@manuscripts/transform 1.3.2 → 1.3.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/cjs/jats/importer/jats-body-dom-parser.js +6 -3
- package/dist/cjs/jats/importer/jats-body-transformations.js +5 -1
- package/dist/cjs/jats/importer/jats-comments.js +2 -1
- package/dist/cjs/jats/importer/jats-front-parser.js +27 -24
- package/dist/cjs/jats/importer/jats-journal-meta-parser.js +10 -6
- package/dist/cjs/jats/importer/jats-reference-parser.js +18 -17
- package/dist/cjs/lib/utils.js +9 -1
- package/dist/cjs/transformer/labels.js +2 -1
- package/dist/es/jats/importer/jats-body-dom-parser.js +6 -3
- package/dist/es/jats/importer/jats-body-transformations.js +5 -1
- package/dist/es/jats/importer/jats-comments.js +2 -1
- package/dist/es/jats/importer/jats-front-parser.js +27 -24
- package/dist/es/jats/importer/jats-journal-meta-parser.js +10 -6
- package/dist/es/jats/importer/jats-reference-parser.js +18 -17
- package/dist/es/lib/utils.js +7 -0
- package/dist/es/transformer/labels.js +2 -1
- package/dist/types/lib/utils.d.ts +1 -0
- package/package.json +1 -1
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@@ -649,10 +649,11 @@ const nodes = [
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tag: 'xref[ref-type="bibr"]',
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node: 'citation',
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getAttrs: (node) => {
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var _a;
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const element = node;
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return {
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rid: element.getAttribute('rid'),
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contents: element.textContent,
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contents: (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
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};
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},
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},
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@@ -660,10 +661,11 @@ const nodes = [
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tag: 'xref[ref-type="fn"]',
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node: 'inline_footnote',
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getAttrs: (node) => {
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var _a;
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const element = node;
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return {
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rid: element.getAttribute('rid'),
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contents: element.textContent,
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contents: (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
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};
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},
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},
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@@ -671,10 +673,11 @@ const nodes = [
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tag: 'xref',
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node: 'cross_reference',
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getAttrs: (node) => {
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var _a;
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const element = node;
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return {
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rid: element.getAttribute('rid'),
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label: element.textContent,
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label: (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
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};
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},
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},
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@@ -215,6 +215,7 @@ exports.jatsBodyTransformations = {
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body.append(backmatterContainer);
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},
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mapFootnotesToSections(doc, backmatterContainer, createElement) {
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var _a;
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const footnoteGroups = [...doc.querySelectorAll('fn[fn-type]')];
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for (const footnote of footnoteGroups) {
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const type = footnote.getAttribute('fn-type') || '';
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@@ -224,7 +225,10 @@ exports.jatsBodyTransformations = {
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const title = footnote.querySelector('p[content-type="fn-title"]');
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if (title) {
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const sectionTitleElement = createElement('title');
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-
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const titleTextContent = (_a = title.textContent) === null || _a === void 0 ? void 0 : _a.trim();
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if (titleTextContent) {
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sectionTitleElement.textContent = titleTextContent;
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}
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removeNodeFromParent(title);
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section.append(sectionTitleElement);
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}
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@@ -21,7 +21,8 @@ const transformer_1 = require("../../transformer");
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const DEFAULT_ANNOTATION_COLOR = 'rgb(250, 224, 150)';
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const DEFAULT_PROFILE_ID = 'MPUserProfile:0000000000000000000000000000000000000001';
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const parseProcessingInstruction = (node) => {
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var _a;
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const value = `<AuthorQuery ${(_a = node.textContent) === null || _a === void 0 ? void 0 : _a.trim()} />`;
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const processingInstruction = new DOMParser().parseFromString(value, 'application/xml').firstElementChild;
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if (processingInstruction) {
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const queryText = processingInstruction.getAttribute('queryText');
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@@ -20,6 +20,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.jatsFrontParser = void 0;
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const debug_1 = __importDefault(require("debug"));
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const utils_1 = require("../../lib/utils");
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const builders_1 = require("../../transformer/builders");
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const jats_journal_meta_parser_1 = require("./jats-journal-meta-parser");
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const warn = (0, debug_1.default)('manuscripts-transform');
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@@ -74,11 +75,10 @@ exports.jatsFrontParser = {
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}
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const history = {};
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const dateToTimestamp = (dateElement) => {
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var _a, _b;
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const selectors = ['year', 'month', 'day'];
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const values = [];
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for (const selector of selectors) {
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const value = (
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const value = (0, utils_1.getTrimmedTextContent)(dateElement, selector);
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if (!value || isNaN(+value)) {
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return;
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}
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@@ -118,17 +118,17 @@ exports.jatsFrontParser = {
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return history;
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},
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parseSupplements(supplementNodes) {
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var _a, _b, _c, _d
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var _a, _b, _c, _d;
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if (!supplementNodes || supplementNodes.length === 0) {
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return [];
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}
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const supplements = [];
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for (const supplementNode of supplementNodes) {
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const supplTitle = (
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const href = (
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const supplTitle = (_a = (0, utils_1.getTrimmedTextContent)(supplementNode, 'caption > title')) !== null && _a !== void 0 ? _a : '';
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const href = (_b = supplementNode.getAttributeNS(XLINK_NAMESPACE, 'href')) !== null && _b !== void 0 ? _b : '';
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const supplementaryMaterial = (0, builders_1.buildSupplementaryMaterial)(supplTitle, href);
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const mimeType = (
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const mimeSubtype = (
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const mimeType = (_c = supplementNode.getAttribute('mimetype')) !== null && _c !== void 0 ? _c : '';
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const mimeSubtype = (_d = supplementNode.getAttribute('mime-subtype')) !== null && _d !== void 0 ? _d : '';
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if (mimeType && mimeSubtype) {
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supplementaryMaterial.MIME = [mimeType, mimeSubtype].join('/');
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}
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@@ -139,10 +139,10 @@ exports.jatsFrontParser = {
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parseAffiliationNodes(affiliationNodes) {
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const affiliationIDs = new Map();
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const affiliations = affiliationNodes.map((affiliationNode, priority) => {
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var _a, _b
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var _a, _b;
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const affiliation = (0, builders_1.buildAffiliation)('', priority);
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for (const node of affiliationNode.querySelectorAll('institution')) {
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const content = node.textContent;
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const content = (_a = node.textContent) === null || _a === void 0 ? void 0 : _a.trim();
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if (!content) {
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continue;
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}
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}
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}
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affiliation.addressLine1 =
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(
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(0, utils_1.getTrimmedTextContent)(affiliationNode, 'addr-line:nth-of-type(1)') ||
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undefined;
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affiliation.addressLine2 =
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(
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(0, utils_1.getTrimmedTextContent)(affiliationNode, 'addr-line:nth-of-type(2)') ||
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undefined;
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affiliation.addressLine3 =
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(
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(0, utils_1.getTrimmedTextContent)(affiliationNode, 'addr-line:nth-of-type(3)') ||
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undefined;
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const emailNode = affiliationNode.querySelector('email');
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if (emailNode) {
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affiliation.email = {
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href: emailNode.getAttributeNS(XLINK_NAMESPACE, 'href') || undefined,
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text: emailNode.textContent || undefined,
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text: ((_b = emailNode.textContent) === null || _b === void 0 ? void 0 : _b.trim()) || undefined,
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};
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}
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affiliation.postCode =
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(
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(0, utils_1.getTrimmedTextContent)(affiliationNode, 'postal-code') || undefined;
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affiliation.country =
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(0, utils_1.getTrimmedTextContent)(affiliationNode, 'country') || undefined;
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const id = affiliationNode.getAttribute('id');
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affiliationIDs.set(id, affiliation._id);
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parseCorrespNodes(correspNodes) {
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const correspondingIDs = new Map();
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const correspondingList = correspNodes.map((correspNode) => {
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const label = correspNode.querySelector('label');
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label.remove();
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}
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const corresponding = (0, builders_1.buildCorresp)((_a = correspNode.textContent) !== null &&
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corresponding.label = (label === null || label === void 0 ? void 0 : label.textContent) || undefined;
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const corresponding = (0, builders_1.buildCorresp)((_b = (_a = correspNode.textContent) === null || _a === void 0 ? void 0 : _a.trim()) !== null && _b !== void 0 ? _b : '');
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corresponding.label = ((_c = label === null || label === void 0 ? void 0 : label.textContent) === null || _c === void 0 ? void 0 : _c.trim()) || undefined;
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const id = correspNode.getAttribute('id');
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},
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parseAuthorNodes(authorNodes, affiliationIDs, footnoteIDs, correspondingIDs) {
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return authorNodes.map((authorNode, priority) => {
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const name = (0, builders_1.buildBibliographicName)({});
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const given = (
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const given = (0, utils_1.getTrimmedTextContent)(authorNode, 'name > given-names');
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name.given = given;
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}
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const surname = (
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const surname = (0, utils_1.getTrimmedTextContent)(authorNode, 'name > surname');
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}
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if (corresponding) {
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contributor.isCorresponding = corresponding;
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}
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const orcid = (
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const orcid = (0, utils_1.getTrimmedTextContent)(authorNode, 'contrib-id[contrib-id-type="orcid"]');
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if (orcid) {
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contributor.ORCIDIdentifier = orcid;
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}
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if (footnoteId) {
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const authorFootNoteRef = {
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noteID: footnoteId,
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noteLabel: xrefNode.textContent || '',
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noteLabel: ((_a = xrefNode.textContent) === null || _a === void 0 ? void 0 : _a.trim()) || '',
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};
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contributor.footnote.push(authorFootNoteRef);
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}
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const authorCorrespRef = {
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correspID: correspId,
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correspLabel: xrefNode.textContent || '',
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correspLabel: ((_b = xrefNode.textContent) === null || _b === void 0 ? void 0 : _b.trim()) || '',
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};
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contributor.corresp.push(authorCorrespRef);
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}
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*/
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.parseJournalMeta = exports.parseJournalISSNs = exports.parseJournalAbbreviatedTitles = exports.parseJournalIdentifiers = void 0;
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const utils_1 = require("../../lib/utils");
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const parseJournalIdentifiers = (journalMeta) => {
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const output = [];
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const elements = journalMeta.querySelectorAll('journal-id');
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for (const element of elements) {
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const journalIDType = element.getAttribute('journal-id-type');
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const journalID = (_b = (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim()) !== null && _b !== void 0 ? _b : element.textContent;
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exports.parseJournalIdentifiers = parseJournalIdentifiers;
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const parseJournalAbbreviatedTitles = (journalMeta) => {
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const abbreviatedTitle = (_b = (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim()) !== null && _b !== void 0 ? _b : element.textContent;
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if (abbreviatedTitle !== null && abbrevType !== null) {
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output.push({ abbreviatedTitle, abbrevType });
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exports.parseJournalAbbreviatedTitles = parseJournalAbbreviatedTitles;
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const parseJournalISSNs = (journalMeta) => {
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const output = [];
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const elements = journalMeta.querySelectorAll('issn');
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for (const element of elements) {
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const publicationType = element.getAttribute('pub-type');
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const ISSN = element.textContent;
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const ISSN = (_b = (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim()) !== null && _b !== void 0 ? _b : element.textContent;
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if (publicationType !== null && ISSN !== null) {
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output.push({ publicationType, ISSN });
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exports.parseJournalISSNs = parseJournalISSNs;
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const parseJournalMeta = (journalMeta) => {
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var _a, _b;
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return {
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abbreviatedTitles: (0, exports.parseJournalAbbreviatedTitles)(journalMeta),
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journalIdentifiers: (0, exports.parseJournalIdentifiers)(journalMeta),
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ISSNs: (0, exports.parseJournalISSNs)(journalMeta),
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publisherName: (
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title: (
|
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+
publisherName: (_a = (0, utils_1.getTrimmedTextContent)(journalMeta, 'publisher > publisher-name')) !== null && _a !== void 0 ? _a : undefined,
|
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title: (_b = (0, utils_1.getTrimmedTextContent)(journalMeta, 'journal-title-group > journal-title')) !== null && _b !== void 0 ? _b : undefined,
|
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};
|
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exports.parseJournalMeta = parseJournalMeta;
|
|
@@ -16,6 +16,7 @@
|
|
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16
16
|
*/
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Object.defineProperty(exports, "__esModule", { value: true });
|
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exports.jatsReferenceParser = void 0;
|
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+
const utils_1 = require("../../lib/utils");
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const builders_1 = require("../../transformer/builders");
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const jats_comments_1 = require("./jats-comments");
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const jats_parser_utils_1 = require("./jats-parser-utils");
|
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@@ -34,7 +35,7 @@ exports.jatsReferenceParser = {
|
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35
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const referenceIDs = new Map();
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36
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const referenceQueries = new Map();
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const references = referenceNodes.map((referenceNode) => {
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var _a
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var _a;
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const publicationType = referenceNode.getAttribute('publication-type');
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const authorNodes = [
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...referenceNode.querySelectorAll('person-group[person-group-type="author"] > *'),
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});
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const titleNode = referenceNode.querySelector('article-title');
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if (titleNode) {
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bibliographyItem.title = (0, jats_parser_utils_1.htmlFromJatsNode)(titleNode, createElement);
|
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bibliographyItem.title = (_a = (0, jats_parser_utils_1.htmlFromJatsNode)(titleNode, createElement)) === null || _a === void 0 ? void 0 : _a.trim();
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}
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const queriesText = [];
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}
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65
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if (item.nodeType === Node.TEXT_NODE &&
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69
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((_a = item.textContent) === null || _a === void 0 ? void 0 : _a.match(/[A-Za-z]+/g))) {
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bibliographyItem.literal = (_b = mixedCitation.textContent) !== null &&
|
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+
bibliographyItem.literal = (_c = (_b = mixedCitation.textContent) === null || _b === void 0 ? void 0 : _b.trim()) !== null && _c !== void 0 ? _c : '';
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return bibliographyItem;
|
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});
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}
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const source = (
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const source = (0, utils_1.getTrimmedTextContent)(referenceNode, 'source');
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76
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if (source) {
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bibliographyItem['container-title'] = source;
|
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}
|
|
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const volume = (
|
|
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+
const volume = (0, utils_1.getTrimmedTextContent)(referenceNode, 'volume');
|
|
79
80
|
if (volume) {
|
|
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81
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bibliographyItem.volume = volume;
|
|
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82
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}
|
|
82
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-
const issue = (
|
|
83
|
+
const issue = (0, utils_1.getTrimmedTextContent)(referenceNode, 'issue');
|
|
83
84
|
if (issue) {
|
|
84
85
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bibliographyItem.issue = issue;
|
|
85
86
|
}
|
|
86
|
-
const supplement = (
|
|
87
|
+
const supplement = (0, utils_1.getTrimmedTextContent)(referenceNode, 'supplement');
|
|
87
88
|
if (supplement) {
|
|
88
89
|
bibliographyItem.supplement = supplement;
|
|
89
90
|
}
|
|
90
|
-
const fpage = (
|
|
91
|
-
const lpage = (
|
|
91
|
+
const fpage = (0, utils_1.getTrimmedTextContent)(referenceNode, 'fpage');
|
|
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|
+
const lpage = (0, utils_1.getTrimmedTextContent)(referenceNode, 'lpage');
|
|
92
93
|
if (fpage) {
|
|
93
94
|
bibliographyItem.page = lpage ? `${fpage}-${lpage}` : fpage;
|
|
94
95
|
}
|
|
95
|
-
const year = (
|
|
96
|
+
const year = (0, utils_1.getTrimmedTextContent)(referenceNode, 'year');
|
|
96
97
|
if (year) {
|
|
97
98
|
bibliographyItem.issued = (0, builders_1.buildBibliographicDate)({
|
|
98
99
|
'date-parts': [[year]],
|
|
99
100
|
});
|
|
100
101
|
}
|
|
101
|
-
const doi = (
|
|
102
|
+
const doi = (0, utils_1.getTrimmedTextContent)(referenceNode, 'pub-id[pub-id-type="doi"]');
|
|
102
103
|
if (doi) {
|
|
103
104
|
bibliographyItem.DOI = doi;
|
|
104
105
|
}
|
|
105
106
|
const authors = [];
|
|
106
107
|
authorNodes.forEach((authorNode) => {
|
|
107
|
-
var _a
|
|
108
|
+
var _a;
|
|
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109
|
const name = (0, builders_1.buildBibliographicName)({});
|
|
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|
-
const given = (
|
|
110
|
+
const given = (0, utils_1.getTrimmedTextContent)(authorNode, 'given-names');
|
|
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111
|
if (given) {
|
|
111
112
|
name.given = given;
|
|
112
113
|
}
|
|
113
|
-
const family = (
|
|
114
|
+
const family = (0, utils_1.getTrimmedTextContent)(authorNode, 'surname');
|
|
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115
|
if (family) {
|
|
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116
|
name.family = family;
|
|
116
117
|
}
|
|
117
|
-
const suffix = (
|
|
118
|
+
const suffix = (0, utils_1.getTrimmedTextContent)(authorNode, 'suffix');
|
|
118
119
|
if (suffix) {
|
|
119
120
|
name.suffix = suffix;
|
|
120
121
|
}
|
|
121
122
|
if (authorNode.nodeName === 'collab') {
|
|
122
|
-
name.literal = authorNode.textContent;
|
|
123
|
+
name.literal = (_a = authorNode.textContent) === null || _a === void 0 ? void 0 : _a.trim();
|
|
123
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|
}
|
|
124
125
|
authors.push(name);
|
|
125
126
|
});
|
package/dist/cjs/lib/utils.js
CHANGED
|
@@ -15,7 +15,7 @@
|
|
|
15
15
|
* limitations under the License.
|
|
16
16
|
*/
|
|
17
17
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
18
|
-
exports.findParentNodeClosestToPos = exports.isInBibliographySection = exports.isInGraphicalAbstractSection = exports.findNodePositions = exports.iterateChildren = void 0;
|
|
18
|
+
exports.getTrimmedTextContent = exports.findParentNodeClosestToPos = exports.isInBibliographySection = exports.isInGraphicalAbstractSection = exports.findNodePositions = exports.iterateChildren = void 0;
|
|
19
19
|
const bibliography_section_1 = require("../schema/nodes/bibliography_section");
|
|
20
20
|
const graphical_abstract_section_1 = require("../schema/nodes/graphical_abstract_section");
|
|
21
21
|
function* iterateChildren(node, recurse = false) {
|
|
@@ -75,3 +75,11 @@ const findParentNodeClosestToPos = ($pos, predicate) => {
|
|
|
75
75
|
}
|
|
76
76
|
};
|
|
77
77
|
exports.findParentNodeClosestToPos = findParentNodeClosestToPos;
|
|
78
|
+
const getTrimmedTextContent = (node, querySelector) => {
|
|
79
|
+
var _a, _b;
|
|
80
|
+
if (!node) {
|
|
81
|
+
return null;
|
|
82
|
+
}
|
|
83
|
+
return (_b = (_a = node.querySelector(querySelector)) === null || _a === void 0 ? void 0 : _a.textContent) === null || _b === void 0 ? void 0 : _b.trim();
|
|
84
|
+
};
|
|
85
|
+
exports.getTrimmedTextContent = getTrimmedTextContent;
|
|
@@ -65,6 +65,7 @@ const buildTargets = (fragment, manuscript) => {
|
|
|
65
65
|
}
|
|
66
66
|
});
|
|
67
67
|
fragment.descendants((node) => {
|
|
68
|
+
var _a;
|
|
68
69
|
if (node.type.name in counters) {
|
|
69
70
|
const isInGraphicalAbstract = figures.indexOf(node.attrs.id) > -1;
|
|
70
71
|
if (isInGraphicalAbstract) {
|
|
@@ -75,7 +76,7 @@ const buildTargets = (fragment, manuscript) => {
|
|
|
75
76
|
type: node.type.name,
|
|
76
77
|
id: node.attrs.id,
|
|
77
78
|
label,
|
|
78
|
-
caption: node.textContent,
|
|
79
|
+
caption: (_a = node.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
|
|
79
80
|
});
|
|
80
81
|
}
|
|
81
82
|
});
|
|
@@ -643,10 +643,11 @@ const nodes = [
|
|
|
643
643
|
tag: 'xref[ref-type="bibr"]',
|
|
644
644
|
node: 'citation',
|
|
645
645
|
getAttrs: (node) => {
|
|
646
|
+
var _a;
|
|
646
647
|
const element = node;
|
|
647
648
|
return {
|
|
648
649
|
rid: element.getAttribute('rid'),
|
|
649
|
-
contents: element.textContent,
|
|
650
|
+
contents: (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
|
|
650
651
|
};
|
|
651
652
|
},
|
|
652
653
|
},
|
|
@@ -654,10 +655,11 @@ const nodes = [
|
|
|
654
655
|
tag: 'xref[ref-type="fn"]',
|
|
655
656
|
node: 'inline_footnote',
|
|
656
657
|
getAttrs: (node) => {
|
|
658
|
+
var _a;
|
|
657
659
|
const element = node;
|
|
658
660
|
return {
|
|
659
661
|
rid: element.getAttribute('rid'),
|
|
660
|
-
contents: element.textContent,
|
|
662
|
+
contents: (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
|
|
661
663
|
};
|
|
662
664
|
},
|
|
663
665
|
},
|
|
@@ -665,10 +667,11 @@ const nodes = [
|
|
|
665
667
|
tag: 'xref',
|
|
666
668
|
node: 'cross_reference',
|
|
667
669
|
getAttrs: (node) => {
|
|
670
|
+
var _a;
|
|
668
671
|
const element = node;
|
|
669
672
|
return {
|
|
670
673
|
rid: element.getAttribute('rid'),
|
|
671
|
-
label: element.textContent,
|
|
674
|
+
label: (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
|
|
672
675
|
};
|
|
673
676
|
},
|
|
674
677
|
},
|
|
@@ -212,6 +212,7 @@ export const jatsBodyTransformations = {
|
|
|
212
212
|
body.append(backmatterContainer);
|
|
213
213
|
},
|
|
214
214
|
mapFootnotesToSections(doc, backmatterContainer, createElement) {
|
|
215
|
+
var _a;
|
|
215
216
|
const footnoteGroups = [...doc.querySelectorAll('fn[fn-type]')];
|
|
216
217
|
for (const footnote of footnoteGroups) {
|
|
217
218
|
const type = footnote.getAttribute('fn-type') || '';
|
|
@@ -221,7 +222,10 @@ export const jatsBodyTransformations = {
|
|
|
221
222
|
const title = footnote.querySelector('p[content-type="fn-title"]');
|
|
222
223
|
if (title) {
|
|
223
224
|
const sectionTitleElement = createElement('title');
|
|
224
|
-
|
|
225
|
+
const titleTextContent = (_a = title.textContent) === null || _a === void 0 ? void 0 : _a.trim();
|
|
226
|
+
if (titleTextContent) {
|
|
227
|
+
sectionTitleElement.textContent = titleTextContent;
|
|
228
|
+
}
|
|
225
229
|
removeNodeFromParent(title);
|
|
226
230
|
section.append(sectionTitleElement);
|
|
227
231
|
}
|
|
@@ -18,7 +18,8 @@ import { buildComment, buildContribution, isCommentAnnotation, isHighlightableMo
|
|
|
18
18
|
const DEFAULT_ANNOTATION_COLOR = 'rgb(250, 224, 150)';
|
|
19
19
|
const DEFAULT_PROFILE_ID = 'MPUserProfile:0000000000000000000000000000000000000001';
|
|
20
20
|
export const parseProcessingInstruction = (node) => {
|
|
21
|
-
|
|
21
|
+
var _a;
|
|
22
|
+
const value = `<AuthorQuery ${(_a = node.textContent) === null || _a === void 0 ? void 0 : _a.trim()} />`;
|
|
22
23
|
const processingInstruction = new DOMParser().parseFromString(value, 'application/xml').firstElementChild;
|
|
23
24
|
if (processingInstruction) {
|
|
24
25
|
const queryText = processingInstruction.getAttribute('queryText');
|
|
@@ -14,6 +14,7 @@
|
|
|
14
14
|
* limitations under the License.
|
|
15
15
|
*/
|
|
16
16
|
import debug from 'debug';
|
|
17
|
+
import { getTrimmedTextContent } from '../../lib/utils';
|
|
17
18
|
import { buildAffiliation, buildBibliographicName, buildContributor, buildCorresp, buildFootnote, buildSupplementaryMaterial, } from '../../transformer/builders';
|
|
18
19
|
import { parseJournalMeta } from './jats-journal-meta-parser';
|
|
19
20
|
const warn = debug('manuscripts-transform');
|
|
@@ -68,11 +69,10 @@ export const jatsFrontParser = {
|
|
|
68
69
|
}
|
|
69
70
|
const history = {};
|
|
70
71
|
const dateToTimestamp = (dateElement) => {
|
|
71
|
-
var _a, _b;
|
|
72
72
|
const selectors = ['year', 'month', 'day'];
|
|
73
73
|
const values = [];
|
|
74
74
|
for (const selector of selectors) {
|
|
75
|
-
const value = (
|
|
75
|
+
const value = getTrimmedTextContent(dateElement, selector);
|
|
76
76
|
if (!value || isNaN(+value)) {
|
|
77
77
|
return;
|
|
78
78
|
}
|
|
@@ -112,17 +112,17 @@ export const jatsFrontParser = {
|
|
|
112
112
|
return history;
|
|
113
113
|
},
|
|
114
114
|
parseSupplements(supplementNodes) {
|
|
115
|
-
var _a, _b, _c, _d
|
|
115
|
+
var _a, _b, _c, _d;
|
|
116
116
|
if (!supplementNodes || supplementNodes.length === 0) {
|
|
117
117
|
return [];
|
|
118
118
|
}
|
|
119
119
|
const supplements = [];
|
|
120
120
|
for (const supplementNode of supplementNodes) {
|
|
121
|
-
const supplTitle = (
|
|
122
|
-
const href = (
|
|
121
|
+
const supplTitle = (_a = getTrimmedTextContent(supplementNode, 'caption > title')) !== null && _a !== void 0 ? _a : '';
|
|
122
|
+
const href = (_b = supplementNode.getAttributeNS(XLINK_NAMESPACE, 'href')) !== null && _b !== void 0 ? _b : '';
|
|
123
123
|
const supplementaryMaterial = buildSupplementaryMaterial(supplTitle, href);
|
|
124
|
-
const mimeType = (
|
|
125
|
-
const mimeSubtype = (
|
|
124
|
+
const mimeType = (_c = supplementNode.getAttribute('mimetype')) !== null && _c !== void 0 ? _c : '';
|
|
125
|
+
const mimeSubtype = (_d = supplementNode.getAttribute('mime-subtype')) !== null && _d !== void 0 ? _d : '';
|
|
126
126
|
if (mimeType && mimeSubtype) {
|
|
127
127
|
supplementaryMaterial.MIME = [mimeType, mimeSubtype].join('/');
|
|
128
128
|
}
|
|
@@ -133,10 +133,10 @@ export const jatsFrontParser = {
|
|
|
133
133
|
parseAffiliationNodes(affiliationNodes) {
|
|
134
134
|
const affiliationIDs = new Map();
|
|
135
135
|
const affiliations = affiliationNodes.map((affiliationNode, priority) => {
|
|
136
|
-
var _a, _b
|
|
136
|
+
var _a, _b;
|
|
137
137
|
const affiliation = buildAffiliation('', priority);
|
|
138
138
|
for (const node of affiliationNode.querySelectorAll('institution')) {
|
|
139
|
-
const content = node.textContent;
|
|
139
|
+
const content = (_a = node.textContent) === null || _a === void 0 ? void 0 : _a.trim();
|
|
140
140
|
if (!content) {
|
|
141
141
|
continue;
|
|
142
142
|
}
|
|
@@ -151,22 +151,25 @@ export const jatsFrontParser = {
|
|
|
151
151
|
}
|
|
152
152
|
}
|
|
153
153
|
affiliation.addressLine1 =
|
|
154
|
-
(
|
|
154
|
+
getTrimmedTextContent(affiliationNode, 'addr-line:nth-of-type(1)') ||
|
|
155
|
+
undefined;
|
|
155
156
|
affiliation.addressLine2 =
|
|
156
|
-
(
|
|
157
|
+
getTrimmedTextContent(affiliationNode, 'addr-line:nth-of-type(2)') ||
|
|
158
|
+
undefined;
|
|
157
159
|
affiliation.addressLine3 =
|
|
158
|
-
(
|
|
160
|
+
getTrimmedTextContent(affiliationNode, 'addr-line:nth-of-type(3)') ||
|
|
161
|
+
undefined;
|
|
159
162
|
const emailNode = affiliationNode.querySelector('email');
|
|
160
163
|
if (emailNode) {
|
|
161
164
|
affiliation.email = {
|
|
162
165
|
href: emailNode.getAttributeNS(XLINK_NAMESPACE, 'href') || undefined,
|
|
163
|
-
text: emailNode.textContent || undefined,
|
|
166
|
+
text: ((_b = emailNode.textContent) === null || _b === void 0 ? void 0 : _b.trim()) || undefined,
|
|
164
167
|
};
|
|
165
168
|
}
|
|
166
169
|
affiliation.postCode =
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affiliation.country =
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(
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affiliationIDs.set(id, affiliation._id);
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@@ -196,13 +199,13 @@ export const jatsFrontParser = {
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parseCorrespNodes(correspNodes) {
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const correspondingList = correspNodes.map((correspNode) => {
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label.remove();
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}
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const corresponding = buildCorresp((_b = (_a = correspNode.textContent) === null || _a === void 0 ? void 0 : _a.trim()) !== null && _b !== void 0 ? _b : '');
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corresponding.label = ((_c = label === null || label === void 0 ? void 0 : label.textContent) === null || _c === void 0 ? void 0 : _c.trim()) || undefined;
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correspondingIDs.set(id, corresponding._id);
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@@ -216,13 +219,13 @@ export const jatsFrontParser = {
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},
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parseAuthorNodes(authorNodes, affiliationIDs, footnoteIDs, correspondingIDs) {
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return authorNodes.map((authorNode, priority) => {
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var _a, _b;
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const name = buildBibliographicName({});
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name.given = given;
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}
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const surname = (
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name.family = surname;
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}
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@@ -231,7 +234,7 @@ export const jatsFrontParser = {
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contributor.isCorresponding = corresponding;
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}
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const orcid = (
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contributor.ORCIDIdentifier = orcid;
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}
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@@ -247,7 +250,7 @@ export const jatsFrontParser = {
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if (footnoteId) {
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const authorFootNoteRef = {
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noteID: footnoteId,
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noteLabel: xrefNode.textContent || '',
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noteLabel: ((_a = xrefNode.textContent) === null || _a === void 0 ? void 0 : _a.trim()) || '',
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};
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contributor.footnote.push(authorFootNoteRef);
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}
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@@ -258,7 +261,7 @@ export const jatsFrontParser = {
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if (correspId) {
|
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const authorCorrespRef = {
|
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|
correspID: correspId,
|
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correspLabel: xrefNode.textContent || '',
|
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correspLabel: ((_b = xrefNode.textContent) === null || _b === void 0 ? void 0 : _b.trim()) || '',
|
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|
};
|
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|
contributor.corresp.push(authorCorrespRef);
|
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}
|
|
@@ -13,12 +13,14 @@
|
|
|
13
13
|
* See the License for the specific language governing permissions and
|
|
14
14
|
* limitations under the License.
|
|
15
15
|
*/
|
|
16
|
+
import { getTrimmedTextContent } from '../../lib/utils';
|
|
16
17
|
export const parseJournalIdentifiers = (journalMeta) => {
|
|
18
|
+
var _a, _b;
|
|
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19
|
const output = [];
|
|
18
20
|
const elements = journalMeta.querySelectorAll('journal-id');
|
|
19
21
|
for (const element of elements) {
|
|
20
22
|
const journalIDType = element.getAttribute('journal-id-type');
|
|
21
|
-
const journalID = element.textContent;
|
|
23
|
+
const journalID = (_b = (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim()) !== null && _b !== void 0 ? _b : element.textContent;
|
|
22
24
|
if (journalID !== null && journalIDType != null) {
|
|
23
25
|
output.push({ journalIDType, journalID });
|
|
24
26
|
}
|
|
@@ -29,11 +31,12 @@ export const parseJournalIdentifiers = (journalMeta) => {
|
|
|
29
31
|
return output;
|
|
30
32
|
};
|
|
31
33
|
export const parseJournalAbbreviatedTitles = (journalMeta) => {
|
|
34
|
+
var _a, _b;
|
|
32
35
|
const output = [];
|
|
33
36
|
const elements = journalMeta.querySelectorAll('journal-title-group > abbrev-journal-title');
|
|
34
37
|
for (const element of elements) {
|
|
35
38
|
const abbrevType = element.getAttribute('abbrev-type');
|
|
36
|
-
const abbreviatedTitle = element.textContent;
|
|
39
|
+
const abbreviatedTitle = (_b = (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim()) !== null && _b !== void 0 ? _b : element.textContent;
|
|
37
40
|
if (abbreviatedTitle !== null && abbrevType !== null) {
|
|
38
41
|
output.push({ abbreviatedTitle, abbrevType });
|
|
39
42
|
}
|
|
@@ -44,11 +47,12 @@ export const parseJournalAbbreviatedTitles = (journalMeta) => {
|
|
|
44
47
|
return output;
|
|
45
48
|
};
|
|
46
49
|
export const parseJournalISSNs = (journalMeta) => {
|
|
50
|
+
var _a, _b;
|
|
47
51
|
const output = [];
|
|
48
52
|
const elements = journalMeta.querySelectorAll('issn');
|
|
49
53
|
for (const element of elements) {
|
|
50
54
|
const publicationType = element.getAttribute('pub-type');
|
|
51
|
-
const ISSN = element.textContent;
|
|
55
|
+
const ISSN = (_b = (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim()) !== null && _b !== void 0 ? _b : element.textContent;
|
|
52
56
|
if (publicationType !== null && ISSN !== null) {
|
|
53
57
|
output.push({ publicationType, ISSN });
|
|
54
58
|
}
|
|
@@ -59,12 +63,12 @@ export const parseJournalISSNs = (journalMeta) => {
|
|
|
59
63
|
return output;
|
|
60
64
|
};
|
|
61
65
|
export const parseJournalMeta = (journalMeta) => {
|
|
62
|
-
var _a, _b
|
|
66
|
+
var _a, _b;
|
|
63
67
|
return {
|
|
64
68
|
abbreviatedTitles: parseJournalAbbreviatedTitles(journalMeta),
|
|
65
69
|
journalIdentifiers: parseJournalIdentifiers(journalMeta),
|
|
66
70
|
ISSNs: parseJournalISSNs(journalMeta),
|
|
67
|
-
publisherName: (
|
|
68
|
-
title: (
|
|
71
|
+
publisherName: (_a = getTrimmedTextContent(journalMeta, 'publisher > publisher-name')) !== null && _a !== void 0 ? _a : undefined,
|
|
72
|
+
title: (_b = getTrimmedTextContent(journalMeta, 'journal-title-group > journal-title')) !== null && _b !== void 0 ? _b : undefined,
|
|
69
73
|
};
|
|
70
74
|
};
|
|
@@ -13,6 +13,7 @@
|
|
|
13
13
|
* See the License for the specific language governing permissions and
|
|
14
14
|
* limitations under the License.
|
|
15
15
|
*/
|
|
16
|
+
import { getTrimmedTextContent } from '../../lib/utils';
|
|
16
17
|
import { buildAuxiliaryObjectReference, buildBibliographicDate, buildBibliographicName, buildBibliographyItem, buildCitation, } from '../../transformer/builders';
|
|
17
18
|
import { parseProcessingInstruction } from './jats-comments';
|
|
18
19
|
import { flatten, htmlFromJatsNode } from './jats-parser-utils';
|
|
@@ -31,7 +32,7 @@ export const jatsReferenceParser = {
|
|
|
31
32
|
const referenceIDs = new Map();
|
|
32
33
|
const referenceQueries = new Map();
|
|
33
34
|
const references = referenceNodes.map((referenceNode) => {
|
|
34
|
-
var _a
|
|
35
|
+
var _a;
|
|
35
36
|
const publicationType = referenceNode.getAttribute('publication-type');
|
|
36
37
|
const authorNodes = [
|
|
37
38
|
...referenceNode.querySelectorAll('person-group[person-group-type="author"] > *'),
|
|
@@ -41,7 +42,7 @@ export const jatsReferenceParser = {
|
|
|
41
42
|
});
|
|
42
43
|
const titleNode = referenceNode.querySelector('article-title');
|
|
43
44
|
if (titleNode) {
|
|
44
|
-
bibliographyItem.title = htmlFromJatsNode(titleNode, createElement);
|
|
45
|
+
bibliographyItem.title = (_a = htmlFromJatsNode(titleNode, createElement)) === null || _a === void 0 ? void 0 : _a.trim();
|
|
45
46
|
}
|
|
46
47
|
const queriesText = [];
|
|
47
48
|
const mixedCitation = referenceNode.querySelector('mixed-citation');
|
|
@@ -60,63 +61,63 @@ export const jatsReferenceParser = {
|
|
|
60
61
|
}
|
|
61
62
|
if (authorNodes.length <= 0) {
|
|
62
63
|
mixedCitation === null || mixedCitation === void 0 ? void 0 : mixedCitation.childNodes.forEach((item) => {
|
|
63
|
-
var _a, _b;
|
|
64
|
+
var _a, _b, _c;
|
|
64
65
|
if (item.nodeType === Node.TEXT_NODE &&
|
|
65
66
|
((_a = item.textContent) === null || _a === void 0 ? void 0 : _a.match(/[A-Za-z]+/g))) {
|
|
66
|
-
bibliographyItem.literal = (_b = mixedCitation.textContent) !== null &&
|
|
67
|
+
bibliographyItem.literal = (_c = (_b = mixedCitation.textContent) === null || _b === void 0 ? void 0 : _b.trim()) !== null && _c !== void 0 ? _c : '';
|
|
67
68
|
return bibliographyItem;
|
|
68
69
|
}
|
|
69
70
|
});
|
|
70
71
|
}
|
|
71
|
-
const source = (
|
|
72
|
+
const source = getTrimmedTextContent(referenceNode, 'source');
|
|
72
73
|
if (source) {
|
|
73
74
|
bibliographyItem['container-title'] = source;
|
|
74
75
|
}
|
|
75
|
-
const volume = (
|
|
76
|
+
const volume = getTrimmedTextContent(referenceNode, 'volume');
|
|
76
77
|
if (volume) {
|
|
77
78
|
bibliographyItem.volume = volume;
|
|
78
79
|
}
|
|
79
|
-
const issue = (
|
|
80
|
+
const issue = getTrimmedTextContent(referenceNode, 'issue');
|
|
80
81
|
if (issue) {
|
|
81
82
|
bibliographyItem.issue = issue;
|
|
82
83
|
}
|
|
83
|
-
const supplement = (
|
|
84
|
+
const supplement = getTrimmedTextContent(referenceNode, 'supplement');
|
|
84
85
|
if (supplement) {
|
|
85
86
|
bibliographyItem.supplement = supplement;
|
|
86
87
|
}
|
|
87
|
-
const fpage = (
|
|
88
|
-
const lpage = (
|
|
88
|
+
const fpage = getTrimmedTextContent(referenceNode, 'fpage');
|
|
89
|
+
const lpage = getTrimmedTextContent(referenceNode, 'lpage');
|
|
89
90
|
if (fpage) {
|
|
90
91
|
bibliographyItem.page = lpage ? `${fpage}-${lpage}` : fpage;
|
|
91
92
|
}
|
|
92
|
-
const year = (
|
|
93
|
+
const year = getTrimmedTextContent(referenceNode, 'year');
|
|
93
94
|
if (year) {
|
|
94
95
|
bibliographyItem.issued = buildBibliographicDate({
|
|
95
96
|
'date-parts': [[year]],
|
|
96
97
|
});
|
|
97
98
|
}
|
|
98
|
-
const doi = (
|
|
99
|
+
const doi = getTrimmedTextContent(referenceNode, 'pub-id[pub-id-type="doi"]');
|
|
99
100
|
if (doi) {
|
|
100
101
|
bibliographyItem.DOI = doi;
|
|
101
102
|
}
|
|
102
103
|
const authors = [];
|
|
103
104
|
authorNodes.forEach((authorNode) => {
|
|
104
|
-
var _a
|
|
105
|
+
var _a;
|
|
105
106
|
const name = buildBibliographicName({});
|
|
106
|
-
const given = (
|
|
107
|
+
const given = getTrimmedTextContent(authorNode, 'given-names');
|
|
107
108
|
if (given) {
|
|
108
109
|
name.given = given;
|
|
109
110
|
}
|
|
110
|
-
const family = (
|
|
111
|
+
const family = getTrimmedTextContent(authorNode, 'surname');
|
|
111
112
|
if (family) {
|
|
112
113
|
name.family = family;
|
|
113
114
|
}
|
|
114
|
-
const suffix = (
|
|
115
|
+
const suffix = getTrimmedTextContent(authorNode, 'suffix');
|
|
115
116
|
if (suffix) {
|
|
116
117
|
name.suffix = suffix;
|
|
117
118
|
}
|
|
118
119
|
if (authorNode.nodeName === 'collab') {
|
|
119
|
-
name.literal = authorNode.textContent;
|
|
120
|
+
name.literal = (_a = authorNode.textContent) === null || _a === void 0 ? void 0 : _a.trim();
|
|
120
121
|
}
|
|
121
122
|
authors.push(name);
|
|
122
123
|
});
|
package/dist/es/lib/utils.js
CHANGED
|
@@ -67,3 +67,10 @@ export const findParentNodeClosestToPos = ($pos, predicate) => {
|
|
|
67
67
|
}
|
|
68
68
|
}
|
|
69
69
|
};
|
|
70
|
+
export const getTrimmedTextContent = (node, querySelector) => {
|
|
71
|
+
var _a, _b;
|
|
72
|
+
if (!node) {
|
|
73
|
+
return null;
|
|
74
|
+
}
|
|
75
|
+
return (_b = (_a = node.querySelector(querySelector)) === null || _a === void 0 ? void 0 : _a.textContent) === null || _b === void 0 ? void 0 : _b.trim();
|
|
76
|
+
};
|
|
@@ -62,6 +62,7 @@ export const buildTargets = (fragment, manuscript) => {
|
|
|
62
62
|
}
|
|
63
63
|
});
|
|
64
64
|
fragment.descendants((node) => {
|
|
65
|
+
var _a;
|
|
65
66
|
if (node.type.name in counters) {
|
|
66
67
|
const isInGraphicalAbstract = figures.indexOf(node.attrs.id) > -1;
|
|
67
68
|
if (isInGraphicalAbstract) {
|
|
@@ -72,7 +73,7 @@ export const buildTargets = (fragment, manuscript) => {
|
|
|
72
73
|
type: node.type.name,
|
|
73
74
|
id: node.attrs.id,
|
|
74
75
|
label,
|
|
75
|
-
caption: node.textContent,
|
|
76
|
+
caption: (_a = node.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
|
|
76
77
|
});
|
|
77
78
|
}
|
|
78
79
|
});
|
package/package.json
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@manuscripts/transform",
|
|
3
3
|
"description": "ProseMirror transformer for Manuscripts applications",
|
|
4
|
-
"version": "1.3.
|
|
4
|
+
"version": "1.3.3",
|
|
5
5
|
"repository": "github:Atypon-OpenSource/manuscripts-transform",
|
|
6
6
|
"license": "Apache-2.0",
|
|
7
7
|
"main": "dist/cjs",
|