@manuscripts/transform 2.3.32 → 2.3.34-LEAN-3911.2

package/dist/cjs/jats/importer/jats-front-transformations.js

@@ -0,0 +1,262 @@
+"use strict";
+/*!
+ * © 2024 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.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.jatsFrontTransformations = exports.defaultTitle = void 0;
+const json_schema_1 = require("@manuscripts/json-schema");
+const utils_1 = require("../../lib/utils");
+const transformer_1 = require("../../transformer");
+const jats_parser_utils_1 = require("./jats-parser-utils");
+exports.defaultTitle = 'Untitled Manuscript';
+exports.jatsFrontTransformations = {
+    setArticleAttrs(doc, template) {
+        var _a;
+        const doi = (_a = doc.querySelector('article-meta > article-id[pub-id-type="doi"]')) === null || _a === void 0 ? void 0 : _a.textContent;
+        const Attrs = {
+            DOI: doi !== null && doi !== void 0 ? doi : '',
+            prototype: template !== null && template !== void 0 ? template : '',
+            id: (0, transformer_1.generateID)(json_schema_1.ObjectTypes.Manuscript),
+        };
+        Object.entries(Attrs).forEach(([key, value]) => {
+            var _a;
+            if (value) {
+                (_a = doc.querySelector('article')) === null || _a === void 0 ? void 0 : _a.setAttribute(key, value);
+            }
+        });
+    },
+    createTitle(front, createElement) {
+        var _a;
+        let title = front.querySelector('article-meta > title-group > article-title');
+        if (title) {
+            title.innerHTML = (_a = (0, jats_parser_utils_1.htmlFromJatsNode)(title, createElement)) !== null && _a !== void 0 ? _a : exports.defaultTitle;
+        }
+        else {
+            title = createElement('article-title');
+            title.textContent = exports.defaultTitle;
+        }
+        return title;
+    },
+    createAuthorNotes(document, createElement) {
+        const authornotes = document.querySelector('article-meta > author-notes');
+        if (!authornotes) {
+            return;
+        }
+        const authorNotesEl = createElement('author-notes');
+        authornotes
+            .querySelectorAll('fn:not([fn-type]), :scope > p, corresp')
+            .forEach((node) => {
+            switch (node.nodeName) {
+                case 'fn': {
+                    this.appendFootnote(node, authorNotesEl, createElement);
+                    break;
+                }
+                case 'p': {
+                    this.appendParagraph(document, node, authorNotesEl);
+                    break;
+                }
+                case 'corresp': {
+                    this.appendCorresp(node, authorNotesEl, createElement);
+                    break;
+                }
+            }
+        });
+        return authorNotesEl;
+    },
+    appendFootnote(node, element, createElement) {
+        const fnEl = createElement('fn-author');
+        fnEl.innerHTML = node.innerHTML;
+        fnEl.setAttribute('kind', 'footnote');
+        const id = node.getAttribute('id');
+        if (id) {
+            fnEl.setAttribute('id', id);
+        }
+        element.append(fnEl);
+    },
+    appendParagraph(document, node, element) {
+        const pEl = document.createElementNS(null, 'p');
+        pEl.innerHTML = node.innerHTML;
+        element.append(pEl);
+    },
+    appendCorresp(node, element, createElement) {
+        var _a, _b;
+        const correspEl = createElement('corresp');
+        const label = node.querySelector('label');
+        if (label) {
+            label.remove();
+        }
+        correspEl.textContent = ((_a = node.textContent) === null || _a === void 0 ? void 0 : _a.trim()) || '';
+        correspEl.setAttribute('label', ((_b = label === null || label === void 0 ? void 0 : label.textContent) === null || _b === void 0 ? void 0 : _b.trim()) || '');
+        const id = node.getAttribute('id');
+        if (id) {
+            correspEl.setAttribute('id', id);
+        }
+        element.append(correspEl);
+    },
+    createContributors(front, createElement) {
+        const contribs = front.querySelectorAll('article-meta > contrib-group > contrib[contrib-type="author"]');
+        const contributors = createElement('contributors');
+        contribs.forEach((element, priority) => {
+            const contributor = this.createContributorElement(priority, createElement);
+            this.setNameAttrs(element, contributor);
+            this.setOrcidAttribute(element, contributor);
+            this.setIsCorrespondingAttribute(element, contributor);
+            this.setContributorReferences(element, contributor, createElement);
+            contributors.append(contributor);
+        });
+        return contributors;
+    },
+    createContributorElement(priority, createElement) {
+        const contributor = createElement('contributor');
+        contributor.setAttribute('priority', priority.toString());
+        contributor.setAttribute('role', 'author');
+        return contributor;
+    },
+    setNameAttrs(node, element) {
+        const given = (0, utils_1.getTrimmedTextContent)(node, 'name > given-names');
+        if (given) {
+            element.setAttribute('given', given);
+        }
+        const surname = (0, utils_1.getTrimmedTextContent)(node, 'name > surname');
+        if (surname) {
+            element.setAttribute('family', surname);
+        }
+    },
+    setOrcidAttribute(node, element) {
+        const orcid = (0, utils_1.getTrimmedTextContent)(node, 'contrib-id[contrib-id-type="orcid"]');
+        if (orcid) {
+            element.setAttribute('ORCIDIdentifier', orcid);
+        }
+    },
+    setIsCorrespondingAttribute(node, element) {
+        const isCorresponding = node.getAttribute('corresp') === 'yes';
+        if (isCorresponding) {
+            element.setAttribute('isCorresponding', isCorresponding.toString());
+        }
+    },
+    setContributorReferences(node, element, createElement) {
+        const xrefs = node.querySelectorAll('xref');
+        const footnotes = createElement('fns');
+        const corresps = createElement('corresps');
+        const affs = createElement('affs');
+        xrefs.forEach((xref) => {
+            const rid = xref.getAttribute('rid');
+            const type = xref.getAttribute('ref-type');
+            if (rid) {
+                switch (type) {
+                    case 'fn':
+                        this.appendFootnoteID(xref, footnotes, rid, createElement);
+                        break;
+                    case 'corresp':
+                        this.appendCorrespID(xref, corresps, rid, createElement);
+                        break;
+                    case 'aff':
+                        this.appendAffiliationID(affs, rid, createElement);
+                        break;
+                }
+            }
+        });
+        element.append(footnotes, corresps, affs);
+    },
+    appendFootnoteID(xref, footnotes, rid, createElement) {
+        var _a;
+        const fn = createElement('fn');
+        fn.setAttribute('noteID', rid);
+        fn.setAttribute('noteLabel', ((_a = xref.textContent) === null || _a === void 0 ? void 0 : _a.trim()) || '');
+        footnotes.append(fn);
+    },
+    appendCorrespID(xref, corresps, rid, createElement) {
+        var _a;
+        const corresp = createElement('corresp');
+        corresp.setAttribute('correspID', rid);
+        corresp.setAttribute('correspLabel', ((_a = xref.textContent) === null || _a === void 0 ? void 0 : _a.trim()) || '');
+        corresps.append(corresp);
+    },
+    appendAffiliationID(affs, rid, createElement) {
+        const rids = rid.split(/\s+/).filter(Boolean);
+        if (rids.length) {
+            rids.forEach((affID) => {
+                const aff = createElement('aff');
+                aff.setAttribute('affiliationID', affID);
+                affs.append(aff);
+            });
+        }
+    },
+    createAffiliations(front, createElement) {
+        const affiliations = front.querySelectorAll('article-meta > contrib-group > aff');
+        const affiliationGroup = createElement('affiliations');
+        affiliations.forEach((element, priority) => {
+            const affiliation = this.createAffiliationElement(element, priority, createElement);
+            this.setInstitutionAttrs(element, affiliation);
+            this.setAddressAttrs(element, affiliation);
+            this.appendEmail(element, affiliation);
+            affiliationGroup.append(affiliation);
+        });
+        return affiliationGroup;
+    },
+    createAffiliationElement(element, priority, createElement) {
+        const affiliation = createElement('affiliation');
+        affiliation.setAttribute('priority', priority.toString());
+        const id = element.getAttribute('id');
+        if (id) {
+            affiliation.setAttribute('id', id);
+        }
+        return affiliation;
+    },
+    appendEmail(element, affiliation) {
+        const emailEl = element.querySelector('email');
+        if (emailEl) {
+            affiliation.appendChild(emailEl);
+        }
+    },
+    setInstitutionAttrs(element, affiliation) {
+        var _a;
+        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.setAttribute('department', content);
+            }
+            else {
+                affiliation.setAttribute('institution', content);
+            }
+        }
+    },
+    setAddressAttrs(element, affiliation) {
+        const addressLine1 = (0, utils_1.getTrimmedTextContent)(element, 'addr-line:nth-of-type(1)');
+        const addressLine2 = (0, utils_1.getTrimmedTextContent)(element, 'addr-line:nth-of-type(2)');
+        const addressLine3 = (0, utils_1.getTrimmedTextContent)(element, 'addr-line:nth-of-type(3)');
+        const postCode = (0, utils_1.getTrimmedTextContent)(element, 'postal-code');
+        const country = (0, utils_1.getTrimmedTextContent)(element, 'country');
+        if (addressLine1) {
+            affiliation.setAttribute('addressLine1', addressLine1);
+        }
+        if (addressLine2) {
+            affiliation.setAttribute('addressLine2', addressLine2);
+        }
+        if (addressLine3) {
+            affiliation.setAttribute('addressLine3', addressLine3);
+        }
+        if (postCode) {
+            affiliation.setAttribute('postCode', postCode);
+        }
+        if (country) {
+            affiliation.setAttribute('country', country);
+        }
+    },
+};

package/dist/cjs/jats/importer/jats-journal-meta-parser.js

@@ -15,8 +15,10 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseJournalMeta = exports.parseJournalISSNs = exports.parseJournalAbbreviatedTitles = exports.parseJournalIdentifiers = void 0;
+exports.parseJournal = exports.parseJournalMeta = exports.parseJournalISSNs = exports.parseJournalAbbreviatedTitles = exports.parseJournalIdentifiers = void 0;
+const json_schema_1 = require("@manuscripts/json-schema");
 const utils_1 = require("../../lib/utils");
+const transformer_1 = require("../../transformer");
 const parseJournalIdentifiers = (element) => {
     var _a;
     if (!element) {
@@ -91,3 +93,8 @@ const parseJournalMeta = (element) => {
     };
 };
 exports.parseJournalMeta = parseJournalMeta;
+const parseJournal = (element) => {
+    const meta = (0, exports.parseJournalMeta)(element);
+    return Object.assign(Object.assign({}, meta), { _id: (0, transformer_1.generateID)(json_schema_1.ObjectTypes.Journal), objectType: json_schema_1.ObjectTypes.Journal });
+};
+exports.parseJournal = parseJournal;

package/dist/cjs/jats/importer/jats-parser-utils.js

@@ -21,21 +21,35 @@ const schema_1 = require("../../schema");
 const transformer_1 = require("../../transformer");
 const updateDocumentIDs = (node, replacements) => {
     const warnings = [];
-    recurseDoc(node, (n) => updateNodeID(n, replacements, warnings));
+    const highlightNodes = [];
+    recurseDoc(node, (n, parent) => updateNodeID(n, parent, replacements, warnings, highlightNodes));
     recurseDoc(node, (n) => updateNodeRID(n, replacements, warnings));
     recurseDoc(node, (n) => updateNodeRIDS(n, replacements, warnings));
+    recurseDoc(node, (n) => updateContributorNodesIDS(n, replacements, warnings));
     return warnings;
 };
 exports.updateDocumentIDs = updateDocumentIDs;
-function recurseDoc(node, fn) {
-    fn(node);
-    node.descendants((n) => fn(n));
+function recurseDoc(node, fn, parent = null) {
+    fn(node, parent);
+    node.descendants((n, pos, parent) => fn(n, parent));
 }
-const updateNodeID = (node, replacements, warnings) => {
+const updateNodeID = (node, parent, replacements, warnings, highlightNodes) => {
     if (node.type === schema_1.schema.nodes.inline_equation) {
         node.attrs = Object.assign(Object.assign({}, node.attrs), { id: `InlineMathFragment:${(0, uuid_1.v4)()}` });
         return;
     }
+    if (node.type === schema_1.schema.nodes.highlight_marker) {
+        node.attrs = Object.assign(Object.assign({}, node.attrs), { tid: parent === null || parent === void 0 ? void 0 : parent.attrs.id });
+        highlightNodes.push(node);
+        return;
+    }
+    if (node.type === schema_1.schema.nodes.comment) {
+        const highlightNode = highlightNodes.find((n) => n.attrs.id === node.attrs.id);
+        if (highlightNode) {
+            node.attrs = Object.assign(Object.assign({}, node.attrs), { target: highlightNode.attrs.tid });
+        }
+        return;
+    }
     if (node.type === schema_1.schema.nodes.general_table_footnote) {
         node.attrs = Object.assign(Object.assign({}, node.attrs), { id: `GeneralTableFootnote:${(0, uuid_1.v4)()}` });
         return;
@@ -78,6 +92,26 @@ const updateNodeRIDS = (node, replacements, warnings) => {
     }
     node.attrs = Object.assign(Object.assign({}, node.attrs), { rids: previousRIDs.map((r) => replacements.get(r) || r) });
 };
+const updateContributorNodesIDS = (node, replacements, warnings) => {
+    var _a, _b;
+    if (node.type === schema_1.schema.nodes.contributor) {
+        const footnote = (_a = node.attrs.footnote) === null || _a === void 0 ? void 0 : _a.map((fn) => {
+            return Object.assign(Object.assign({}, fn), { noteID: replacements.get(fn.noteID) });
+        });
+        const corresp = (_b = node.attrs.corresp) === null || _b === void 0 ? void 0 : _b.map((corresp) => {
+            return Object.assign(Object.assign({}, corresp), { correspID: replacements.get(corresp.correspID) });
+        });
+        const affiliations = node.attrs.affiliations.map((affiliation) => {
+            return replacements.get(affiliation);
+        });
+        node.attrs = Object.assign(Object.assign({}, node.attrs), { footnote,
+            corresp,
+            affiliations });
+    }
+    if (node.type !== schema_1.schema.nodes.contributors) {
+        return false;
+    }
+};
 const JATS_TO_HTML_MAPPING = new Map([
     ['bold', 'b'],
     ['italic', 'i'],

package/dist/cjs/jats/importer/jats-reference-parser.js

@@ -16,9 +16,9 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.jatsReferenceParser = void 0;
+const json_schema_1 = require("@manuscripts/json-schema");
 const utils_1 = require("../../lib/utils");
-const builders_1 = require("../../transformer/builders");
-const jats_comments_1 = require("./jats-comments");
+const transformer_1 = require("../../transformer");
 const jats_parser_utils_1 = require("./jats-parser-utils");
 const jats_references_1 = require("./jats-references");
 const chooseBibliographyItemType = (publicationType) => {
@@ -40,23 +40,15 @@ exports.jatsReferenceParser = {
             const authorNodes = [
                 ...element.querySelectorAll('person-group[person-group-type="author"] > *'),
             ];
-            const bibliographyItem = (0, builders_1.buildBibliographyItem)({
+            const bibliographyItem = {
+                id: (0, transformer_1.generateID)(json_schema_1.ObjectTypes.BibliographyItem),
                 type: chooseBibliographyItemType(publicationType),
-            });
+            };
             const titleNode = element.querySelector('article-title');
             if (titleNode) {
                 bibliographyItem.title = (_a = (0, jats_parser_utils_1.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 ((0, jats_comments_1.isJATSComment)(item)) {
-                    const comment = (0, jats_comments_1.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;
@@ -69,7 +61,7 @@ exports.jatsReferenceParser = {
             }
             const source = (0, utils_1.getTrimmedTextContent)(element, 'source');
             if (source) {
-                bibliographyItem['container-title'] = source;
+                bibliographyItem.containerTitle = source;
             }
             const volume = (0, utils_1.getTrimmedTextContent)(element, 'volume');
             if (volume) {
@@ -90,18 +82,22 @@ exports.jatsReferenceParser = {
             }
             const year = (0, utils_1.getTrimmedTextContent)(element, 'year');
             if (year) {
-                bibliographyItem.issued = (0, builders_1.buildBibliographicDate)({
+                bibliographyItem.issued = {
                     'date-parts': [[year]],
-                });
+                    _id: (0, transformer_1.generateID)(json_schema_1.ObjectTypes.BibliographicDate),
+                    objectType: json_schema_1.ObjectTypes.BibliographicDate,
+                };
             }
             const doi = (0, utils_1.getTrimmedTextContent)(element, 'pub-id[pub-id-type="doi"]');
             if (doi) {
-                bibliographyItem.DOI = doi;
+                bibliographyItem.doi = doi;
             }
             const authors = [];
             authorNodes.forEach((authorNode) => {
-                var _a;
-                const name = (0, builders_1.buildBibliographicName)({});
+                const name = {
+                    _id: (0, transformer_1.generateID)(json_schema_1.ObjectTypes.BibliographicName),
+                    objectType: json_schema_1.ObjectTypes.BibliographicName,
+                };
                 const given = (0, utils_1.getTrimmedTextContent)(authorNode, 'given-names');
                 if (given) {
                     name.given = given;
@@ -110,20 +106,13 @@ exports.jatsReferenceParser = {
                 if (family) {
                     name.family = family;
                 }
-                const suffix = (0, utils_1.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);
+            references.add(bibliographyItem, id);
         });
         return references;
     },

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

@@ -1,34 +1,34 @@
 "use strict";
+/*!
+ * © 2023 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.
+ */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.References = void 0;
 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);
+    add(item, id) {
+        this.items.set(item.id, item);
         if (id) {
-            this.IDs.set(id, item._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);
-        }
-    }
 }
 exports.References = References;

package/dist/cjs/jats/importer/parse-jats-article.js

@@ -15,46 +15,15 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseJATSArticle = exports.parseJATSBody = exports.parseJATSFront = void 0;
+exports.parseJATSArticle = void 0;
 const errors_1 = require("../../errors");
-const transformer_1 = require("../../transformer");
-const builders_1 = require("../../transformer/builders");
-const id_1 = require("../../transformer/id");
-const project_bundle_1 = require("../../transformer/project-bundle");
-const jats_body_dom_parser_1 = require("./jats-body-dom-parser");
 const jats_body_transformations_1 = require("./jats-body-transformations");
 const jats_comments_1 = require("./jats-comments");
-const jats_front_parser_1 = require("./jats-front-parser");
+const jats_dom_parser_1 = require("./jats-dom-parser");
+const jats_front_transformations_1 = require("./jats-front-transformations");
+const jats_journal_meta_parser_1 = require("./jats-journal-meta-parser");
 const jats_parser_utils_1 = require("./jats-parser-utils");
 const jats_reference_parser_1 = require("./jats-reference-parser");
-const parseJATSFront = (doc, front) => {
-    const createElement = createElementFn(doc);
-    const journal = jats_front_parser_1.jatsFrontParser.parseJournal(front.querySelector('journal-meta'));
-    const titles = jats_front_parser_1.jatsFrontParser.parseTitles(front.querySelector('article-meta > title-group'), createElement);
-    const DOI = jats_front_parser_1.jatsFrontParser.parseDOI(front);
-    const { affiliations, affiliationIDs } = jats_front_parser_1.jatsFrontParser.parseAffiliations([
-        ...front.querySelectorAll('article-meta > contrib-group > aff'),
-    ]);
-    const { footnotes, footnoteIDs, authorNotes, authorNotesParagraphs, correspondingIDs, correspondingList, } = jats_front_parser_1.jatsFrontParser.parseAuthorNotes(front.querySelector('article-meta > author-notes'));
-    const authors = jats_front_parser_1.jatsFrontParser.parseContributors([
-        ...front.querySelectorAll('article-meta > contrib-group > contrib[contrib-type="author"]'),
-    ], affiliationIDs, footnoteIDs, correspondingIDs);
-    const history = jats_front_parser_1.jatsFrontParser.parseDates(front.querySelector('article-meta > history'));
-    const counts = jats_front_parser_1.jatsFrontParser.parseCounts(front.querySelector('article-meta counts'));
-    const manuscript = Object.assign(Object.assign(Object.assign(Object.assign({}, (0, builders_1.buildManuscript)()), counts), history), { DOI });
-    return generateIDs([
-        manuscript,
-        titles,
-        journal,
-        ...authorNotesParagraphs,
-        ...authorNotes,
-        ...footnotes,
-        ...authors,
-        ...affiliations,
-        ...correspondingList,
-    ]);
-};
-exports.parseJATSFront = parseJATSFront;
 const parseJATSBody = (doc, body, references) => {
     const createElement = createElementFn(doc);
     jats_body_transformations_1.jatsBodyTransformations.ensureSection(body, createElement);
@@ -66,64 +35,59 @@ const parseJATSBody = (doc, body, references) => {
     jats_body_transformations_1.jatsBodyTransformations.createSuppleMaterials(doc, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.createKeywords(doc, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.orderTableFootnote(doc, body);
-    const node = jats_body_dom_parser_1.jatsBodyDOMParser.parse(body).firstChild;
-    if (!node) {
-        throw new Error('No content was parsed from the JATS article body');
-    }
-    const replacements = new Map(references === null || references === void 0 ? void 0 : references.IDs);
-    (0, jats_parser_utils_1.updateDocumentIDs)(node, replacements);
-    return (0, transformer_1.encode)(node).values();
+    jats_body_transformations_1.jatsBodyTransformations.moveReferencesToBackmatter(body, references, createElement);
 };
-exports.parseJATSBody = parseJATSBody;
-const createBibliographyModels = (references) => {
-    const models = [];
-    const bibliographyItems = references.getBibliographyItems();
-    const bibliographyElement = (0, transformer_1.buildBibliographyElement)(bibliographyItems);
-    const bibliographySection = Object.assign(Object.assign({}, (0, transformer_1.buildSection)(99)), { category: 'MPSectionCategory:bibliography', elementIDs: [bibliographyElement._id], title: 'References' });
-    const comments = (0, jats_comments_1.createReferenceComments)(references);
-    models.push(bibliographySection);
-    models.push(bibliographyElement);
-    models.push(...bibliographyItems);
-    models.push(...comments);
-    return models;
+const parseJATSFront = (doc, front, template) => {
+    var _a;
+    const createElement = createElementFn(doc);
+    jats_front_transformations_1.jatsFrontTransformations.setArticleAttrs(doc, template);
+    const authorNotes = jats_front_transformations_1.jatsFrontTransformations.createAuthorNotes(doc, createElement);
+    if (authorNotes) {
+        doc.documentElement.prepend(authorNotes);
+    }
+    const affiliations = jats_front_transformations_1.jatsFrontTransformations.createAffiliations(front, createElement);
+    if (affiliations) {
+        doc.documentElement.prepend(affiliations);
+    }
+    const contributors = jats_front_transformations_1.jatsFrontTransformations.createContributors(front, createElement);
+    if (contributors) {
+        doc.documentElement.prepend(contributors);
+    }
+    const title = jats_front_transformations_1.jatsFrontTransformations.createTitle(front, createElement);
+    if (title) {
+        doc.documentElement.prepend(title);
+    }
+    (_a = doc.querySelector('front')) === null || _a === void 0 ? void 0 : _a.remove();
 };
 const createElementFn = (doc) => (tagName) => doc.createElement(tagName);
-const generateIDs = (models) => models.map((m) => m._id ? m : Object.assign(Object.assign({}, m), { _id: (0, id_1.generateID)(m.objectType) }));
-const parseJATSArticle = (doc) => {
+const parseJATSArticle = (doc, template) => {
     const article = doc.querySelector('article');
     const front = doc.querySelector('front');
     const body = doc.querySelector('body');
     const back = doc.querySelector('back');
-    if (!front) {
-        throw new errors_1.InvalidInput('Invalid JATS format! Missing front element');
-    }
-    if (!article) {
-        throw new errors_1.InvalidInput('Invalid JATS format! Missing article element');
+    if (!article || !front) {
+        throw new errors_1.InvalidInput('invalid JATS format');
     }
-    const marks = (0, jats_comments_1.markComments)(doc);
+    (0, jats_comments_1.markComments)(doc);
+    const journal = (0, jats_journal_meta_parser_1.parseJournal)(front.querySelector('journal-meta'));
     const createElement = createElementFn(doc);
-    const models = [];
     let references;
     if (back) {
         references = jats_reference_parser_1.jatsReferenceParser.parseReferences([...back.querySelectorAll('ref-list > ref')], createElement);
     }
-    models.push(...(0, exports.parseJATSFront)(doc, front));
+    const replacements = new Map(references === null || references === void 0 ? void 0 : references.IDs);
+    parseJATSFront(doc, front, template);
     if (body) {
-        models.push(...(0, exports.parseJATSBody)(doc, body, references));
-    }
-    const modelMap = new Map(models.map((model) => [model._id, model]));
-    const manuscript = (0, project_bundle_1.findManuscript)(modelMap);
-    if (manuscript) {
-        const type = article.getAttribute('article-type');
-        manuscript.articleType = type || 'other';
+        parseJATSBody(doc, body, references);
     }
-    if (references && references.items.size) {
-        models.push(...createBibliographyModels(references));
-    }
-    if (marks.length) {
-        const comments = (0, jats_comments_1.createComments)(models, marks);
-        models.push(...comments);
+    const node = jats_dom_parser_1.jatsDOMParser.parse(doc).firstChild;
+    if (!node) {
+        throw new Error('No content was parsed from the JATS article body');
     }
-    return models;
+    (0, jats_parser_utils_1.updateDocumentIDs)(node, replacements);
+    return {
+        node: node,
+        journal,
+    };
 };
 exports.parseJATSArticle = parseJATSArticle;