@manuscripts/transform 4.3.53 → 4.4.1

package/src/jats/exporter/jats-versions.ts

@@ -0,0 +1,50 @@
+/*!
+ * © 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.
+ */
+
+interface VersionIds {
+  publicId: string
+  systemId: string
+}
+
+export type Version = '1.1' | '1.2d1' | '1.2'
+
+const versions: { [key in Version]: VersionIds } = {
+  '1.1': {
+    publicId:
+      '-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.1 20151215//EN',
+    systemId:
+      'http://jats.nlm.nih.gov/archiving/1.1/JATS-archive-oasis-article1-mathml3.dtd',
+  },
+  '1.2d1': {
+    publicId:
+      '-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.2d1 20170631//EN',
+    systemId:
+      'http://jats.nlm.nih.gov/archiving/1.2d1/JATS-archive-oasis-article1-mathml3.dtd',
+  },
+  '1.2': {
+    publicId:
+      '-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.2 20190208//EN',
+    systemId:
+      'http://jats.nlm.nih.gov/archiving/1.2/JATS-archive-oasis-article1-mathml3.dtd',
+  },
+}
+
+export const selectVersionIds = (version: Version): VersionIds => {
+  if (!(version in versions)) {
+    throw new Error(`Unknown version ${version}`)
+  }
+  return versions[version]
+}

package/src/jats/exporter/labels.ts

@@ -0,0 +1,101 @@
+/*!
+ * © 2020 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import { ManuscriptNode, ManuscriptNodeType, schema } from '../../schema'
+import { nodeNames } from '../../transformer/node-names'
+
+export interface Target {
+  type: string
+  id: string
+  label: string
+  caption: string
+}
+
+interface Counter {
+  label: string
+  index: number
+}
+
+interface Counters {
+  [key: string]: Counter
+}
+
+const labelledNodeTypes: ManuscriptNodeType[] = [
+  schema.nodes.figure_element,
+  schema.nodes.table_element,
+  schema.nodes.equation_element,
+  schema.nodes.listing_element,
+  schema.nodes.box_element,
+  schema.nodes.embed,
+  schema.nodes.image_element,
+]
+
+const excludedTypes = [schema.nodes.graphical_abstract_section]
+
+const chooseLabel = (nodeType: ManuscriptNodeType): string => {
+  return nodeNames.get(nodeType) as string
+}
+
+type iterator = (
+  node: ManuscriptNode,
+  pos: number,
+  parent: ManuscriptNode | null,
+  index: number
+) => void | boolean
+
+export const buildTargets = (
+  iterator: (fn: iterator) => void
+): Map<string, Target> => {
+  const counters: Counters = {}
+
+  for (const nodeType of labelledNodeTypes) {
+    counters[nodeType.name] = {
+      label: chooseLabel(nodeType), // choosing label name: "Figure", "Table", etc.
+      index: 0, // TODO: use manuscript.figureElementNumberingScheme
+    }
+  }
+
+  const buildLabel = (type: ManuscriptNodeType) => {
+    const counter = counters[type.name]
+    counter.index++
+    return `${counter.label} ${counter.index}`
+  }
+
+  const targets: Map<string, Target> = new Map()
+
+  iterator((node, pos, parent) => {
+    if (node.type.name in counters) {
+      if (parent && excludedTypes.includes(parent.type)) {
+        return
+      }
+      if (node.type === schema.nodes.box_element) {
+        const child = node.firstChild
+        if (!child || child.type !== schema.nodes.caption_title) {
+          return
+        }
+      }
+      const label = buildLabel(node.type)
+
+      targets.set(node.attrs.id, {
+        type: node.type.name,
+        id: node.attrs.id,
+        label,
+        caption: node.textContent?.trim(), // TODO: HTML?
+      })
+    }
+  })
+  return targets
+}

package/src/jats/importer/create-article-node.ts

@@ -0,0 +1,52 @@
+/*!
+ * © 2024 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import { ManuscriptAttrs, ManuscriptNode, schema } from '../../schema'
+import { generateNodeID } from '../../transformer'
+
+export const createArticleNode = (
+  attrs: Partial<ManuscriptAttrs> & { id: string }
+): ManuscriptNode => {
+  const title = schema.nodes.title.createChecked({
+    id: generateNodeID(schema.nodes.title),
+  })
+  const abstracts = schema.nodes.abstracts.createChecked({
+    id: generateNodeID(schema.nodes.abstracts),
+  })
+  const paragraph = schema.nodes.paragraph.createChecked({
+    id: generateNodeID(schema.nodes.paragraph),
+  })
+  const body = schema.nodes.body.createChecked(
+    {
+      id: generateNodeID(schema.nodes.body),
+    },
+    paragraph
+  )
+  const backmatter = schema.nodes.backmatter.createChecked({
+    id: generateNodeID(schema.nodes.backmatter),
+  })
+  const comments = schema.nodes.comments.createChecked({
+    id: generateNodeID(schema.nodes.comments),
+  })
+
+  return schema.nodes.manuscript.createChecked(attrs, [
+    title,
+    abstracts,
+    body,
+    backmatter,
+    comments,
+  ])
+}

package/src/jats/importer/jats-comments.ts

@@ -0,0 +1,111 @@
+/*!
+ * © 2020 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import { v4 as uuid } from 'uuid'
+
+import { schema } from '../../schema'
+import { generateNodeID } from '../../transformer'
+
+export const DEFAULT_PROFILE_ID =
+  'MPUserProfile:0000000000000000000000000000000000000001'
+
+const isJATSComment = (node: Node) => {
+  return (
+    node.nodeType === node.PROCESSING_INSTRUCTION_NODE &&
+    node.nodeName === 'AuthorQuery'
+  )
+}
+
+const parseJATSComment = (node: Node): string | undefined => {
+  const text = node.textContent
+  if (text) {
+    const queryText = /queryText="(.+)"/.exec(text)
+    return (queryText && queryText[1]) || undefined
+  }
+}
+
+const isHighlightable = (node: Element) => {
+  //todo find a better way to do this
+  return node.nodeName === 'p'
+}
+
+const findTarget = (node: Element) => {
+  const target = node.closest('ref, kwd-group')
+  if (target) {
+    return target
+  }
+  return node
+}
+
+export const markComments = (doc: Document) => {
+  const root = doc.getRootNode() as Element
+  const queue: Element[] = [root]
+  const comments = doc.createElement('comments')
+  while (queue.length !== 0) {
+    const node = queue.shift()
+    if (node) {
+      if (isJATSComment(node)) {
+        const text = parseJATSComment(node)
+        if (text) {
+          const id = generateNodeID(schema.nodes.comment)
+          let target
+          const parent = node.parentNode as Element
+          if (isHighlightable(parent)) {
+            const marker = createHighlightMarkerElement(doc, id)
+            parent.insertBefore(marker, node)
+            target = parent
+          } else {
+            target = findTarget(parent)
+          }
+          // if the target has no ID, generate one here and rely on
+          // updateDocumentIDs to fix it
+          if (!target.id) {
+            target.id = uuid()
+          }
+          const comment = createCommentElement(doc, id, target.id, text)
+          comments.appendChild(comment)
+        }
+      }
+      node.childNodes.forEach((child) => {
+        queue.push(child as Element)
+      })
+    }
+  }
+
+  doc.documentElement.appendChild(comments)
+}
+
+const createHighlightMarkerElement = (doc: Document, id: string) => {
+  const highlightMarker = doc.createElement('highlight-marker')
+  highlightMarker.setAttribute('id', id)
+  highlightMarker.setAttribute('position', 'point')
+  return highlightMarker
+}
+
+const createCommentElement = (
+  doc: Document,
+  id: string,
+  targetID: string | undefined,
+  text: string
+) => {
+  const commentElement = doc.createElement('comment')
+  commentElement.setAttribute('id', id)
+  if (targetID) {
+    commentElement.setAttribute('target-id', targetID)
+  }
+  commentElement.textContent = text
+  return commentElement
+}