@manuscripts/transform 1.3.2 → 1.3.4-LEAN-2501-test

package/dist/cjs/jats/importer/jats-body-dom-parser.js

@@ -649,10 +649,11 @@ const nodes = [
         tag: 'xref[ref-type="bibr"]',
         node: 'citation',
         getAttrs: (node) => {
+            var _a;
             const element = node;
             return {
                 rid: element.getAttribute('rid'),
-                contents: element.textContent,
+                contents: (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
             };
         },
     },
@@ -660,10 +661,11 @@ const nodes = [
         tag: 'xref[ref-type="fn"]',
         node: 'inline_footnote',
         getAttrs: (node) => {
+            var _a;
             const element = node;
             return {
                 rid: element.getAttribute('rid'),
-                contents: element.textContent,
+                contents: (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
             };
         },
     },
@@ -671,10 +673,11 @@ const nodes = [
         tag: 'xref',
         node: 'cross_reference',
         getAttrs: (node) => {
+            var _a;
             const element = node;
             return {
                 rid: element.getAttribute('rid'),
-                label: element.textContent,
+                label: (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
             };
         },
     },

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

@@ -215,6 +215,7 @@ exports.jatsBodyTransformations = {
         body.append(backmatterContainer);
     },
     mapFootnotesToSections(doc, backmatterContainer, createElement) {
+        var _a;
         const footnoteGroups = [...doc.querySelectorAll('fn[fn-type]')];
         for (const footnote of footnoteGroups) {
             const type = footnote.getAttribute('fn-type') || '';
@@ -224,7 +225,10 @@ exports.jatsBodyTransformations = {
                 const title = footnote.querySelector('p[content-type="fn-title"]');
                 if (title) {
                     const sectionTitleElement = createElement('title');
-                    sectionTitleElement.textContent = title.textContent;
+                    const titleTextContent = (_a = title.textContent) === null || _a === void 0 ? void 0 : _a.trim();
+                    if (titleTextContent) {
+                        sectionTitleElement.textContent = titleTextContent;
+                    }
                     removeNodeFromParent(title);
                     section.append(sectionTitleElement);
                 }

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

@@ -21,7 +21,8 @@ const transformer_1 = require("../../transformer");
 const DEFAULT_ANNOTATION_COLOR = 'rgb(250, 224, 150)';
 const DEFAULT_PROFILE_ID = 'MPUserProfile:0000000000000000000000000000000000000001';
 const parseProcessingInstruction = (node) => {
-    const value = `<AuthorQuery ${node.textContent} />`;
+    var _a;
+    const value = `<AuthorQuery ${(_a = node.textContent) === null || _a === void 0 ? void 0 : _a.trim()} />`;
     const processingInstruction = new DOMParser().parseFromString(value, 'application/xml').firstElementChild;
     if (processingInstruction) {
         const queryText = processingInstruction.getAttribute('queryText');

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

@@ -20,6 +20,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.jatsFrontParser = void 0;
 const debug_1 = __importDefault(require("debug"));
+const utils_1 = require("../../lib/utils");
 const builders_1 = require("../../transformer/builders");
 const jats_journal_meta_parser_1 = require("./jats-journal-meta-parser");
 const warn = (0, debug_1.default)('manuscripts-transform');
@@ -74,11 +75,10 @@ exports.jatsFrontParser = {
         }
         const history = {};
         const dateToTimestamp = (dateElement) => {
-            var _a, _b;
             const selectors = ['year', 'month', 'day'];
             const values = [];
             for (const selector of selectors) {
-                const value = (_b = (_a = dateElement.querySelector(selector)) === null || _a === void 0 ? void 0 : _a.textContent) === null || _b === void 0 ? void 0 : _b.trim();
+                const value = (0, utils_1.getTrimmedTextContent)(dateElement, selector);
                 if (!value || isNaN(+value)) {
                     return;
                 }
@@ -118,17 +118,17 @@ exports.jatsFrontParser = {
         return history;
     },
     parseSupplements(supplementNodes) {
-        var _a, _b, _c, _d, _e;
+        var _a, _b, _c, _d;
         if (!supplementNodes || supplementNodes.length === 0) {
             return [];
         }
         const supplements = [];
         for (const supplementNode of supplementNodes) {
-            const supplTitle = (_b = (_a = supplementNode.querySelector('caption > title')) === null || _a === void 0 ? void 0 : _a.textContent) !== null && _b !== void 0 ? _b : '';
-            const href = (_c = supplementNode.getAttributeNS(XLINK_NAMESPACE, 'href')) !== null && _c !== void 0 ? _c : '';
+            const supplTitle = (_a = (0, utils_1.getTrimmedTextContent)(supplementNode, 'caption > title')) !== null && _a !== void 0 ? _a : '';
+            const href = (_b = supplementNode.getAttributeNS(XLINK_NAMESPACE, 'href')) !== null && _b !== void 0 ? _b : '';
             const supplementaryMaterial = (0, builders_1.buildSupplementaryMaterial)(supplTitle, href);
-            const mimeType = (_d = supplementNode.getAttribute('mimetype')) !== null && _d !== void 0 ? _d : '';
-            const mimeSubtype = (_e = supplementNode.getAttribute('mime-subtype')) !== null && _e !== void 0 ? _e : '';
+            const mimeType = (_c = supplementNode.getAttribute('mimetype')) !== null && _c !== void 0 ? _c : '';
+            const mimeSubtype = (_d = supplementNode.getAttribute('mime-subtype')) !== null && _d !== void 0 ? _d : '';
             if (mimeType && mimeSubtype) {
                 supplementaryMaterial.MIME = [mimeType, mimeSubtype].join('/');
             }
@@ -139,10 +139,10 @@ exports.jatsFrontParser = {
     parseAffiliationNodes(affiliationNodes) {
         const affiliationIDs = new Map();
         const affiliations = affiliationNodes.map((affiliationNode, priority) => {
-            var _a, _b, _c, _d, _e;
+            var _a, _b;
             const affiliation = (0, builders_1.buildAffiliation)('', priority);
             for (const node of affiliationNode.querySelectorAll('institution')) {
-                const content = node.textContent;
+                const content = (_a = node.textContent) === null || _a === void 0 ? void 0 : _a.trim();
                 if (!content) {
                     continue;
                 }
@@ -157,22 +157,25 @@ exports.jatsFrontParser = {
                 }
             }
             affiliation.addressLine1 =
-                ((_a = affiliationNode.querySelector('addr-line:nth-of-type(1)')) === null || _a === void 0 ? void 0 : _a.textContent) || undefined;
+                (0, utils_1.getTrimmedTextContent)(affiliationNode, 'addr-line:nth-of-type(1)') ||
+                    undefined;
             affiliation.addressLine2 =
-                ((_b = affiliationNode.querySelector('addr-line:nth-of-type(2)')) === null || _b === void 0 ? void 0 : _b.textContent) || undefined;
+                (0, utils_1.getTrimmedTextContent)(affiliationNode, 'addr-line:nth-of-type(2)') ||
+                    undefined;
             affiliation.addressLine3 =
-                ((_c = affiliationNode.querySelector('addr-line:nth-of-type(3)')) === null || _c === void 0 ? void 0 : _c.textContent) || undefined;
+                (0, utils_1.getTrimmedTextContent)(affiliationNode, 'addr-line:nth-of-type(3)') ||
+                    undefined;
             const emailNode = affiliationNode.querySelector('email');
             if (emailNode) {
                 affiliation.email = {
                     href: emailNode.getAttributeNS(XLINK_NAMESPACE, 'href') || undefined,
-                    text: emailNode.textContent || undefined,
+                    text: ((_b = emailNode.textContent) === null || _b === void 0 ? void 0 : _b.trim()) || undefined,
                 };
             }
             affiliation.postCode =
-                ((_d = affiliationNode.querySelector('postal-code')) === null || _d === void 0 ? void 0 : _d.textContent) || undefined;
+                (0, utils_1.getTrimmedTextContent)(affiliationNode, 'postal-code') || undefined;
             affiliation.country =
-                ((_e = affiliationNode.querySelector('country')) === null || _e === void 0 ? void 0 : _e.textContent) || undefined;
+                (0, utils_1.getTrimmedTextContent)(affiliationNode, 'country') || undefined;
             const id = affiliationNode.getAttribute('id');
             if (id) {
                 affiliationIDs.set(id, affiliation._id);
@@ -202,13 +205,13 @@ exports.jatsFrontParser = {
     parseCorrespNodes(correspNodes) {
         const correspondingIDs = new Map();
         const correspondingList = correspNodes.map((correspNode) => {
-            var _a;
+            var _a, _b, _c;
             const label = correspNode.querySelector('label');
             if (label) {
                 label.remove();
             }
-            const corresponding = (0, builders_1.buildCorresp)((_a = correspNode.textContent) !== null && _a !== void 0 ? _a : '');
-            corresponding.label = (label === null || label === void 0 ? void 0 : label.textContent) || undefined;
+            const corresponding = (0, builders_1.buildCorresp)((_b = (_a = correspNode.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 = correspNode.getAttribute('id');
             if (id) {
                 correspondingIDs.set(id, corresponding._id);
@@ -222,13 +225,13 @@ exports.jatsFrontParser = {
     },
     parseAuthorNodes(authorNodes, affiliationIDs, footnoteIDs, correspondingIDs) {
         return authorNodes.map((authorNode, priority) => {
-            var _a, _b, _c;
+            var _a, _b;
             const name = (0, builders_1.buildBibliographicName)({});
-            const given = (_a = authorNode.querySelector('name > given-names')) === null || _a === void 0 ? void 0 : _a.textContent;
+            const given = (0, utils_1.getTrimmedTextContent)(authorNode, 'name > given-names');
             if (given) {
                 name.given = given;
             }
-            const surname = (_b = authorNode.querySelector('name > surname')) === null || _b === void 0 ? void 0 : _b.textContent;
+            const surname = (0, utils_1.getTrimmedTextContent)(authorNode, 'name > surname');
             if (surname) {
                 name.family = surname;
             }
@@ -237,7 +240,7 @@ exports.jatsFrontParser = {
             if (corresponding) {
                 contributor.isCorresponding = corresponding;
             }
-            const orcid = (_c = authorNode.querySelector('contrib-id[contrib-id-type="orcid"]')) === null || _c === void 0 ? void 0 : _c.textContent;
+            const orcid = (0, utils_1.getTrimmedTextContent)(authorNode, 'contrib-id[contrib-id-type="orcid"]');
             if (orcid) {
                 contributor.ORCIDIdentifier = orcid;
             }
@@ -253,7 +256,7 @@ exports.jatsFrontParser = {
                             if (footnoteId) {
                                 const authorFootNoteRef = {
                                     noteID: footnoteId,
-                                    noteLabel: xrefNode.textContent || '',
+                                    noteLabel: ((_a = xrefNode.textContent) === null || _a === void 0 ? void 0 : _a.trim()) || '',
                                 };
                                 contributor.footnote.push(authorFootNoteRef);
                             }
@@ -264,7 +267,7 @@ exports.jatsFrontParser = {
                             if (correspId) {
                                 const authorCorrespRef = {
                                     correspID: correspId,
-                                    correspLabel: xrefNode.textContent || '',
+                                    correspLabel: ((_b = xrefNode.textContent) === null || _b === void 0 ? void 0 : _b.trim()) || '',
                                 };
                                 contributor.corresp.push(authorCorrespRef);
                             }

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

@@ -16,12 +16,14 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseJournalMeta = exports.parseJournalISSNs = exports.parseJournalAbbreviatedTitles = exports.parseJournalIdentifiers = void 0;
+const utils_1 = require("../../lib/utils");
 const parseJournalIdentifiers = (journalMeta) => {
+    var _a, _b;
     const output = [];
     const elements = journalMeta.querySelectorAll('journal-id');
     for (const element of elements) {
         const journalIDType = element.getAttribute('journal-id-type');
-        const journalID = element.textContent;
+        const journalID = (_b = (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim()) !== null && _b !== void 0 ? _b : element.textContent;
         if (journalID !== null && journalIDType != null) {
             output.push({ journalIDType, journalID });
         }
@@ -33,11 +35,12 @@ const parseJournalIdentifiers = (journalMeta) => {
 };
 exports.parseJournalIdentifiers = parseJournalIdentifiers;
 const parseJournalAbbreviatedTitles = (journalMeta) => {
+    var _a, _b;
     const output = [];
     const elements = journalMeta.querySelectorAll('journal-title-group > abbrev-journal-title');
     for (const element of elements) {
         const abbrevType = element.getAttribute('abbrev-type');
-        const abbreviatedTitle = element.textContent;
+        const abbreviatedTitle = (_b = (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim()) !== null && _b !== void 0 ? _b : element.textContent;
         if (abbreviatedTitle !== null && abbrevType !== null) {
             output.push({ abbreviatedTitle, abbrevType });
         }
@@ -49,11 +52,12 @@ const parseJournalAbbreviatedTitles = (journalMeta) => {
 };
 exports.parseJournalAbbreviatedTitles = parseJournalAbbreviatedTitles;
 const parseJournalISSNs = (journalMeta) => {
+    var _a, _b;
     const output = [];
     const elements = journalMeta.querySelectorAll('issn');
     for (const element of elements) {
         const publicationType = element.getAttribute('pub-type');
-        const ISSN = element.textContent;
+        const ISSN = (_b = (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim()) !== null && _b !== void 0 ? _b : element.textContent;
         if (publicationType !== null && ISSN !== null) {
             output.push({ publicationType, ISSN });
         }
@@ -65,13 +69,13 @@ const parseJournalISSNs = (journalMeta) => {
 };
 exports.parseJournalISSNs = parseJournalISSNs;
 const parseJournalMeta = (journalMeta) => {
-    var _a, _b, _c, _d;
+    var _a, _b;
     return {
         abbreviatedTitles: (0, exports.parseJournalAbbreviatedTitles)(journalMeta),
         journalIdentifiers: (0, exports.parseJournalIdentifiers)(journalMeta),
         ISSNs: (0, exports.parseJournalISSNs)(journalMeta),
-        publisherName: (_b = (_a = journalMeta.querySelector('publisher > publisher-name')) === null || _a === void 0 ? void 0 : _a.textContent) !== null && _b !== void 0 ? _b : undefined,
-        title: (_d = (_c = journalMeta.querySelector('journal-title-group > journal-title')) === null || _c === void 0 ? void 0 : _c.textContent) !== null && _d !== void 0 ? _d : undefined,
+        publisherName: (_a = (0, utils_1.getTrimmedTextContent)(journalMeta, 'publisher > publisher-name')) !== null && _a !== void 0 ? _a : undefined,
+        title: (_b = (0, utils_1.getTrimmedTextContent)(journalMeta, 'journal-title-group > journal-title')) !== null && _b !== void 0 ? _b : undefined,
     };
 };
 exports.parseJournalMeta = parseJournalMeta;

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

@@ -16,6 +16,7 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.jatsReferenceParser = void 0;
+const utils_1 = require("../../lib/utils");
 const builders_1 = require("../../transformer/builders");
 const jats_comments_1 = require("./jats-comments");
 const jats_parser_utils_1 = require("./jats-parser-utils");
@@ -34,7 +35,7 @@ exports.jatsReferenceParser = {
         const referenceIDs = new Map();
         const referenceQueries = new Map();
         const references = referenceNodes.map((referenceNode) => {
-            var _a, _b, _c, _d, _e, _f, _g, _h;
+            var _a;
             const publicationType = referenceNode.getAttribute('publication-type');
             const authorNodes = [
                 ...referenceNode.querySelectorAll('person-group[person-group-type="author"] > *'),
@@ -44,7 +45,7 @@ exports.jatsReferenceParser = {
             });
             const titleNode = referenceNode.querySelector('article-title');
             if (titleNode) {
-                bibliographyItem.title = (0, jats_parser_utils_1.htmlFromJatsNode)(titleNode, createElement);
+                bibliographyItem.title = (_a = (0, jats_parser_utils_1.htmlFromJatsNode)(titleNode, createElement)) === null || _a === void 0 ? void 0 : _a.trim();
             }
             const queriesText = [];
             const mixedCitation = referenceNode.querySelector('mixed-citation');
@@ -63,63 +64,63 @@ exports.jatsReferenceParser = {
             }
             if (authorNodes.length <= 0) {
                 mixedCitation === null || mixedCitation === void 0 ? void 0 : mixedCitation.childNodes.forEach((item) => {
-                    var _a, _b;
+                    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 = (_b = mixedCitation.textContent) !== null && _b !== void 0 ? _b : '';
+                        bibliographyItem.literal = (_c = (_b = mixedCitation.textContent) === null || _b === void 0 ? void 0 : _b.trim()) !== null && _c !== void 0 ? _c : '';
                         return bibliographyItem;
                     }
                 });
             }
-            const source = (_a = referenceNode.querySelector('source')) === null || _a === void 0 ? void 0 : _a.textContent;
+            const source = (0, utils_1.getTrimmedTextContent)(referenceNode, 'source');
             if (source) {
                 bibliographyItem['container-title'] = source;
             }
-            const volume = (_b = referenceNode.querySelector('volume')) === null || _b === void 0 ? void 0 : _b.textContent;
+            const volume = (0, utils_1.getTrimmedTextContent)(referenceNode, 'volume');
             if (volume) {
                 bibliographyItem.volume = volume;
             }
-            const issue = (_c = referenceNode.querySelector('issue')) === null || _c === void 0 ? void 0 : _c.textContent;
+            const issue = (0, utils_1.getTrimmedTextContent)(referenceNode, 'issue');
             if (issue) {
                 bibliographyItem.issue = issue;
             }
-            const supplement = (_d = referenceNode.querySelector('supplement')) === null || _d === void 0 ? void 0 : _d.textContent;
+            const supplement = (0, utils_1.getTrimmedTextContent)(referenceNode, 'supplement');
             if (supplement) {
                 bibliographyItem.supplement = supplement;
             }
-            const fpage = (_e = referenceNode.querySelector('fpage')) === null || _e === void 0 ? void 0 : _e.textContent;
-            const lpage = (_f = referenceNode.querySelector('lpage')) === null || _f === void 0 ? void 0 : _f.textContent;
+            const fpage = (0, utils_1.getTrimmedTextContent)(referenceNode, 'fpage');
+            const lpage = (0, utils_1.getTrimmedTextContent)(referenceNode, 'lpage');
             if (fpage) {
                 bibliographyItem.page = lpage ? `${fpage}-${lpage}` : fpage;
             }
-            const year = (_g = referenceNode.querySelector('year')) === null || _g === void 0 ? void 0 : _g.textContent;
+            const year = (0, utils_1.getTrimmedTextContent)(referenceNode, 'year');
             if (year) {
                 bibliographyItem.issued = (0, builders_1.buildBibliographicDate)({
                     'date-parts': [[year]],
                 });
             }
-            const doi = (_h = referenceNode.querySelector('pub-id[pub-id-type="doi"]')) === null || _h === void 0 ? void 0 : _h.textContent;
+            const doi = (0, utils_1.getTrimmedTextContent)(referenceNode, 'pub-id[pub-id-type="doi"]');
             if (doi) {
                 bibliographyItem.DOI = doi;
             }
             const authors = [];
             authorNodes.forEach((authorNode) => {
-                var _a, _b, _c;
+                var _a;
                 const name = (0, builders_1.buildBibliographicName)({});
-                const given = (_a = authorNode.querySelector('given-names')) === null || _a === void 0 ? void 0 : _a.textContent;
+                const given = (0, utils_1.getTrimmedTextContent)(authorNode, 'given-names');
                 if (given) {
                     name.given = given;
                 }
-                const family = (_b = authorNode.querySelector('surname')) === null || _b === void 0 ? void 0 : _b.textContent;
+                const family = (0, utils_1.getTrimmedTextContent)(authorNode, 'surname');
                 if (family) {
                     name.family = family;
                 }
-                const suffix = (_c = authorNode.querySelector('suffix')) === null || _c === void 0 ? void 0 : _c.textContent;
+                const suffix = (0, utils_1.getTrimmedTextContent)(authorNode, 'suffix');
                 if (suffix) {
                     name.suffix = suffix;
                 }
                 if (authorNode.nodeName === 'collab') {
-                    name.literal = authorNode.textContent;
+                    name.literal = (_a = authorNode.textContent) === null || _a === void 0 ? void 0 : _a.trim();
                 }
                 authors.push(name);
             });

package/dist/cjs/jats/jats-exporter.js

@@ -236,7 +236,6 @@ class JATSExporter {
         this.buildFront = (doi, id, links) => {
             var _a, _b, _c, _d;
             const manuscript = (0, project_bundle_1.findManuscript)(this.modelMap);
-            const submission = (0, project_bundle_1.findLatestManuscriptSubmission)(this.modelMap, manuscript);
             const front = this.document.createElement('front');
             const journalMeta = this.document.createElement('journal-meta');
             front.appendChild(journalMeta);
@@ -291,29 +290,6 @@ class JATSExporter {
                     journalMeta.appendChild(publisher);
                 }
             }
-            else {
-                if (submission) {
-                    if (submission.journalCode) {
-                        const journalID = this.document.createElement('journal-id');
-                        journalID.setAttribute('journal-id-type', 'publisher-id');
-                        journalID.textContent = submission.journalCode;
-                        journalMeta.appendChild(journalID);
-                    }
-                    if (submission.journalTitle) {
-                        const journalTitleGroup = this.document.createElement('journal-title-group');
-                        journalMeta.appendChild(journalTitleGroup);
-                        const journalTitle = this.document.createElement('journal-title');
-                        journalTitle.textContent = submission.journalTitle;
-                        journalTitleGroup.appendChild(journalTitle);
-                    }
-                    if (submission.issn) {
-                        const issn = this.document.createElement('issn');
-                        issn.setAttribute('pub-type', 'epub');
-                        issn.textContent = submission.issn;
-                        journalMeta.appendChild(issn);
-                    }
-                }
-            }
             if (id) {
                 const articleID = this.document.createElement('article-id');
                 articleID.setAttribute('pub-id-type', 'publisher-id');

package/dist/cjs/lib/utils.js

@@ -15,7 +15,7 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.findParentNodeClosestToPos = exports.isInBibliographySection = exports.isInGraphicalAbstractSection = exports.findNodePositions = exports.iterateChildren = void 0;
+exports.getTrimmedTextContent = exports.findParentNodeClosestToPos = exports.isInBibliographySection = exports.isInGraphicalAbstractSection = exports.findNodePositions = exports.iterateChildren = void 0;
 const bibliography_section_1 = require("../schema/nodes/bibliography_section");
 const graphical_abstract_section_1 = require("../schema/nodes/graphical_abstract_section");
 function* iterateChildren(node, recurse = false) {
@@ -75,3 +75,11 @@ const findParentNodeClosestToPos = ($pos, predicate) => {
     }
 };
 exports.findParentNodeClosestToPos = findParentNodeClosestToPos;
+const getTrimmedTextContent = (node, querySelector) => {
+    var _a, _b;
+    if (!node) {
+        return null;
+    }
+    return (_b = (_a = node.querySelector(querySelector)) === null || _a === void 0 ? void 0 : _a.textContent) === null || _b === void 0 ? void 0 : _b.trim();
+};
+exports.getTrimmedTextContent = getTrimmedTextContent;

package/dist/cjs/transformer/builders.js

@@ -18,7 +18,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.buildElementsOrder = exports.auxiliaryObjectTypes = exports.buildUserFootNote = exports.buildStatusLabel = exports.buildJournal = exports.buildSubmission = exports.buildAttribution = exports.buildInlineStyle = exports.buildContributorRole = exports.buildContribution = exports.buildHighlightMarker = exports.buildHighlight = exports.buildColor = exports.buildParagraph = exports.buildSection = exports.buildCorresp = exports.buildFootnotesOrder = exports.buildFootnote = exports.buildInlineMathFragment = exports.buildValidation = exports.buildNote = exports.buildComment = exports.buildUserProfileAffiliation = exports.buildSupplementaryMaterial = exports.buildAffiliation = exports.buildFigure = exports.buildLibraryCollection = exports.buildManuscriptKeyword = exports.buildKeywordGroup = exports.buildKeyword = exports.buildCitation = exports.buildEmbeddedCitationItem = exports.buildAuxiliaryObjectReference = exports.buildBibliographicDate = exports.buildBibliographicName = exports.buildBibliographyItem = exports.buildContributor = exports.buildManuscript = exports.buildProject = exports.DEFAULT_PAGE_LAYOUT = exports.DEFAULT_BUNDLE = void 0;
+exports.buildElementsOrder = exports.auxiliaryObjectTypes = exports.buildStatusLabel = exports.buildJournal = exports.buildAttribution = exports.buildInlineStyle = exports.buildContributorRole = exports.buildContribution = exports.buildHighlightMarker = exports.buildHighlight = exports.buildColor = exports.buildParagraph = exports.buildSection = exports.buildCorresp = exports.buildFootnotesOrder = exports.buildFootnote = exports.buildInlineMathFragment = exports.buildValidation = exports.buildNote = exports.buildComment = exports.buildUserProfileAffiliation = exports.buildSupplementaryMaterial = exports.buildAffiliation = exports.buildFigure = exports.buildLibraryCollection = exports.buildManuscriptKeyword = exports.buildKeywordGroup = exports.buildKeyword = exports.buildCitation = exports.buildEmbeddedCitationItem = exports.buildAuxiliaryObjectReference = exports.buildBibliographicDate = exports.buildBibliographicName = exports.buildBibliographyItem = exports.buildContributor = exports.buildManuscript = exports.buildProject = exports.DEFAULT_PAGE_LAYOUT = exports.DEFAULT_BUNDLE = void 0;
 const json_schema_1 = require("@manuscripts/json-schema");
 const w3c_xmlserializer_1 = __importDefault(require("w3c-xmlserializer"));
 const schema_1 = require("../schema");
@@ -267,11 +267,6 @@ const buildAttribution = () => ({
     objectType: json_schema_1.ObjectTypes.Attribution,
 });
 exports.buildAttribution = buildAttribution;
-const buildSubmission = () => ({
-    _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.Submission),
-    objectType: json_schema_1.ObjectTypes.Submission,
-});
-exports.buildSubmission = buildSubmission;
 const buildJournal = () => ({
     _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.Journal),
     objectType: json_schema_1.ObjectTypes.Journal,
@@ -283,13 +278,6 @@ const buildStatusLabel = (name) => ({
     name,
 });
 exports.buildStatusLabel = buildStatusLabel;
-const buildUserFootNote = (noteId, content) => ({
-    _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.UserProfileFootNote),
-    objectType: json_schema_1.ObjectTypes.UserProfileFootNote,
-    noteId,
-    content,
-});
-exports.buildUserFootNote = buildUserFootNote;
 exports.auxiliaryObjectTypes = new Set([
     schema_1.schema.nodes.figure_element,
     schema_1.schema.nodes.table_element,

package/dist/cjs/transformer/decode.js

@@ -43,7 +43,7 @@ const timestamp_1 = require("./timestamp");
 const warn = (0, debug_1.default)('manuscripts-transform');
 const parser = prosemirror_model_1.DOMParser.fromSchema(schema_1.schema);
 const getModelData = (model) => {
-    const { _rev, _deleted, updatedAt, createdAt, sessionID } = model, data = __rest(model, ["_rev", "_deleted", "updatedAt", "createdAt", "sessionID"]);
+    const { updatedAt, createdAt } = model, data = __rest(model, ["updatedAt", "createdAt"]);
     return data;
 };
 exports.getModelData = getModelData;

package/dist/cjs/transformer/labels.js

@@ -65,6 +65,7 @@ const buildTargets = (fragment, manuscript) => {
         }
     });
     fragment.descendants((node) => {
+        var _a;
         if (node.type.name in counters) {
             const isInGraphicalAbstract = figures.indexOf(node.attrs.id) > -1;
             if (isInGraphicalAbstract) {
@@ -75,7 +76,7 @@ const buildTargets = (fragment, manuscript) => {
                 type: node.type.name,
                 id: node.attrs.id,
                 label,
-                caption: node.textContent,
+                caption: (_a = node.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
             });
         }
     });

package/dist/cjs/transformer/manuscript-dependencies.js

@@ -14,7 +14,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.fromPrototype = void 0;
 const id_1 = require("./id");
 const fromPrototype = (model) => {
-    const { _id, _rev } = model, data = __rest(model, ["_id", "_rev"]);
+    const { _id } = model, data = __rest(model, ["_id"]);
     const output = Object.assign(Object.assign({}, data), { prototype: _id, _id: (0, id_1.generateID)(model.objectType) });
     return output;
 };

package/dist/cjs/transformer/project-bundle.js

@@ -15,7 +15,7 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.findManuscriptById = exports.findLatestManuscriptSubmission = exports.findManuscriptModelByType = exports.findJournal = exports.findManuscript = exports.parseProjectBundle = void 0;
+exports.findManuscriptById = exports.findManuscriptModelByType = exports.findJournal = exports.findManuscript = exports.parseProjectBundle = void 0;
 const json_schema_1 = require("@manuscripts/json-schema");
 const decode_1 = require("./decode");
 const object_types_1 = require("./object-types");
@@ -63,19 +63,6 @@ const findManuscriptModelByType = (modelMap, manuscript, objectType) => {
     }
 };
 exports.findManuscriptModelByType = findManuscriptModelByType;
-const isSubmission = (0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.Submission);
-const newestFirst = (a, b) => b.createdAt - a.createdAt;
-const findLatestManuscriptSubmission = (modelMap, manuscript) => {
-    const submissions = [];
-    for (const model of modelMap.values()) {
-        if (isSubmission(model) && model.manuscriptID === manuscript._id) {
-            submissions.push(model);
-        }
-    }
-    submissions.sort(newestFirst);
-    return submissions.length ? submissions[0] : undefined;
-};
-exports.findLatestManuscriptSubmission = findLatestManuscriptSubmission;
 const findManuscriptById = (modelMap, manuscriptID) => {
     const manuscript = modelMap.get(manuscriptID);
     if (manuscript && isManuscript(manuscript)) {

package/dist/es/jats/importer/jats-body-dom-parser.js

@@ -643,10 +643,11 @@ const nodes = [
         tag: 'xref[ref-type="bibr"]',
         node: 'citation',
         getAttrs: (node) => {
+            var _a;
             const element = node;
             return {
                 rid: element.getAttribute('rid'),
-                contents: element.textContent,
+                contents: (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
             };
         },
     },
@@ -654,10 +655,11 @@ const nodes = [
         tag: 'xref[ref-type="fn"]',
         node: 'inline_footnote',
         getAttrs: (node) => {
+            var _a;
             const element = node;
             return {
                 rid: element.getAttribute('rid'),
-                contents: element.textContent,
+                contents: (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
             };
         },
     },
@@ -665,10 +667,11 @@ const nodes = [
         tag: 'xref',
         node: 'cross_reference',
         getAttrs: (node) => {
+            var _a;
             const element = node;
             return {
                 rid: element.getAttribute('rid'),
-                label: element.textContent,
+                label: (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
             };
         },
     },

package/dist/es/jats/importer/jats-body-transformations.js

@@ -212,6 +212,7 @@ export const jatsBodyTransformations = {
         body.append(backmatterContainer);
     },
     mapFootnotesToSections(doc, backmatterContainer, createElement) {
+        var _a;
         const footnoteGroups = [...doc.querySelectorAll('fn[fn-type]')];
         for (const footnote of footnoteGroups) {
             const type = footnote.getAttribute('fn-type') || '';
@@ -221,7 +222,10 @@ export const jatsBodyTransformations = {
                 const title = footnote.querySelector('p[content-type="fn-title"]');
                 if (title) {
                     const sectionTitleElement = createElement('title');
-                    sectionTitleElement.textContent = title.textContent;
+                    const titleTextContent = (_a = title.textContent) === null || _a === void 0 ? void 0 : _a.trim();
+                    if (titleTextContent) {
+                        sectionTitleElement.textContent = titleTextContent;
+                    }
                     removeNodeFromParent(title);
                     section.append(sectionTitleElement);
                 }

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

@@ -18,7 +18,8 @@ import { buildComment, buildContribution, isCommentAnnotation, isHighlightableMo
 const DEFAULT_ANNOTATION_COLOR = 'rgb(250, 224, 150)';
 const DEFAULT_PROFILE_ID = 'MPUserProfile:0000000000000000000000000000000000000001';
 export const parseProcessingInstruction = (node) => {
-    const value = `<AuthorQuery ${node.textContent} />`;
+    var _a;
+    const value = `<AuthorQuery ${(_a = node.textContent) === null || _a === void 0 ? void 0 : _a.trim()} />`;
     const processingInstruction = new DOMParser().parseFromString(value, 'application/xml').firstElementChild;
     if (processingInstruction) {
         const queryText = processingInstruction.getAttribute('queryText');

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

@@ -14,6 +14,7 @@
  * limitations under the License.
  */
 import debug from 'debug';
+import { getTrimmedTextContent } from '../../lib/utils';
 import { buildAffiliation, buildBibliographicName, buildContributor, buildCorresp, buildFootnote, buildSupplementaryMaterial, } from '../../transformer/builders';
 import { parseJournalMeta } from './jats-journal-meta-parser';
 const warn = debug('manuscripts-transform');
@@ -68,11 +69,10 @@ export const jatsFrontParser = {
         }
         const history = {};
         const dateToTimestamp = (dateElement) => {
-            var _a, _b;
             const selectors = ['year', 'month', 'day'];
             const values = [];
             for (const selector of selectors) {
-                const value = (_b = (_a = dateElement.querySelector(selector)) === null || _a === void 0 ? void 0 : _a.textContent) === null || _b === void 0 ? void 0 : _b.trim();
+                const value = getTrimmedTextContent(dateElement, selector);
                 if (!value || isNaN(+value)) {
                     return;
                 }
@@ -112,17 +112,17 @@ export const jatsFrontParser = {
         return history;
     },
     parseSupplements(supplementNodes) {
-        var _a, _b, _c, _d, _e;
+        var _a, _b, _c, _d;
         if (!supplementNodes || supplementNodes.length === 0) {
             return [];
         }
         const supplements = [];
         for (const supplementNode of supplementNodes) {
-            const supplTitle = (_b = (_a = supplementNode.querySelector('caption > title')) === null || _a === void 0 ? void 0 : _a.textContent) !== null && _b !== void 0 ? _b : '';
-            const href = (_c = supplementNode.getAttributeNS(XLINK_NAMESPACE, 'href')) !== null && _c !== void 0 ? _c : '';
+            const supplTitle = (_a = getTrimmedTextContent(supplementNode, 'caption > title')) !== null && _a !== void 0 ? _a : '';
+            const href = (_b = supplementNode.getAttributeNS(XLINK_NAMESPACE, 'href')) !== null && _b !== void 0 ? _b : '';
             const supplementaryMaterial = buildSupplementaryMaterial(supplTitle, href);
-            const mimeType = (_d = supplementNode.getAttribute('mimetype')) !== null && _d !== void 0 ? _d : '';
-            const mimeSubtype = (_e = supplementNode.getAttribute('mime-subtype')) !== null && _e !== void 0 ? _e : '';
+            const mimeType = (_c = supplementNode.getAttribute('mimetype')) !== null && _c !== void 0 ? _c : '';
+            const mimeSubtype = (_d = supplementNode.getAttribute('mime-subtype')) !== null && _d !== void 0 ? _d : '';
             if (mimeType && mimeSubtype) {
                 supplementaryMaterial.MIME = [mimeType, mimeSubtype].join('/');
             }
@@ -133,10 +133,10 @@ export const jatsFrontParser = {
     parseAffiliationNodes(affiliationNodes) {
         const affiliationIDs = new Map();
         const affiliations = affiliationNodes.map((affiliationNode, priority) => {
-            var _a, _b, _c, _d, _e;
+            var _a, _b;
             const affiliation = buildAffiliation('', priority);
             for (const node of affiliationNode.querySelectorAll('institution')) {
-                const content = node.textContent;
+                const content = (_a = node.textContent) === null || _a === void 0 ? void 0 : _a.trim();
                 if (!content) {
                     continue;
                 }
@@ -151,22 +151,25 @@ export const jatsFrontParser = {
                 }
             }
             affiliation.addressLine1 =
-                ((_a = affiliationNode.querySelector('addr-line:nth-of-type(1)')) === null || _a === void 0 ? void 0 : _a.textContent) || undefined;
+                getTrimmedTextContent(affiliationNode, 'addr-line:nth-of-type(1)') ||
+                    undefined;
             affiliation.addressLine2 =
-                ((_b = affiliationNode.querySelector('addr-line:nth-of-type(2)')) === null || _b === void 0 ? void 0 : _b.textContent) || undefined;
+                getTrimmedTextContent(affiliationNode, 'addr-line:nth-of-type(2)') ||
+                    undefined;
             affiliation.addressLine3 =
-                ((_c = affiliationNode.querySelector('addr-line:nth-of-type(3)')) === null || _c === void 0 ? void 0 : _c.textContent) || undefined;
+                getTrimmedTextContent(affiliationNode, 'addr-line:nth-of-type(3)') ||
+                    undefined;
             const emailNode = affiliationNode.querySelector('email');
             if (emailNode) {
                 affiliation.email = {
                     href: emailNode.getAttributeNS(XLINK_NAMESPACE, 'href') || undefined,
-                    text: emailNode.textContent || undefined,
+                    text: ((_b = emailNode.textContent) === null || _b === void 0 ? void 0 : _b.trim()) || undefined,
                 };
             }
             affiliation.postCode =
-                ((_d = affiliationNode.querySelector('postal-code')) === null || _d === void 0 ? void 0 : _d.textContent) || undefined;
+                getTrimmedTextContent(affiliationNode, 'postal-code') || undefined;
             affiliation.country =
-                ((_e = affiliationNode.querySelector('country')) === null || _e === void 0 ? void 0 : _e.textContent) || undefined;
+                getTrimmedTextContent(affiliationNode, 'country') || undefined;
             const id = affiliationNode.getAttribute('id');
             if (id) {
                 affiliationIDs.set(id, affiliation._id);
@@ -196,13 +199,13 @@ export const jatsFrontParser = {
     parseCorrespNodes(correspNodes) {
         const correspondingIDs = new Map();
         const correspondingList = correspNodes.map((correspNode) => {
-            var _a;
+            var _a, _b, _c;
             const label = correspNode.querySelector('label');
             if (label) {
                 label.remove();
             }
-            const corresponding = buildCorresp((_a = correspNode.textContent) !== null && _a !== void 0 ? _a : '');
-            corresponding.label = (label === null || label === void 0 ? void 0 : label.textContent) || undefined;
+            const corresponding = buildCorresp((_b = (_a = correspNode.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 = correspNode.getAttribute('id');
             if (id) {
                 correspondingIDs.set(id, corresponding._id);
@@ -216,13 +219,13 @@ export const jatsFrontParser = {
     },
     parseAuthorNodes(authorNodes, affiliationIDs, footnoteIDs, correspondingIDs) {
         return authorNodes.map((authorNode, priority) => {
-            var _a, _b, _c;
+            var _a, _b;
             const name = buildBibliographicName({});
-            const given = (_a = authorNode.querySelector('name > given-names')) === null || _a === void 0 ? void 0 : _a.textContent;
+            const given = getTrimmedTextContent(authorNode, 'name > given-names');
             if (given) {
                 name.given = given;
             }
-            const surname = (_b = authorNode.querySelector('name > surname')) === null || _b === void 0 ? void 0 : _b.textContent;
+            const surname = getTrimmedTextContent(authorNode, 'name > surname');
             if (surname) {
                 name.family = surname;
             }
@@ -231,7 +234,7 @@ export const jatsFrontParser = {
             if (corresponding) {
                 contributor.isCorresponding = corresponding;
             }
-            const orcid = (_c = authorNode.querySelector('contrib-id[contrib-id-type="orcid"]')) === null || _c === void 0 ? void 0 : _c.textContent;
+            const orcid = getTrimmedTextContent(authorNode, 'contrib-id[contrib-id-type="orcid"]');
             if (orcid) {
                 contributor.ORCIDIdentifier = orcid;
             }
@@ -247,7 +250,7 @@ export const jatsFrontParser = {
                             if (footnoteId) {
                                 const authorFootNoteRef = {
                                     noteID: footnoteId,
-                                    noteLabel: xrefNode.textContent || '',
+                                    noteLabel: ((_a = xrefNode.textContent) === null || _a === void 0 ? void 0 : _a.trim()) || '',
                                 };
                                 contributor.footnote.push(authorFootNoteRef);
                             }
@@ -258,7 +261,7 @@ export const jatsFrontParser = {
                             if (correspId) {
                                 const authorCorrespRef = {
                                     correspID: correspId,
-                                    correspLabel: xrefNode.textContent || '',
+                                    correspLabel: ((_b = xrefNode.textContent) === null || _b === void 0 ? void 0 : _b.trim()) || '',
                                 };
                                 contributor.corresp.push(authorCorrespRef);
                             }

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

@@ -13,12 +13,14 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+import { getTrimmedTextContent } from '../../lib/utils';
 export const parseJournalIdentifiers = (journalMeta) => {
+    var _a, _b;
     const output = [];
     const elements = journalMeta.querySelectorAll('journal-id');
     for (const element of elements) {
         const journalIDType = element.getAttribute('journal-id-type');
-        const journalID = element.textContent;
+        const journalID = (_b = (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim()) !== null && _b !== void 0 ? _b : element.textContent;
         if (journalID !== null && journalIDType != null) {
             output.push({ journalIDType, journalID });
         }
@@ -29,11 +31,12 @@ export const parseJournalIdentifiers = (journalMeta) => {
     return output;
 };
 export const parseJournalAbbreviatedTitles = (journalMeta) => {
+    var _a, _b;
     const output = [];
     const elements = journalMeta.querySelectorAll('journal-title-group > abbrev-journal-title');
     for (const element of elements) {
         const abbrevType = element.getAttribute('abbrev-type');
-        const abbreviatedTitle = element.textContent;
+        const abbreviatedTitle = (_b = (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim()) !== null && _b !== void 0 ? _b : element.textContent;
         if (abbreviatedTitle !== null && abbrevType !== null) {
             output.push({ abbreviatedTitle, abbrevType });
         }
@@ -44,11 +47,12 @@ export const parseJournalAbbreviatedTitles = (journalMeta) => {
     return output;
 };
 export const parseJournalISSNs = (journalMeta) => {
+    var _a, _b;
     const output = [];
     const elements = journalMeta.querySelectorAll('issn');
     for (const element of elements) {
         const publicationType = element.getAttribute('pub-type');
-        const ISSN = element.textContent;
+        const ISSN = (_b = (_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim()) !== null && _b !== void 0 ? _b : element.textContent;
         if (publicationType !== null && ISSN !== null) {
             output.push({ publicationType, ISSN });
         }
@@ -59,12 +63,12 @@ export const parseJournalISSNs = (journalMeta) => {
     return output;
 };
 export const parseJournalMeta = (journalMeta) => {
-    var _a, _b, _c, _d;
+    var _a, _b;
     return {
         abbreviatedTitles: parseJournalAbbreviatedTitles(journalMeta),
         journalIdentifiers: parseJournalIdentifiers(journalMeta),
         ISSNs: parseJournalISSNs(journalMeta),
-        publisherName: (_b = (_a = journalMeta.querySelector('publisher > publisher-name')) === null || _a === void 0 ? void 0 : _a.textContent) !== null && _b !== void 0 ? _b : undefined,
-        title: (_d = (_c = journalMeta.querySelector('journal-title-group > journal-title')) === null || _c === void 0 ? void 0 : _c.textContent) !== null && _d !== void 0 ? _d : undefined,
+        publisherName: (_a = getTrimmedTextContent(journalMeta, 'publisher > publisher-name')) !== null && _a !== void 0 ? _a : undefined,
+        title: (_b = getTrimmedTextContent(journalMeta, 'journal-title-group > journal-title')) !== null && _b !== void 0 ? _b : undefined,
     };
 };

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

@@ -13,6 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+import { getTrimmedTextContent } from '../../lib/utils';
 import { buildAuxiliaryObjectReference, buildBibliographicDate, buildBibliographicName, buildBibliographyItem, buildCitation, } from '../../transformer/builders';
 import { parseProcessingInstruction } from './jats-comments';
 import { flatten, htmlFromJatsNode } from './jats-parser-utils';
@@ -31,7 +32,7 @@ export const jatsReferenceParser = {
         const referenceIDs = new Map();
         const referenceQueries = new Map();
         const references = referenceNodes.map((referenceNode) => {
-            var _a, _b, _c, _d, _e, _f, _g, _h;
+            var _a;
             const publicationType = referenceNode.getAttribute('publication-type');
             const authorNodes = [
                 ...referenceNode.querySelectorAll('person-group[person-group-type="author"] > *'),
@@ -41,7 +42,7 @@ export const jatsReferenceParser = {
             });
             const titleNode = referenceNode.querySelector('article-title');
             if (titleNode) {
-                bibliographyItem.title = htmlFromJatsNode(titleNode, createElement);
+                bibliographyItem.title = (_a = htmlFromJatsNode(titleNode, createElement)) === null || _a === void 0 ? void 0 : _a.trim();
             }
             const queriesText = [];
             const mixedCitation = referenceNode.querySelector('mixed-citation');
@@ -60,63 +61,63 @@ export const jatsReferenceParser = {
             }
             if (authorNodes.length <= 0) {
                 mixedCitation === null || mixedCitation === void 0 ? void 0 : mixedCitation.childNodes.forEach((item) => {
-                    var _a, _b;
+                    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 = (_b = mixedCitation.textContent) !== null && _b !== void 0 ? _b : '';
+                        bibliographyItem.literal = (_c = (_b = mixedCitation.textContent) === null || _b === void 0 ? void 0 : _b.trim()) !== null && _c !== void 0 ? _c : '';
                         return bibliographyItem;
                     }
                 });
             }
-            const source = (_a = referenceNode.querySelector('source')) === null || _a === void 0 ? void 0 : _a.textContent;
+            const source = getTrimmedTextContent(referenceNode, 'source');
             if (source) {
                 bibliographyItem['container-title'] = source;
             }
-            const volume = (_b = referenceNode.querySelector('volume')) === null || _b === void 0 ? void 0 : _b.textContent;
+            const volume = getTrimmedTextContent(referenceNode, 'volume');
             if (volume) {
                 bibliographyItem.volume = volume;
             }
-            const issue = (_c = referenceNode.querySelector('issue')) === null || _c === void 0 ? void 0 : _c.textContent;
+            const issue = getTrimmedTextContent(referenceNode, 'issue');
             if (issue) {
                 bibliographyItem.issue = issue;
             }
-            const supplement = (_d = referenceNode.querySelector('supplement')) === null || _d === void 0 ? void 0 : _d.textContent;
+            const supplement = getTrimmedTextContent(referenceNode, 'supplement');
             if (supplement) {
                 bibliographyItem.supplement = supplement;
             }
-            const fpage = (_e = referenceNode.querySelector('fpage')) === null || _e === void 0 ? void 0 : _e.textContent;
-            const lpage = (_f = referenceNode.querySelector('lpage')) === null || _f === void 0 ? void 0 : _f.textContent;
+            const fpage = getTrimmedTextContent(referenceNode, 'fpage');
+            const lpage = getTrimmedTextContent(referenceNode, 'lpage');
             if (fpage) {
                 bibliographyItem.page = lpage ? `${fpage}-${lpage}` : fpage;
             }
-            const year = (_g = referenceNode.querySelector('year')) === null || _g === void 0 ? void 0 : _g.textContent;
+            const year = getTrimmedTextContent(referenceNode, 'year');
             if (year) {
                 bibliographyItem.issued = buildBibliographicDate({
                     'date-parts': [[year]],
                 });
             }
-            const doi = (_h = referenceNode.querySelector('pub-id[pub-id-type="doi"]')) === null || _h === void 0 ? void 0 : _h.textContent;
+            const doi = getTrimmedTextContent(referenceNode, 'pub-id[pub-id-type="doi"]');
             if (doi) {
                 bibliographyItem.DOI = doi;
             }
             const authors = [];
             authorNodes.forEach((authorNode) => {
-                var _a, _b, _c;
+                var _a;
                 const name = buildBibliographicName({});
-                const given = (_a = authorNode.querySelector('given-names')) === null || _a === void 0 ? void 0 : _a.textContent;
+                const given = getTrimmedTextContent(authorNode, 'given-names');
                 if (given) {
                     name.given = given;
                 }
-                const family = (_b = authorNode.querySelector('surname')) === null || _b === void 0 ? void 0 : _b.textContent;
+                const family = getTrimmedTextContent(authorNode, 'surname');
                 if (family) {
                     name.family = family;
                 }
-                const suffix = (_c = authorNode.querySelector('suffix')) === null || _c === void 0 ? void 0 : _c.textContent;
+                const suffix = getTrimmedTextContent(authorNode, 'suffix');
                 if (suffix) {
                     name.suffix = suffix;
                 }
                 if (authorNode.nodeName === 'collab') {
-                    name.literal = authorNode.textContent;
+                    name.literal = (_a = authorNode.textContent) === null || _a === void 0 ? void 0 : _a.trim();
                 }
                 authors.push(name);
             });

package/dist/es/jats/jats-exporter.js

@@ -25,7 +25,7 @@ import { generateAttachmentFilename } from '../transformer/filename';
 import { buildTargets } from '../transformer/labels';
 import { isExecutableNodeType, isNodeType } from '../transformer/node-types';
 import { hasObjectType } from '../transformer/object-types';
-import { findLatestManuscriptSubmission, findManuscript, findManuscriptById, } from '../transformer/project-bundle';
+import { findManuscript, findManuscriptById, } from '../transformer/project-bundle';
 import { chooseSecType } from '../transformer/section-category';
 import { selectVersionIds } from './jats-versions';
 const warn = debug('manuscripts-transform');
@@ -229,7 +229,6 @@ export class JATSExporter {
         this.buildFront = (doi, id, links) => {
             var _a, _b, _c, _d;
             const manuscript = findManuscript(this.modelMap);
-            const submission = findLatestManuscriptSubmission(this.modelMap, manuscript);
             const front = this.document.createElement('front');
             const journalMeta = this.document.createElement('journal-meta');
             front.appendChild(journalMeta);
@@ -284,29 +283,6 @@ export class JATSExporter {
                     journalMeta.appendChild(publisher);
                 }
             }
-            else {
-                if (submission) {
-                    if (submission.journalCode) {
-                        const journalID = this.document.createElement('journal-id');
-                        journalID.setAttribute('journal-id-type', 'publisher-id');
-                        journalID.textContent = submission.journalCode;
-                        journalMeta.appendChild(journalID);
-                    }
-                    if (submission.journalTitle) {
-                        const journalTitleGroup = this.document.createElement('journal-title-group');
-                        journalMeta.appendChild(journalTitleGroup);
-                        const journalTitle = this.document.createElement('journal-title');
-                        journalTitle.textContent = submission.journalTitle;
-                        journalTitleGroup.appendChild(journalTitle);
-                    }
-                    if (submission.issn) {
-                        const issn = this.document.createElement('issn');
-                        issn.setAttribute('pub-type', 'epub');
-                        issn.textContent = submission.issn;
-                        journalMeta.appendChild(issn);
-                    }
-                }
-            }
             if (id) {
                 const articleID = this.document.createElement('article-id');
                 articleID.setAttribute('pub-id-type', 'publisher-id');

package/dist/es/lib/utils.js

@@ -67,3 +67,10 @@ export const findParentNodeClosestToPos = ($pos, predicate) => {
         }
     }
 };
+export const getTrimmedTextContent = (node, querySelector) => {
+    var _a, _b;
+    if (!node) {
+        return null;
+    }
+    return (_b = (_a = node.querySelector(querySelector)) === null || _a === void 0 ? void 0 : _a.textContent) === null || _b === void 0 ? void 0 : _b.trim();
+};

package/dist/es/transformer/builders.js

@@ -228,10 +228,6 @@ export const buildAttribution = () => ({
     _id: generateID(ObjectTypes.Attribution),
     objectType: ObjectTypes.Attribution,
 });
-export const buildSubmission = () => ({
-    _id: generateID(ObjectTypes.Submission),
-    objectType: ObjectTypes.Submission,
-});
 export const buildJournal = () => ({
     _id: generateID(ObjectTypes.Journal),
     objectType: ObjectTypes.Journal,
@@ -241,12 +237,6 @@ export const buildStatusLabel = (name) => ({
     objectType: ObjectTypes.StatusLabel,
     name,
 });
-export const buildUserFootNote = (noteId, content) => ({
-    _id: generateID(ObjectTypes.UserProfileFootNote),
-    objectType: ObjectTypes.UserProfileFootNote,
-    noteId,
-    content,
-});
 export const auxiliaryObjectTypes = new Set([
     schema.nodes.figure_element,
     schema.nodes.table_element,

package/dist/es/transformer/decode.js

@@ -37,7 +37,7 @@ import { timestamp } from './timestamp';
 const warn = debug('manuscripts-transform');
 const parser = DOMParser.fromSchema(schema);
 export const getModelData = (model) => {
-    const { _rev, _deleted, updatedAt, createdAt, sessionID } = model, data = __rest(model, ["_rev", "_deleted", "updatedAt", "createdAt", "sessionID"]);
+    const { updatedAt, createdAt } = model, data = __rest(model, ["updatedAt", "createdAt"]);
     return data;
 };
 export const getModelsByType = (modelMap, objectType) => {

package/dist/es/transformer/labels.js

@@ -62,6 +62,7 @@ export const buildTargets = (fragment, manuscript) => {
         }
     });
     fragment.descendants((node) => {
+        var _a;
         if (node.type.name in counters) {
             const isInGraphicalAbstract = figures.indexOf(node.attrs.id) > -1;
             if (isInGraphicalAbstract) {
@@ -72,7 +73,7 @@ export const buildTargets = (fragment, manuscript) => {
                 type: node.type.name,
                 id: node.attrs.id,
                 label,
-                caption: node.textContent,
+                caption: (_a = node.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
             });
         }
     });

package/dist/es/transformer/manuscript-dependencies.js

@@ -11,7 +11,7 @@ var __rest = (this && this.__rest) || function (s, e) {
 };
 import { generateID } from './id';
 export const fromPrototype = (model) => {
-    const { _id, _rev } = model, data = __rest(model, ["_id", "_rev"]);
+    const { _id } = model, data = __rest(model, ["_id"]);
     const output = Object.assign(Object.assign({}, data), { prototype: _id, _id: generateID(model.objectType) });
     return output;
 };

package/dist/es/transformer/project-bundle.js

@@ -56,18 +56,6 @@ export const findManuscriptModelByType = (modelMap, manuscript, objectType) => {
         }
     }
 };
-const isSubmission = hasObjectType(ObjectTypes.Submission);
-const newestFirst = (a, b) => b.createdAt - a.createdAt;
-export const findLatestManuscriptSubmission = (modelMap, manuscript) => {
-    const submissions = [];
-    for (const model of modelMap.values()) {
-        if (isSubmission(model) && model.manuscriptID === manuscript._id) {
-            submissions.push(model);
-        }
-    }
-    submissions.sort(newestFirst);
-    return submissions.length ? submissions[0] : undefined;
-};
 export const findManuscriptById = (modelMap, manuscriptID) => {
     const manuscript = modelMap.get(manuscriptID);
     if (manuscript && isManuscript(manuscript)) {

package/dist/types/lib/utils.d.ts

@@ -25,3 +25,4 @@ export declare const findParentNodeClosestToPos: ($pos: ResolvedPos, predicate:
     depth: number;
     node: ProsemirrorNode;
 } | undefined;
+export declare const getTrimmedTextContent: (node: Element | Document, querySelector: string) => string | null | undefined;

package/dist/types/transformer/builders.d.ts

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { Affiliation, Attribution, AuxiliaryObjectReference, BibliographicDate, BibliographicName, BibliographyItem, Citation, CitationItem, Color, CommentAnnotation, Contribution, Contributor, ContributorRole, Corresponding, ElementsOrder, EmbeddedModel, Figure, Footnote, FootnotesOrder, Highlight, HighlightMarker, InlineMathFragment, InlineStyle, Journal, Keyword, KeywordGroup, LibraryCollection, Manuscript, ManuscriptKeyword, ManuscriptNote, ObjectTypes, ParagraphElement, Project, RequirementsValidation, RequirementsValidationData, Section, StatusLabel, Submission, Supplement, UserProfileAffiliation, UserProfileFootNote } from '@manuscripts/json-schema';
+import { Affiliation, Attribution, AuxiliaryObjectReference, BibliographicDate, BibliographicName, BibliographyItem, Citation, CitationItem, Color, CommentAnnotation, Contribution, Contributor, ContributorRole, Corresponding, ElementsOrder, EmbeddedModel, Figure, Footnote, FootnotesOrder, Highlight, HighlightMarker, InlineMathFragment, InlineStyle, Journal, Keyword, KeywordGroup, LibraryCollection, Manuscript, ManuscriptKeyword, ManuscriptNote, ObjectTypes, ParagraphElement, Project, RequirementsValidation, RequirementsValidationData, Section, StatusLabel, Supplement, UserProfileAffiliation } from '@manuscripts/json-schema';
 import { FootnotesOrderIndexList } from './footnotes-order';
 import { CommentSelector, ManuscriptModel, ModelAttachment } from './models';
 export declare const DEFAULT_BUNDLE = "MPBundle:www-zotero-org-styles-nature";
@@ -65,10 +65,8 @@ export declare const buildContribution: (profileID: string) => Contribution;
 export declare const buildContributorRole: (name: string) => Build<ContributorRole>;
 export declare const buildInlineStyle: (priority: number, title?: string) => Build<InlineStyle>;
 export declare const buildAttribution: () => Build<Attribution>;
-export declare const buildSubmission: () => Build<Submission>;
 export declare const buildJournal: () => Build<Journal>;
 export declare const buildStatusLabel: (name: string) => Build<StatusLabel>;
-export declare const buildUserFootNote: (noteId: string, content: string) => Build<UserProfileFootNote>;
 export type AuxiliaryObjects = 'MPFigureElement' | 'MPTableElement' | 'MPListingElement' | 'MPEquationElement';
 export declare const auxiliaryObjectTypes: Set<import("prosemirror-model").NodeType>;
 export declare const buildElementsOrder: (elementType: AuxiliaryObjects) => Build<ElementsOrder>;

package/dist/types/transformer/project-bundle.d.ts

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { Journal, Manuscript, Model, ObjectTypes, Submission } from '@manuscripts/json-schema';
+import { Journal, Manuscript, Model, ObjectTypes } from '@manuscripts/json-schema';
 import { ManuscriptModel } from './models';
 export interface ProjectBundle {
     version: string;
@@ -26,5 +26,4 @@ export declare const parseProjectBundle: (projectBundle: ProjectBundle, manuscri
 export declare const findManuscript: (modelMap: Map<string, Model>) => Manuscript;
 export declare const findJournal: (modelMap: Map<string, Model>) => Journal | null;
 export declare const findManuscriptModelByType: <T extends ManuscriptModel>(modelMap: Map<string, Model>, manuscript: Manuscript, objectType: ObjectTypes) => T | undefined;
-export declare const findLatestManuscriptSubmission: (modelMap: Map<string, Model>, manuscript: Manuscript) => Submission | undefined;
 export declare const findManuscriptById: (modelMap: Map<string, Model>, manuscriptID: string) => Manuscript;

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "1.3.2",
+  "version": "1.3.4-LEAN-2501-test",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",
@@ -29,7 +29,7 @@
     "version": "yarn build"
   },
   "dependencies": {
-    "@manuscripts/json-schema": "^2.0.2",
+    "@manuscripts/json-schema": "^2.1.0",
     "debug": "^4.3.4",
     "jszip": "^3.10.1",
     "mathjax-full": "^3.2.2",