@manuscripts/transform 2.3.38-LEAN-3911.0 → 2.6.0

package/dist/cjs/transformer/index.js

@@ -29,8 +29,26 @@ var __exportStar = (this && this.__exportStar) || function(m, exports) {
     for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.createTestDoc = void 0;
+__exportStar(require("./builders"), exports);
+__exportStar(require("./decode"), exports);
+__exportStar(require("./document-object-types"), exports);
+__exportStar(require("./encode"), exports);
+__exportStar(require("./filename"), exports);
+__exportStar(require("./highlight-markers"), exports);
+__exportStar(require("./html"), exports);
 __exportStar(require("./id"), exports);
+__exportStar(require("./labels"), exports);
+__exportStar(require("./manuscript-dependencies"), exports);
+__exportStar(require("./models"), exports);
 __exportStar(require("./node-names"), exports);
 __exportStar(require("./node-title"), exports);
 __exportStar(require("./node-types"), exports);
+__exportStar(require("./object-types"), exports);
+__exportStar(require("./project-bundle"), exports);
 __exportStar(require("./section-category"), exports);
+__exportStar(require("./serializer"), exports);
+__exportStar(require("./timestamp"), exports);
+__exportStar(require("./update-identifiers"), exports);
+var doc_1 = require("./__tests__/__helpers__/doc");
+Object.defineProperty(exports, "createTestDoc", { enumerable: true, get: function () { return doc_1.createTestDoc; } });

package/dist/cjs/{jats/exporter → transformer}/labels.js

@@ -16,19 +16,20 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.buildTargets = void 0;
-const schema_1 = require("../../schema");
-const node_names_1 = require("../../transformer/node-names");
+const schema_1 = require("../schema");
+const node_names_1 = require("./node-names");
 const labelledNodeTypes = [
     schema_1.schema.nodes.figure_element,
     schema_1.schema.nodes.table_element,
     schema_1.schema.nodes.equation_element,
     schema_1.schema.nodes.listing_element,
+    schema_1.schema.nodes.box_element,
 ];
 const excludedTypes = [schema_1.schema.nodes.graphical_abstract_section];
 const chooseLabel = (nodeType) => {
     return node_names_1.nodeNames.get(nodeType);
 };
-const buildTargets = (node) => {
+const buildTargets = (fragment) => {
     const counters = {};
     for (const nodeType of labelledNodeTypes) {
         counters[nodeType.name] = {
@@ -42,7 +43,7 @@ const buildTargets = (node) => {
         return `${counter.label} ${counter.index}`;
     };
     const targets = new Map();
-    node.descendants((node, pos, parent) => {
+    fragment.descendants((node, pos, parent) => {
         var _a;
         if (node.type.name in counters) {
             if (parent && excludedTypes.includes(parent.type)) {

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

@@ -0,0 +1,21 @@
+"use strict";
+var __rest = (this && this.__rest) || function (s, e) {
+    var t = {};
+    for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)
+        t[p] = s[p];
+    if (s != null && typeof Object.getOwnPropertySymbols === "function")
+        for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {
+            if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))
+                t[p[i]] = s[p[i]];
+        }
+    return t;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.fromPrototype = void 0;
+const id_1 = require("./id");
+const fromPrototype = (model) => {
+    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;
+};
+exports.fromPrototype = fromPrototype;

package/dist/cjs/transformer/model-map.js

@@ -0,0 +1,26 @@
+"use strict";
+/*!
+ * © 2020 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.addModelToMap = void 0;
+const id_1 = require("./id");
+const addModelToMap = (modelMap) => (data) => {
+    if (!data._id) {
+        data._id = (0, id_1.generateID)(data.objectType);
+    }
+    modelMap.set(data._id, data);
+};
+exports.addModelToMap = addModelToMap;

package/dist/cjs/{lib/deafults.js → transformer/models.js}

@@ -1,6 +1,6 @@
 "use strict";
 /*!
- * © 2024 Atypon Systems LLC
+ * © 2019 Atypon Systems LLC
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -15,5 +15,3 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.defaultTitle = void 0;
-exports.defaultTitle = 'Untitled Manuscript';

package/dist/cjs/transformer/node-names.js

@@ -39,4 +39,5 @@ exports.nodeNames = new Map([
     [schema_1.schema.nodes.pullquote_element, 'Pull Quote'],
     [schema_1.schema.nodes.keywords, 'Section'],
     [schema_1.schema.nodes.toc_section, 'Section'],
+    [schema_1.schema.nodes.box_element, 'Box'],
 ]);

package/dist/cjs/transformer/object-types.js

@@ -0,0 +1,57 @@
+"use strict";
+/*!
+ * © 2019 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.isKeyword = exports.isCommentAnnotation = exports.isTable = exports.isManuscript = exports.isFigure = exports.hasObjectType = exports.isManuscriptModel = exports.manuscriptObjects = exports.elementObjects = exports.ExtraObjectTypes = void 0;
+const json_schema_1 = require("@manuscripts/json-schema");
+var ExtraObjectTypes;
+(function (ExtraObjectTypes) {
+    ExtraObjectTypes["PlaceholderElement"] = "MPPlaceholderElement";
+    ExtraObjectTypes["GeneralTableFootnote"] = "MPGeneralTableFootnote";
+})(ExtraObjectTypes = exports.ExtraObjectTypes || (exports.ExtraObjectTypes = {}));
+exports.elementObjects = [
+    json_schema_1.ObjectTypes.BibliographyElement,
+    json_schema_1.ObjectTypes.EquationElement,
+    json_schema_1.ObjectTypes.FigureElement,
+    json_schema_1.ObjectTypes.FootnotesElement,
+    json_schema_1.ObjectTypes.ListElement,
+    json_schema_1.ObjectTypes.ListingElement,
+    json_schema_1.ObjectTypes.ParagraphElement,
+    json_schema_1.ObjectTypes.TableElement,
+    json_schema_1.ObjectTypes.TOCElement,
+];
+exports.manuscriptObjects = [
+    json_schema_1.ObjectTypes.Affiliation,
+    json_schema_1.ObjectTypes.Citation,
+    json_schema_1.ObjectTypes.CommentAnnotation,
+    json_schema_1.ObjectTypes.Contributor,
+    json_schema_1.ObjectTypes.Footnote,
+    json_schema_1.ObjectTypes.Section,
+].concat(exports.elementObjects);
+const isManuscriptModel = (model) => {
+    if (!model.objectType) {
+        throw new Error('Model must have objectType');
+    }
+    return json_schema_1.manuscriptIDTypes.has(model.objectType);
+};
+exports.isManuscriptModel = isManuscriptModel;
+const hasObjectType = (objectType) => (model) => model.objectType === objectType;
+exports.hasObjectType = hasObjectType;
+exports.isFigure = (0, exports.hasObjectType)(json_schema_1.ObjectTypes.Figure);
+exports.isManuscript = (0, exports.hasObjectType)(json_schema_1.ObjectTypes.Manuscript);
+exports.isTable = (0, exports.hasObjectType)(json_schema_1.ObjectTypes.Table);
+exports.isCommentAnnotation = (0, exports.hasObjectType)(json_schema_1.ObjectTypes.CommentAnnotation);
+exports.isKeyword = (0, exports.hasObjectType)(json_schema_1.ObjectTypes.Keyword);

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

@@ -0,0 +1,94 @@
+"use strict";
+/*!
+ * © 2019 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.findTitles = 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");
+const parseProjectBundle = (projectBundle, manuscriptID) => {
+    const manuscriptData = manuscriptID
+        ? projectBundle.data.filter((doc) => !doc.manuscriptID || doc.manuscriptID === manuscriptID)
+        : projectBundle.data;
+    const modelMap = new Map();
+    for (const component of manuscriptData) {
+        modelMap.set(component._id, component);
+    }
+    const decoder = new decode_1.Decoder(modelMap);
+    const doc = decoder.createArticleNode();
+    return { doc, modelMap };
+};
+exports.parseProjectBundle = parseProjectBundle;
+const isManuscript = (0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.Manuscript);
+const findManuscript = (modelMap) => {
+    for (const model of modelMap.values()) {
+        if (isManuscript(model)) {
+            return model;
+        }
+    }
+    throw new Error('No manuscript found');
+};
+exports.findManuscript = findManuscript;
+const isJournal = (0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.Journal);
+const findJournal = (modelMap) => {
+    for (const model of modelMap.values()) {
+        if (isJournal(model)) {
+            return model;
+        }
+    }
+    return null;
+};
+exports.findJournal = findJournal;
+const isManuscriptModel = (model) => 'manuscriptID' in model;
+const findManuscriptModelByType = (modelMap, manuscript, objectType) => {
+    for (const model of modelMap.values()) {
+        if (model.objectType === objectType &&
+            isManuscriptModel(model) &&
+            manuscript._id === model.manuscriptID) {
+            return model;
+        }
+    }
+};
+exports.findManuscriptModelByType = findManuscriptModelByType;
+const findManuscriptById = (modelMap, manuscriptID) => {
+    const manuscript = modelMap.get(manuscriptID);
+    if (manuscript && isManuscript(manuscript)) {
+        return manuscript;
+    }
+    throw new Error(`There is no manuscript found for the following _id (${manuscriptID})`);
+};
+exports.findManuscriptById = findManuscriptById;
+const isTitle = (0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.Titles);
+const findTitles = (modelMap) => {
+    for (const model of modelMap.values()) {
+        if (isTitle(model)) {
+            return model;
+        }
+    }
+    const defaultTitle = {
+        _id: 'MPTitles:8EB79C14-9F61-483A-902F-A0B8EF5973C1',
+        createdAt: 1538472121.690101,
+        updatedAt: 1538472121.690101,
+        objectType: 'MPTitles',
+        title: 'main title',
+        subtitle: 'subtitle',
+        runningTitle: 'running title',
+        manuscriptID: 'MPManuscript:E3830344-E77B-42BA-BD77-3E95489712A0',
+        containerID: 'MPProject:1',
+    };
+    return defaultTitle;
+};
+exports.findTitles = findTitles;

package/dist/cjs/transformer/serializer.js

@@ -0,0 +1,23 @@
+"use strict";
+/*!
+ * © 2019 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.xmlSerializer = void 0;
+const w3c_xmlserializer_1 = __importDefault(require("w3c-xmlserializer"));
+exports.xmlSerializer = { serializeToString: w3c_xmlserializer_1.default };

package/dist/cjs/transformer/timestamp.js

@@ -0,0 +1,20 @@
+"use strict";
+/*!
+ * © 2019 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.timestamp = void 0;
+const timestamp = () => Math.floor(Date.now() / 1000);
+exports.timestamp = timestamp;

package/dist/cjs/transformer/update-identifiers.js

@@ -0,0 +1,93 @@
+"use strict";
+/*!
+ * © 2020 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.updateAttachments = exports.updateAttachmentPath = exports.updateIdentifiers = void 0;
+const id_1 = require("./id");
+const updateIdentifiers = async (data) => {
+    const idMap = new Map();
+    const updateIDs = (model) => {
+        const { _id, objectType } = model;
+        if (!objectType || !_id || !_id.match(/^MP.+:.+/)) {
+            return;
+        }
+        if (idMap.has(_id)) {
+            model._id = idMap.get(_id);
+        }
+        else {
+            model._id = (0, id_1.generateID)(objectType);
+            idMap.set(_id, model._id);
+        }
+        for (const value of Object.values(model)) {
+            if (Array.isArray(value)) {
+                value.forEach(updateIDs);
+            }
+            else {
+                updateIDs(value);
+            }
+        }
+    };
+    const replaceContent = (content) => {
+        content = content.replace(/MP\w+:[\w-]+/g, (match) => {
+            const value = idMap.get(match);
+            return value !== null && value !== void 0 ? value : match;
+        });
+        content = content.replace(/MP\w+_[\w-]+/g, (match) => {
+            const value = idMap.get(match.replace('_', ':'));
+            return value ? value.replace(':', '_') : match;
+        });
+        return content;
+    };
+    const updateContent = (model) => {
+        for (const [key, value] of Object.entries(model)) {
+            if (typeof value === 'object') {
+                updateContent(value);
+            }
+            else if (typeof value === 'string') {
+                model[key] = replaceContent(value);
+            }
+        }
+    };
+    for (const item of data) {
+        updateIDs(item);
+    }
+    for (const item of data) {
+        updateContent(item);
+    }
+    return { data, idMap };
+};
+exports.updateIdentifiers = updateIdentifiers;
+const updateAttachmentPath = (oldPath, idMap) => {
+    const matches = oldPath.match(/^Data\/([^.]+)(.*)/);
+    if (matches) {
+        const [, prefix, suffix] = matches;
+        const id = idMap.get(prefix.replace('_', ':'));
+        if (id) {
+            const newPrefix = id.replace(':', '_');
+            return `Data/${newPrefix}${suffix}`;
+        }
+    }
+};
+exports.updateAttachmentPath = updateAttachmentPath;
+const updateAttachments = async (zip, idMap) => {
+    for (const [oldPath, entry] of Object.entries(zip.files)) {
+        const newPath = (0, exports.updateAttachmentPath)(oldPath, idMap);
+        if (newPath) {
+            zip.file(newPath, await entry.async('blob')).remove(oldPath);
+        }
+    }
+};
+exports.updateAttachments = updateAttachments;

package/dist/cjs/version.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.VERSION = void 0;
-exports.VERSION = "2.3.38-LEAN-3911.0";
+exports.VERSION = "2.6.0";