
2 changed files with 153 additions and 48 deletions
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@ -152,11 +152,10 @@ Zotero_Import_Mendeley.prototype.translate = async function (options = {}) {
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docURLs,
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creators.get(document.id),
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tags.get(document.id),
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collections.get(document.id),
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annotations.get(document.id)
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collections.get(document.id)
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);
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let documentIDMap = await this._saveItems(libraryID, itemJSON);
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// Save the document's attachments and extracted annotations for any of them
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// Save the document's attachments and annotations for any of them
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if (docFiles) {
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await this._saveFilesAndAnnotations(
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docFiles,
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@ -495,34 +494,88 @@ Zotero_Import_Mendeley.prototype._getDocumentFiles = async function (groupID) {
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* Get a Map of document ids to arrays of annotations
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*/
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Zotero_Import_Mendeley.prototype._getDocumentAnnotations = async function (groupID) {
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var map = new Map();
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// Highlights
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var rows = await this._db.queryAsync(
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`SELECT documentId, uuid, fileHash, page, note, color `
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`SELECT documentId, FH.id AS highlightId, uuid, fileHash, color, createdTime, `
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+ `page, x1, y1, x2, y2 `
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+ `FROM FileHighlights FH `
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+ `JOIN RemoteDocuments USING (documentId) `
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+ `JOIN FileHighlightRects FHR ON (FH.id=FHR.highlightId) `
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+ `WHERE groupId=? `
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+ `ORDER BY FH.id, page, y1 DESC, x1`,
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groupID
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);
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var currentHighlight = null;
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for (let i = 0; i < rows.length; i++) {
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let row = rows[i];
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let docAnnotations = map.get(row.documentId);
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if (!docAnnotations) docAnnotations = [];
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// There can be multiple highlight rows per annotation, so add the last annotation when the
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// UUID changes
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if (!currentHighlight || currentHighlight.uuid != row.uuid) {
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if (currentHighlight) {
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docAnnotations.push(currentHighlight);
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map.set(row.documentId, docAnnotations);
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}
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currentHighlight = {
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type: 'highlight',
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uuid: row.uuid,
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hash: row.fileHash,
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color: row.color,
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dateAdded: row.createdTime,
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page: null,
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rects: []
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};
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}
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currentHighlight.page = row.page;
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currentHighlight.rects.push({
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x1: row.x1,
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y1: row.y1,
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x2: row.x2,
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y2: row.y2,
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});
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if (i == rows.length - 1) {
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docAnnotations.push(currentHighlight);
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map.set(row.documentId, docAnnotations);
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}
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}
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// Notes
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rows = await this._db.queryAsync(
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`SELECT documentId, uuid, fileHash, page, x, y, note, color, modifiedTime, createdTime `
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+ `FROM FileNotes `
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+ `JOIN RemoteDocuments USING (documentId) `
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+ `WHERE groupId=? `
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+ `ORDER BY page, y, x`,
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groupID
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);
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var map = new Map();
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for (let row of rows) {
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let docAnnotations = map.get(row.documentId);
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if (!docAnnotations) docAnnotations = [];
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docAnnotations.push({
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type: 'note',
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uuid: row.uuid,
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hash: row.fileHash,
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x: row.x,
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y: row.y,
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note: row.note,
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page: row.page,
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color: row.color
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color: row.color,
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dateAdded: row.createdTime,
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dateModified: row.modifiedTime
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});
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map.set(row.documentId, docAnnotations);
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}
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return map;
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};
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/**
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* Create API JSON array with item and any child attachments or notes
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*/
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Zotero_Import_Mendeley.prototype._documentToAPIJSON = async function (map, documentRow, urls, creators, tags, collections, annotations) {
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Zotero_Import_Mendeley.prototype._documentToAPIJSON = async function (map, documentRow, urls, creators, tags, collections) {
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var parent = {
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key: Zotero.DataObjectUtilities.generateKey()
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};
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@ -982,7 +1035,7 @@ Zotero_Import_Mendeley.prototype._getItemByRelation = async function (libraryID,
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/**
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* Saves attachments and extracted annotations for a given document
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* Saves attachments and annotations for a given document
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*/
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Zotero_Import_Mendeley.prototype._saveFilesAndAnnotations = async function (files, libraryID, parentItemID, annotations) {
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for (let file of files) {
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@ -994,39 +1047,39 @@ Zotero_Import_Mendeley.prototype._saveFilesAndAnnotations = async function (file
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let attachment;
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if (realPath) {
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if (this._findExistingFile(parentItemID, file)) {
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continue;
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}
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let options = {
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libraryID,
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parentItemID,
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file: realPath,
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title: file.title
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};
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// If we're not set to link files or file is in Mendeley downloads folder, import it
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if (!this._linkFiles || this._isDownloadedFile(path)) {
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if (file.url) {
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options.title = file.title;
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options.url = file.url;
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options.contentType = file.contentType;
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options.singleFile = true;
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attachment = await Zotero.Attachments.importSnapshotFromFile(options);
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attachment = this._findExistingFile(parentItemID, file);
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// If file hasn't already been imported, import it
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if (!attachment) {
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let options = {
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libraryID,
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parentItemID,
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file: realPath,
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title: file.title,
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contentType: file.contentType
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};
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// If we're not set to link files or file is in Mendeley downloads folder, import it
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if (!this._linkFiles || this._isDownloadedFile(path)) {
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if (file.url) {
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options.title = file.title;
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options.url = file.url;
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options.singleFile = true;
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attachment = await Zotero.Attachments.importSnapshotFromFile(options);
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}
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else {
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attachment = await Zotero.Attachments.importFromFile(options);
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}
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}
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// Otherwise link it
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else {
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attachment = await Zotero.Attachments.importFromFile(options);
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attachment = await Zotero.Attachments.linkFromFile(options);
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}
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attachment.setRelations({
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'mendeleyDB:fileHash': file.hash
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});
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await attachment.saveTx({
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skipSelect: true
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});
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}
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// Otherwise link it
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else {
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attachment = await Zotero.Attachments.linkFromFile(options);
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}
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attachment.setRelations({
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'mendeleyDB:fileHash': file.hash
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});
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await attachment.saveTx({
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skipSelect: true
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});
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}
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else {
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Zotero.warn(path + " not found -- not importing");
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@ -1038,7 +1091,7 @@ Zotero_Import_Mendeley.prototype._saveFilesAndAnnotations = async function (file
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// this file
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annotations.filter(a => a.hash == file.hash),
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parentItemID,
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attachment ? attachment.id : null,
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(attachment && file.contentType == 'application/pdf') ? attachment.id : null,
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file.hash
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);
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}
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@ -1108,21 +1161,66 @@ Zotero_Import_Mendeley.prototype._saveAnnotations = async function (annotations,
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if (attachmentItemID) {
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var attachmentItem = Zotero.Items.get(attachmentItemID);
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var attachmentURIPath = Zotero.API.getLibraryPrefix(libraryID) + '/items/' + attachmentItem.key;
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if (attachmentItem) {
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let file = await attachmentItem.getFilePathAsync();
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if (file) {
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let annotationMap = new Map();
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for (let annotation of annotations) {
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// 'type', 'uuid', 'hash', 'color', 'dateAdded', 'page'
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// For highlights: 'rects' (array of { x1, y1, x2, y2 })
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// For notes: 'dateModified', 'x', 'y'
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annotationMap.set(annotation.uuid, annotation);
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}
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// PDFWorker needs 'id'
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annotations.forEach(annotation => annotation.id = annotation.uuid);
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// Returns 'id', 'position', 'type', 'pageLabel', 'sortIndex', 'text' (for highlight)
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annotations = await Zotero.PDFWorker.processMendeleyAnnotations(file, annotations);
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for (let annotation of annotations) {
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let o = annotationMap.get(annotation.id);
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Object.assign(o, annotation);
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// Check for existing annotation, and update it if found
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predicate = 'mendeleyDB:annotationUUID';
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let existingItem = await this._getItemByRelation(
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attachmentItem.libraryID,
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predicate,
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o.uuid
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);
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let key = existingItem
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? existingItem.key
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: Zotero.DataObjectUtilities.generateKey();
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await Zotero.Annotations.saveFromJSON(
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attachmentItem,
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{
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key,
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type: o.type,
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text: o.text,
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comment: o.note,
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color: o.color,
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pageLabel: o.pageLabel,
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sortIndex: o.sortIndex,
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position: o.position,
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relations: {
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[predicate]: o.uuid
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}
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},
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{
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skipSelect: true
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}
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);
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}
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return;
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}
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}
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}
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// If no file, create note from extracted annotations instead
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for (let annotation of annotations) {
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if (!annotation.note || !annotation.note.trim()) continue;
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let linkStr;
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let linkText = `note on p. ${annotation.page}`;
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if (attachmentItem) {
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let url = `zotero://open-pdf/${attachmentURIPath}?page=${annotation.page}`;
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linkStr = `<a href="${url}">${linkText}</a>`;
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}
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else {
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linkStr = linkText;
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}
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let linkStr = `note on p. ${annotation.page}`;
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noteStrings.push(
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Zotero.Utilities.text2html(annotation.note.trim())
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+ `<p class="pdf-link" style="margin-top: -0.5em; margin-bottom: 2em; font-size: .9em; text-align: right;">(${linkStr})</p>`
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@ -203,6 +203,13 @@ Zotero.Annotations = new function () {
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// TODO: Can colors be set?
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item.setTags((json.tags || []).map(t => ({ tag: t.name })));
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// For Mendeley import -- additive only
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if (json.relations) {
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for (let predicate in json.relations) {
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item.addRelation(predicate, json.relations[predicate]);
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}
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}
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await item.saveTx(saveOptions);
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return item;
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