@manuscripts/transform 1.0.0

package/LICENSE

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package/README.md

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+# @manuscripts/manuscript-transform
+
+ProseMirror transformer for Manuscripts applications.
+
+It provides a way to import/export [Manuscript JSON Schema](https://gitlab.com/mpapp-public/manuscripts-json-schema) formatted data from and to other formats such as (JATS XML, STS XML, HTML, [ProseMirror Model](https://prosemirror.net/docs/guide/#doc))
+
+# Components 
+
+**Decoder**: converts Manuscript JSON Schema to ProseMirror Model.
+
+**Encoder**: converts ProseMirror Model to Manuscript JSON Schema.
+
+**ManuscriptNode**: a Manuscript definition of a ProseMirror Node which hold a ProseMirror fragment containing zero or more child nodes, for example a section node or a figure node.
+
+**ManuscriptFragment**:  a Manuscript definition of a ProseMirror Fragment represents a node's collection of child nodes.
+
+**ManuscriptMark**:  a Manuscript definition of a ProseMirror mark which is a piece of information that can be attached to a node, such as it being emphasized, in code font, or a link
+
+**JATSExporter**: converts Manuscript JSON Schema to JATS XML via ProseMirror Model.
+
+**JATSImporter** converts JATS XML to Manuscript JSON Schema via ProseMirror Model.
+
+# Usage
+
+### Manuscript JSON Schema to ProseMirror Model
+
+```typescript
+import { Decoder, ContainedModel } from '@manuscripts/manuscript-transform'
+
+
+// Data from Manuscript JSON Schema file
+const data: ContainedModel[]
+const modelMap = new Map<string, ContainedModel>(
+  data.map((model) => [model._id, model])
+)
+const decoder = new Decoder(modelMap)
+// manuscriptID =>  The ID for the manuscript data can be found in MPManuscript Model
+const manuscriptNode = decoder.createArticleNode(manuscriptID)
+```    
+
+### ProseMirror Model to Manuscript JSON Schema
+
+```typescript
+import { encode } from '@manuscripts/manuscript-transform'
+
+const manuscriptNode: ManuscriptNode
+const result = encode(manuscriptNode)
+```
+
+### Manuscript JSON Schema to JATS XML
+
+```typescript
+import {
+  ContainedModel,
+  JATSExporter,
+  JATSExporterOptions,
+  ManuscriptFragment,
+} from '@manuscripts/manuscript-transform'
+
+// Data from Manuscript JSON Schema file
+const data: ContainedModel[]
+const modelMap = new Map<string, ContainedModel>(
+  data.map((model) => [model._id, model])
+)
+const decoder = new Decoder(modelMap)
+// manuscriptID =>  The ID for the manuscript data can be found in MPManuscript Model
+const manuscriptNode = decoder.createArticleNode(manuscriptID)
+
+const options: JATSExporterOptions   
+const result = new JATSExporter().serializeToJATS(manuscriptNode.content, modelMap, manuscriptID, options)
+```
+
+#### JATSExporterOptions
+
+**version**: JATS output version, supported versions ('1.1' , '1.2d1' , '1.2')\
+**doi**: DOI of the article\
+**id**: article id\
+**frontMatterOnly**: to export article front only
+
+### JATS XML to Manuscript JSON Schema
+
+```typescript
+import { parseJATSArticle } from '@manuscripts/manuscript-transform'
+
+// JATS XML document
+const doc: Document
+const result = await parseJATSArticle(doc)
+```
+
+## ProseMirror Schema 
+
+As mentioned in ProseMirror [documentation](https://prosemirror.net/docs/ref/#model.Document_Schema) the schema defined as 
+>Every ProseMirror document conforms to a schema, which describes the set of nodes and marks that it is made out of, 
+along with the relations between those, such as which node may occur as a child node of which other nodes. 
+
+You can find the definition of the schema in **/schema** folder where it is constructed form a set of nodes and marks
+
+### ProseMirror Node 
+
+>This class represents a node in the tree that makes up a ProseMirror document. So a document is an instance of Node, with children that are also instances of Node.
+
+Please check [Node class](https://prosemirror.net/docs/ref/#model.Node) documentation to know more about its attributes and methods
+
+Let's take **figure** node as an example
+
+```typescript
+export const figure: NodeSpec = {
+    content: 'figcaption* paragraph* attribution*',
+   // ...
+   // ...
+```
+
+The content attribute here describe the children of this node, a figure can have captions, paragraphs and attributions and each 
+of these nodes can also have their own content 
+
+```typescript
+ export const figure: NodeSpec = {
+ // ...
+ // ...
+  attrs: {
+    id: { default: '' },
+    originalURL: { default: undefined },
+ ```   
+     
+attrs describe the attributes that can this figure node have for example an ID or a URL        
+  
+```typescript
+toDOM: (node) => {}
+```
+
+ this function defines the default way of the figure node to be serialized to DOM/HTML, the return type is a DOM node or an array structure that describes one, with an optional number zero (“hole”) in it to indicate where the node's content should be inserted.
+
+
+### ProseMirror Mark
+
+>mark is a piece of information that can be attached to a node, such as it being emphasized, in code font, or a link. It has a type and optionally a set of attributes that provide further information (such as the target of the link). 
+>Marks are created through a Schema, which controls which types exist and which attributes they have.
+
+Please check [Mark class](https://prosemirror.net/docs/ref/#model.Mark) documentation to know more about its attributes and methods
+
+Let's take italic mark as an example 
+
+```typescript
+export const italic: MarkSpec = {
+  parseDOM: [{ tag: 'i' }, { tag: 'em' }, { style: 'font-style=italic' }],
+  toDOM: () => ['i'],
+}
+```
+
+parseDOM here define how to deserialize this mark from DOM, for example an **em** tag will be parsed to this italic mark 
+
+## Deserialize JATS to ProseMirror 
+
+in **jats-body-dom-parser.ts** file you can find the rules of how the parser can deserialize JATS XML tags into ProseMirror nodes
+
+for example to map **sec** JATS tag to ProseMirror section node 
+
+```typescript
+      {
+        tag: 'sec',
+        node: 'section',
+        getAttrs: (node) => {
+          const element = node as HTMLElement
+    
+          return {
+            id: element.getAttribute('id'),
+            category: chooseSectionCategory(element),
+          }
+        },
+      },
+```
+
+getAttrs function here extract the attributes of the **sec** tag and map them into section node attributes
+
+## Serialize ProseMirror nodes to JATS XML
+
+in **jats-exporter.ts** file you can find the serialization rules defined in **createSerializer** method
+
+section node to sec tag
+
+```typescript
+section: (node) => {
+  const attrs: { [key: string]: string } = {
+    id: normalizeID(node.attrs.id),
+  }
+
+  if (node.attrs.category) {
+    attrs['sec-type'] = chooseSecType(node.attrs.category)
+  }
+
+  return ['sec', attrs, 0]
+}
+```

package/dist/cjs/errors.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.InvalidInput = exports.MissingElement = void 0;
+class MissingElement extends Error {
+    constructor(elementID) {
+        super(`${elementID} not found in the manuscripts data`);
+        this.name = 'MissingElement';
+    }
+}
+exports.MissingElement = MissingElement;
+class InvalidInput extends Error {
+    constructor(message) {
+        super(message);
+        this.name = 'InvalidInput';
+    }
+}
+exports.InvalidInput = InvalidInput;

package/dist/cjs/index.js

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+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+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.isSectionLabelNode = void 0;
+__exportStar(require("./lib/table-cell-styles"), exports);
+__exportStar(require("./lib/utils"), exports);
+__exportStar(require("./mathjax"), exports);
+__exportStar(require("./schema"), exports);
+__exportStar(require("./transformer"), exports);
+__exportStar(require("./jats"), exports);
+__exportStar(require("./types"), exports);
+__exportStar(require("./errors"), exports);
+var section_label_1 = require("./schema/nodes/section_label");
+Object.defineProperty(exports, "isSectionLabelNode", { enumerable: true, get: function () { return section_label_1.isSectionLabelNode; } });

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

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+"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.getElementsOrder = exports.parseJATSArticle = exports.parseJATSReferences = exports.parseJATSBody = exports.parseJATSFront = void 0;
+var parse_jats_article_1 = require("./parse-jats-article");
+Object.defineProperty(exports, "parseJATSFront", { enumerable: true, get: function () { return parse_jats_article_1.parseJATSFront; } });
+Object.defineProperty(exports, "parseJATSBody", { enumerable: true, get: function () { return parse_jats_article_1.parseJATSBody; } });
+Object.defineProperty(exports, "parseJATSReferences", { enumerable: true, get: function () { return parse_jats_article_1.parseJATSReferences; } });
+Object.defineProperty(exports, "parseJATSArticle", { enumerable: true, get: function () { return parse_jats_article_1.parseJATSArticle; } });
+Object.defineProperty(exports, "getElementsOrder", { enumerable: true, get: function () { return parse_jats_article_1.getElementsOrder; } });