@manuscripts/transform 2.6.0 → 2.6.1-LEAN-3966.1

package/dist/es/jats/importer/index.js

@@ -1,16 +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.
- */
-export { parseJATSFront, parseJATSBody, parseJATSArticle, } from './parse-jats-article';

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/jats/importer/jats-reference-parser.js

@@ -1,127 +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 { getTrimmedTextContent } from '../../lib/utils';
-import { buildBibliographicDate, buildBibliographicName, buildBibliographyItem, } from '../../transformer/builders';
-import { isJATSComment, parseJATSComment } from './jats-comments';
-import { htmlFromJatsNode } from './jats-parser-utils';
-import { References } from './jats-references';
-const chooseBibliographyItemType = (publicationType) => {
-    switch (publicationType) {
-        case 'book':
-        case 'thesis':
-            return publicationType;
-        case 'journal':
-        default:
-            return 'article-journal';
-    }
-};
-export const jatsReferenceParser = {
-    parseReferences(elements, createElement) {
-        const references = new References();
-        elements.forEach((element) => {
-            var _a;
-            const publicationType = element.getAttribute('publication-type');
-            const authorNodes = [
-                ...element.querySelectorAll('person-group[person-group-type="author"] > *'),
-            ];
-            const bibliographyItem = buildBibliographyItem({
-                type: chooseBibliographyItemType(publicationType),
-            });
-            const titleNode = element.querySelector('article-title');
-            if (titleNode) {
-                bibliographyItem.title = (_a = htmlFromJatsNode(titleNode, createElement)) === null || _a === void 0 ? void 0 : _a.trim();
-            }
-            const comments = [];
-            const mixedCitation = element.querySelector('mixed-citation');
-            mixedCitation === null || mixedCitation === void 0 ? void 0 : mixedCitation.childNodes.forEach((item) => {
-                if (isJATSComment(item)) {
-                    const comment = parseJATSComment(item);
-                    if (comment) {
-                        comments.push(comment);
-                    }
-                }
-            });
-            if (authorNodes.length <= 0) {
-                mixedCitation === null || mixedCitation === void 0 ? void 0 : mixedCitation.childNodes.forEach((item) => {
-                    var _a, _b, _c;
-                    if (item.nodeType === Node.TEXT_NODE &&
-                        ((_a = item.textContent) === null || _a === void 0 ? void 0 : _a.match(/[A-Za-z]+/g))) {
-                        bibliographyItem.literal = (_c = (_b = mixedCitation.textContent) === null || _b === void 0 ? void 0 : _b.trim()) !== null && _c !== void 0 ? _c : '';
-                        return bibliographyItem;
-                    }
-                });
-            }
-            const source = getTrimmedTextContent(element, 'source');
-            if (source) {
-                bibliographyItem['container-title'] = source;
-            }
-            const volume = getTrimmedTextContent(element, 'volume');
-            if (volume) {
-                bibliographyItem.volume = volume;
-            }
-            const issue = getTrimmedTextContent(element, 'issue');
-            if (issue) {
-                bibliographyItem.issue = issue;
-            }
-            const supplement = getTrimmedTextContent(element, 'supplement');
-            if (supplement) {
-                bibliographyItem.supplement = supplement;
-            }
-            const fpage = getTrimmedTextContent(element, 'fpage');
-            const lpage = getTrimmedTextContent(element, 'lpage');
-            if (fpage) {
-                bibliographyItem.page = lpage ? `${fpage}-${lpage}` : fpage;
-            }
-            const year = getTrimmedTextContent(element, 'year');
-            if (year) {
-                bibliographyItem.issued = buildBibliographicDate({
-                    'date-parts': [[year]],
-                });
-            }
-            const doi = getTrimmedTextContent(element, 'pub-id[pub-id-type="doi"]');
-            if (doi) {
-                bibliographyItem.DOI = doi;
-            }
-            const authors = [];
-            authorNodes.forEach((authorNode) => {
-                var _a;
-                const name = buildBibliographicName({});
-                const given = getTrimmedTextContent(authorNode, 'given-names');
-                if (given) {
-                    name.given = given;
-                }
-                const family = getTrimmedTextContent(authorNode, 'surname');
-                if (family) {
-                    name.family = family;
-                }
-                const suffix = getTrimmedTextContent(authorNode, 'suffix');
-                if (suffix) {
-                    name.suffix = suffix;
-                }
-                if (authorNode.nodeName === 'collab') {
-                    name.literal = (_a = authorNode.textContent) === null || _a === void 0 ? void 0 : _a.trim();
-                }
-                authors.push(name);
-            });
-            if (authors.length) {
-                bibliographyItem.author = authors;
-            }
-            const id = element.getAttribute('id');
-            references.add(bibliographyItem, id, comments);
-        });
-        return references;
-    },
-};

package/dist/es/jats/importer/jats-references.js

@@ -1,30 +0,0 @@
-export class References {
-    constructor() {
-        this.items = new Map();
-        this.IDs = new Map();
-        this.comments = new Map();
-    }
-    add(item, id, comments) {
-        this.items.set(item._id, item);
-        this.comments.set(item._id, comments);
-        if (id) {
-            this.IDs.set(id, item._id);
-        }
-    }
-    getBibliographyItems() {
-        return [...this.items.values()];
-    }
-    getComments(id) {
-        return this.getValue(id, this.comments) || [];
-    }
-    getValue(id, map) {
-        const value = map.get(id);
-        if (value) {
-            return value;
-        }
-        const id2 = this.IDs.get(id);
-        if (id2) {
-            return map.get(id2);
-        }
-    }
-}

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();
-};