@manuscripts/transform 2.3.36 → 2.3.37-LEAN-3911.0

package/dist/es/jats/importer/jats-front-parser.js

@@ -1,315 +0,0 @@
-/*!
- * © 2020 Atypon Systems LLC
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-import debug from 'debug';
-import { getTrimmedTextContent } from '../../lib/utils';
-import { buildAffiliation, buildAuthorNotes, buildBibliographicName, buildContributor, buildCorresp, buildFootnote, buildJournal, buildParagraph, buildTitles, } from '../../transformer';
-import { parseJournalMeta } from './jats-journal-meta-parser';
-import { htmlFromJatsNode } from './jats-parser-utils';
-const warn = debug('manuscripts-transform');
-const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
-const defaultTitle = 'Untitled Manuscript';
-export const jatsFrontParser = {
-    parseTitles(element, createElement) {
-        var _a;
-        if (!element) {
-            return buildTitles(defaultTitle);
-        }
-        const title = element.querySelector('article-title');
-        const subtitle = element.querySelector('subtitle');
-        const runningTitle = element.querySelector('alt-title[alt-title-type="right-running"]');
-        const titles = buildTitles((_a = htmlFromJatsNode(title, createElement)) !== null && _a !== void 0 ? _a : defaultTitle);
-        if (subtitle) {
-            titles.subtitle = htmlFromJatsNode(subtitle, createElement);
-        }
-        if (runningTitle) {
-            titles.runningTitle = htmlFromJatsNode(runningTitle, createElement);
-        }
-        return titles;
-    },
-    parseDOI(front) {
-        var _a;
-        const doi = front === null || front === void 0 ? void 0 : front.querySelector('article-meta > article-id[pub-id-type="doi"]');
-        return (_a = doi === null || doi === void 0 ? void 0 : doi.textContent) !== null && _a !== void 0 ? _a : undefined;
-    },
-    parseCounts(counts) {
-        var _a, _b, _c, _d, _e;
-        if (counts) {
-            const parseCount = (count) => {
-                if (count && /^-?\d+$/.test(count)) {
-                    return parseInt(count);
-                }
-                else if (count) {
-                    warn(`Invalid count number for ${count}`);
-                }
-            };
-            const genericCounts = [];
-            const countElements = counts.querySelectorAll('count');
-            for (const element of countElements.values()) {
-                const countType = element.getAttribute('count-type');
-                const count = parseCount(element.getAttribute('count'));
-                if (countType) {
-                    const genericCount = { count, countType };
-                    genericCounts.push(genericCount);
-                }
-            }
-            return {
-                wordCount: parseCount((_a = counts.querySelector('word-count')) === null || _a === void 0 ? void 0 : _a.getAttribute('count')),
-                figureCount: parseCount((_b = counts.querySelector('fig-count')) === null || _b === void 0 ? void 0 : _b.getAttribute('count')),
-                tableCount: parseCount((_c = counts.querySelector('table-count')) === null || _c === void 0 ? void 0 : _c.getAttribute('count')),
-                equationCount: parseCount((_d = counts.querySelector('equation-count')) === null || _d === void 0 ? void 0 : _d.getAttribute('count')),
-                referencesCount: parseCount((_e = counts.querySelector('ref-count')) === null || _e === void 0 ? void 0 : _e.getAttribute('count')),
-                genericCounts: genericCounts.length > 0 ? genericCounts : undefined,
-            };
-        }
-    },
-    parseJournal(element) {
-        const meta = parseJournalMeta(element);
-        return Object.assign(Object.assign({}, meta), buildJournal());
-    },
-    parseDates(historyNode) {
-        if (!historyNode) {
-            return undefined;
-        }
-        const history = {};
-        const dateToTimestamp = (dateElement) => {
-            const selectors = ['year', 'month', 'day'];
-            const values = [];
-            for (const selector of selectors) {
-                const value = getTrimmedTextContent(dateElement, selector);
-                if (!value || isNaN(+value)) {
-                    return;
-                }
-                values.push(+value);
-            }
-            return Date.UTC(values[0], values[1], values[2]) / 1000;
-        };
-        for (const date of historyNode.children) {
-            const dateType = date.getAttribute('date-type');
-            switch (dateType) {
-                case 'received': {
-                    history.receiveDate = dateToTimestamp(date);
-                    break;
-                }
-                case 'rev-recd': {
-                    history.revisionReceiveDate = dateToTimestamp(date);
-                    break;
-                }
-                case 'accepted': {
-                    history.acceptanceDate = dateToTimestamp(date);
-                    break;
-                }
-                case 'rev-request': {
-                    history.revisionRequestDate = dateToTimestamp(date);
-                    break;
-                }
-                case 'retracted': {
-                    history.retractionDate = dateToTimestamp(date);
-                    break;
-                }
-                case 'corrected': {
-                    history.correctionDate = dateToTimestamp(date);
-                    break;
-                }
-            }
-        }
-        return history;
-    },
-    parseAffiliations(elements) {
-        const affiliationIDs = new Map();
-        const affiliations = elements.map((element, priority) => {
-            var _a, _b;
-            const affiliation = buildAffiliation('', priority);
-            for (const node of element.querySelectorAll('institution')) {
-                const content = (_a = node.textContent) === null || _a === void 0 ? void 0 : _a.trim();
-                if (!content) {
-                    continue;
-                }
-                const type = node.getAttribute('content-type');
-                if (type === 'dept') {
-                    affiliation.department = content;
-                }
-                else {
-                    affiliation.institution = content;
-                }
-            }
-            affiliation.addressLine1 =
-                getTrimmedTextContent(element, 'addr-line:nth-of-type(1)') || undefined;
-            affiliation.addressLine2 =
-                getTrimmedTextContent(element, 'addr-line:nth-of-type(2)') || undefined;
-            affiliation.addressLine3 =
-                getTrimmedTextContent(element, 'addr-line:nth-of-type(3)') || undefined;
-            affiliation.postCode =
-                getTrimmedTextContent(element, 'postal-code') || undefined;
-            affiliation.country =
-                getTrimmedTextContent(element, 'country') || undefined;
-            const email = element.querySelector('email');
-            if (email) {
-                affiliation.email = {
-                    href: email.getAttributeNS(XLINK_NAMESPACE, 'href') || undefined,
-                    text: ((_b = email.textContent) === null || _b === void 0 ? void 0 : _b.trim()) || undefined,
-                };
-            }
-            const id = element.getAttribute('id');
-            if (id) {
-                affiliationIDs.set(id, affiliation._id);
-            }
-            return affiliation;
-        });
-        return {
-            affiliations,
-            affiliationIDs,
-        };
-    },
-    parseAuthorNotes(element) {
-        if (!element) {
-            return {
-                footnotes: [],
-                footnoteIDs: new Map(),
-                authorNotes: [],
-                authorNotesParagraphs: [],
-                correspondingIDs: new Map(),
-                correspondingList: [],
-            };
-        }
-        const { footnotes, footnoteIDs } = this.parseFootnotes([
-            ...element.querySelectorAll('fn:not([fn-type])'),
-        ]);
-        const authorNotesParagraphs = this.parseParagraphs([
-            ...element.querySelectorAll(':scope > p'),
-        ]);
-        const { correspondingList, correspondingIDs } = this.parseCorresp([
-            ...element.querySelectorAll('corresp'),
-        ]);
-        const authorNotes = [
-            buildAuthorNotes([
-                ...correspondingIDs.values(),
-                ...footnoteIDs.values(),
-                ...authorNotesParagraphs.map((p) => p._id),
-            ]),
-        ];
-        return {
-            footnotes,
-            footnoteIDs,
-            authorNotesParagraphs,
-            authorNotes,
-            correspondingIDs,
-            correspondingList,
-        };
-    },
-    parseParagraphs(elements) {
-        return elements.map((p) => buildParagraph(p.innerHTML));
-    },
-    parseFootnotes(elements) {
-        const footnoteIDs = new Map();
-        const footnotes = elements.map((element) => {
-            const fn = buildFootnote('', element.innerHTML);
-            const id = element.getAttribute('id');
-            if (id) {
-                footnoteIDs.set(id, fn._id);
-            }
-            return fn;
-        });
-        return {
-            footnotes,
-            footnoteIDs,
-        };
-    },
-    parseCorresp(elements) {
-        const correspondingIDs = new Map();
-        const correspondingList = elements.map((element) => {
-            var _a, _b, _c;
-            const label = element.querySelector('label');
-            if (label) {
-                label.remove();
-            }
-            const corresponding = buildCorresp((_b = (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim()) !== null && _b !== void 0 ? _b : '');
-            corresponding.label = ((_c = label === null || label === void 0 ? void 0 : label.textContent) === null || _c === void 0 ? void 0 : _c.trim()) || undefined;
-            const id = element.getAttribute('id');
-            if (id) {
-                correspondingIDs.set(id, corresponding._id);
-            }
-            return corresponding;
-        });
-        return {
-            correspondingList,
-            correspondingIDs,
-        };
-    },
-    parseContributors(elements, affiliationIDs, footnoteIDs, correspondingIDs) {
-        return elements.map((element, priority) => {
-            var _a, _b;
-            const name = buildBibliographicName({});
-            const given = getTrimmedTextContent(element, 'name > given-names');
-            if (given) {
-                name.given = given;
-            }
-            const surname = getTrimmedTextContent(element, 'name > surname');
-            if (surname) {
-                name.family = surname;
-            }
-            const contributor = buildContributor(name, 'author', priority);
-            const corresponding = element.getAttribute('corresp') === 'yes';
-            if (corresponding) {
-                contributor.isCorresponding = corresponding;
-            }
-            const orcid = getTrimmedTextContent(element, 'contrib-id[contrib-id-type="orcid"]');
-            if (orcid) {
-                contributor.ORCIDIdentifier = orcid;
-            }
-            const xrefs = element.querySelectorAll('xref');
-            for (const xref of xrefs) {
-                if (xref) {
-                    const rid = xref.getAttribute('rid');
-                    const type = xref.getAttribute('ref-type');
-                    if (rid) {
-                        if (type === 'fn') {
-                            contributor.footnote = [];
-                            const footnoteID = footnoteIDs.get(rid);
-                            if (footnoteID) {
-                                const authorFootNoteRef = {
-                                    noteID: footnoteID,
-                                    noteLabel: ((_a = xref.textContent) === null || _a === void 0 ? void 0 : _a.trim()) || '',
-                                };
-                                contributor.footnote.push(authorFootNoteRef);
-                            }
-                        }
-                        else if (type === 'corresp') {
-                            contributor.corresp = [];
-                            const correspID = correspondingIDs.get(rid);
-                            if (correspID) {
-                                const authorCorrespRef = {
-                                    correspID: correspID,
-                                    correspLabel: ((_b = xref.textContent) === null || _b === void 0 ? void 0 : _b.trim()) || '',
-                                };
-                                contributor.corresp.push(authorCorrespRef);
-                            }
-                        }
-                        else if (type === 'aff') {
-                            const rids = rid
-                                .split(/\s+/)
-                                .map((id) => affiliationIDs.get(id))
-                                .filter(Boolean);
-                            if (rids.length) {
-                                contributor.affiliations = rids;
-                            }
-                        }
-                    }
-                }
-            }
-            return contributor;
-        });
-    },
-};

package/dist/es/transformer/__tests__/__helpers__/doc.js

@@ -1,29 +0,0 @@
-/*!
- * © 2019 Atypon Systems LLC
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-import projectDump from '../../../__tests__/data/project-dump.json';
-import { Decoder } from '../../decode';
-export const createTestModelMap = () => {
-    const modelMap = new Map();
-    for (const component of projectDump.data) {
-        modelMap.set(component._id, component);
-    }
-    return modelMap;
-};
-export const createTestDoc = () => {
-    const modelMap = createTestModelMap();
-    const decoder = new Decoder(modelMap);
-    return decoder.createArticleNode();
-};

package/dist/es/transformer/builders.js

@@ -1,186 +0,0 @@
-/*!
- * © 2019 Atypon Systems LLC
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-import { ObjectTypes, } from '@manuscripts/json-schema';
-import serializeToXML from 'w3c-xmlserializer';
-import { schema } from '../schema';
-import { generateID } from './id';
-import { timestamp } from './timestamp';
-export const buildProject = (owner) => ({
-    _id: generateID(ObjectTypes.Project),
-    objectType: ObjectTypes.Project,
-    owners: [owner],
-    writers: [],
-    viewers: [],
-    title: '',
-});
-export const buildManuscript = () => ({
-    _id: generateID(ObjectTypes.Manuscript),
-    objectType: ObjectTypes.Manuscript,
-});
-export const buildContributor = (bibliographicName, role = 'author', priority = 0, userID, invitationID) => ({
-    _id: generateID(ObjectTypes.Contributor),
-    objectType: ObjectTypes.Contributor,
-    priority,
-    role,
-    affiliations: [],
-    bibliographicName: buildBibliographicName(bibliographicName),
-    userID,
-    invitationID,
-});
-export const buildBibliographyItem = (data) => (Object.assign(Object.assign({}, data), { type: data.type || 'article-journal', _id: generateID(ObjectTypes.BibliographyItem), objectType: ObjectTypes.BibliographyItem }));
-export const buildBibliographicName = (data) => (Object.assign(Object.assign({}, data), { _id: generateID(ObjectTypes.BibliographicName), objectType: ObjectTypes.BibliographicName }));
-export const buildBibliographicDate = (data) => (Object.assign(Object.assign({}, data), { _id: generateID(ObjectTypes.BibliographicDate), objectType: ObjectTypes.BibliographicDate }));
-export const buildBibliographyElement = (bibliographyItems) => ({
-    _id: generateID(ObjectTypes.BibliographyElement),
-    objectType: ObjectTypes.BibliographyElement,
-    contents: '',
-    elementType: 'div',
-    containedObjectIDs: bibliographyItems.map((b) => b._id),
-});
-export const buildKeyword = (name) => ({
-    _id: generateID(ObjectTypes.Keyword),
-    objectType: ObjectTypes.Keyword,
-    name,
-});
-export const buildKeywordGroup = (attributes) => (Object.assign(Object.assign(Object.assign({ _id: generateID(ObjectTypes.KeywordGroup), objectType: ObjectTypes.KeywordGroup }, (attributes.type && { type: attributes.type })), (attributes.title && { title: attributes.title })), (attributes.label && { label: attributes.label })));
-export const buildFigure = (blob) => ({
-    _id: generateID(ObjectTypes.Figure),
-    objectType: ObjectTypes.Figure,
-    contentType: blob.type,
-    src: window.URL.createObjectURL(blob),
-    attachment: {
-        id: 'image',
-        type: blob.type,
-        data: blob,
-    },
-});
-export const buildAffiliation = (institution, priority = 0) => ({
-    _id: generateID(ObjectTypes.Affiliation),
-    objectType: ObjectTypes.Affiliation,
-    institution,
-    priority,
-});
-export const buildSupplementaryMaterial = (title, href) => ({
-    _id: generateID(ObjectTypes.Supplement),
-    objectType: ObjectTypes.Supplement,
-    title,
-    href,
-});
-export const buildComment = (target, contents = '', selector, contributions, annotationColor) => ({
-    _id: generateID(ObjectTypes.CommentAnnotation),
-    objectType: ObjectTypes.CommentAnnotation,
-    target,
-    selector,
-    contents,
-    contributions,
-    annotationColor,
-});
-export const buildNote = (target, source, contents = '') => ({
-    _id: generateID(ObjectTypes.ManuscriptNote),
-    objectType: ObjectTypes.ManuscriptNote,
-    target,
-    source,
-    contents,
-});
-export const buildFootnote = (containingObject, contents, kind = 'footnote') => ({
-    _id: generateID(ObjectTypes.Footnote),
-    objectType: ObjectTypes.Footnote,
-    containingObject: containingObject || undefined,
-    contents,
-    kind,
-});
-export const buildAuthorNotes = (containedObjectIDs) => ({
-    _id: generateID(ObjectTypes.AuthorNotes),
-    objectType: ObjectTypes.AuthorNotes,
-    containedObjectIDs: containedObjectIDs,
-});
-export const buildFootnotesOrder = (footnotesList, containedObjectID) => ({
-    _id: generateID(ObjectTypes.FootnotesOrder),
-    objectType: ObjectTypes.FootnotesOrder,
-    footnotesList,
-    containedObjectID,
-});
-export const buildCorresp = (contents) => ({
-    _id: generateID(ObjectTypes.Corresponding),
-    objectType: ObjectTypes.Corresponding,
-    contents,
-});
-export const buildSection = (priority = 0, path = []) => {
-    const id = generateID(ObjectTypes.Section);
-    return {
-        _id: id,
-        objectType: ObjectTypes.Section,
-        priority,
-        path: path.concat(id),
-    };
-};
-export const buildParagraph = (innerHTML = '') => {
-    const _id = generateID(ObjectTypes.ParagraphElement);
-    const element = document.createElementNS(null, 'p');
-    element.setAttribute('id', _id);
-    if (innerHTML) {
-        element.innerHTML = innerHTML;
-    }
-    const contents = serializeToXML(element);
-    return {
-        _id,
-        objectType: ObjectTypes.ParagraphElement,
-        elementType: 'p',
-        contents,
-    };
-};
-export const buildColor = (value, priority) => ({
-    _id: generateID(ObjectTypes.Color),
-    objectType: ObjectTypes.Color,
-    priority,
-    value,
-});
-export const buildContribution = (profileID) => ({
-    _id: generateID(ObjectTypes.Contribution),
-    objectType: ObjectTypes.Contribution,
-    profileID,
-    timestamp: timestamp(),
-});
-export const buildContributorRole = (name) => ({
-    _id: generateID(ObjectTypes.ContributorRole),
-    objectType: ObjectTypes.ContributorRole,
-    name,
-});
-export const buildAttribution = () => ({
-    _id: generateID(ObjectTypes.Attribution),
-    objectType: ObjectTypes.Attribution,
-});
-export const buildJournal = () => ({
-    _id: generateID(ObjectTypes.Journal),
-    objectType: ObjectTypes.Journal,
-});
-export const auxiliaryObjectTypes = new Set([
-    schema.nodes.figure_element,
-    schema.nodes.table_element,
-    schema.nodes.equation_element,
-    schema.nodes.listing_element,
-]);
-export const buildElementsOrder = (elementType) => ({
-    _id: generateID(ObjectTypes.ElementsOrder),
-    objectType: ObjectTypes.ElementsOrder,
-    elementType: elementType,
-    elements: [],
-});
-export const buildTitles = (title) => ({
-    _id: generateID(ObjectTypes.Titles),
-    objectType: ObjectTypes.Titles,
-    title: title || '',
-});