@manuscripts/body-editor 3.12.66 → 3.13.0

package/src/lib/copy.ts

@@ -0,0 +1,30 @@
+/*!
+ * © 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 { Slice } from 'prosemirror-model'
+
+// TODO: checking the ability to remove the following logic, after the following ticket LEAN-4118 is resolved
+export const transformCopied = (slice: Slice) => {
+  if (
+    slice.openStart !== slice.openEnd &&
+    (slice.content.firstChild?.type.isBlock ||
+      slice.content.lastChild?.type.isBlock)
+  ) {
+    const cutDepth = Math.min(slice.openStart, slice.openEnd)
+    // rebalance slice sides to be digestible for track changes plugin
+    return new Slice(slice.content, cutDepth, cutDepth)
+  }
+  return slice
+}

package/src/lib/crossref.ts

@@ -0,0 +1,90 @@
+/*!
+ * © 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.
+ */
+
+import { generateNodeID, schema } from '@manuscripts/transform'
+
+import {
+  BibliographyItemSearch,
+  BibliographyItemSource,
+} from '../components/references/BibliographyItemSource'
+
+type CrossrefItem = {
+  [key: string]: unknown
+}
+
+type CrossrefResponse = {
+  message: {
+    items: CrossrefItem[]
+    'total-results': number
+  }
+}
+
+const search = (query: string, limit: number): BibliographyItemSearch => {
+  const controller = new AbortController()
+  const params = new URLSearchParams({
+    filter: 'type:journal-article',
+    query,
+    rows: String(limit),
+  })
+
+  const promise = searchAsync(params, controller)
+
+  return new BibliographyItemSearch((resolve, reject) => {
+    promise.then(resolve).catch(reject)
+  }, controller)
+}
+
+const searchAsync = async (
+  params: URLSearchParams,
+  controller: AbortController
+) => {
+  const response = await fetch(`https://api.crossref.org/works?${params}`, {
+    signal: controller.signal,
+  })
+
+  if (!response.ok) {
+    throw new Error('There was a problem searching for this query.')
+  }
+  const data = (await response.json()) as CrossrefResponse
+  const items = data.message.items.map(fixItem)
+  const total = data.message['total-results']
+
+  return {
+    items,
+    total,
+  }
+}
+
+export const Crossref: BibliographyItemSource = {
+  id: 'crossref',
+  label: 'External sources',
+  search,
+}
+
+const fixItem = (item: CrossrefItem): CSL.Data => {
+  for (const key in item) {
+    if (key === 'author' || key === 'editor') {
+      continue
+    }
+    const value = item[key]
+    if (Array.isArray(value)) {
+      const [data] = item[key] as string[]
+      item[key] = data || undefined
+    }
+  }
+  item.id = generateNodeID(schema.nodes.bibliography_item)
+  return item as CSL.Data
+}

package/src/lib/dnd.ts

@@ -0,0 +1,29 @@
+/*!
+ * © 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 { DropTargetMonitor, XYCoord } from 'react-dnd'
+
+export type DropSide = 'before' | 'after'
+
+export const getDropSide = (element: Element, monitor: DropTargetMonitor) => {
+  const rect = element.getBoundingClientRect()
+
+  // Get vertical middle
+  const middle = (rect.bottom - rect.top) / 2
+
+  const offset = monitor.getClientOffset() as XYCoord
+
+  return offset.y > middle + rect.top ? 'after' : 'before'
+}

package/src/lib/doc.ts

@@ -0,0 +1,167 @@
+/*!
+ * © 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 {
+  AwardsNode,
+  generateNodeID,
+  ManuscriptNode,
+  ManuscriptTransaction,
+  schema,
+  SupplementNode,
+  SupplementsNode,
+} from '@manuscripts/transform'
+import { findChildren, findChildrenByType } from 'prosemirror-utils'
+
+import { findInsertionPosition } from './utils'
+
+export const insertAwardsNode = (tr: ManuscriptTransaction) => {
+  const doc = tr.doc
+  const awards = findChildrenByType(doc, schema.nodes.awards)[0]
+  if (awards) {
+    return awards
+  }
+  const pos = findInsertionPosition(schema.nodes.awards, doc)
+  // const node = schema.nodes.awards.create() as AwardsNode
+  const node = schema.nodes.awards.createAndFill() as AwardsNode
+  tr.insert(pos, node)
+  return {
+    node,
+    pos,
+  }
+}
+
+export const upsertSupplementsSection = (
+  tr: ManuscriptTransaction,
+  supplement: SupplementNode
+) => {
+  const doc = tr.doc
+  const supplements = findChildrenByType(doc, schema.nodes.supplements)[0]
+  if (supplements) {
+    // Section exists -> insert inside it
+    const pos = supplements.pos + supplements.node.nodeSize - 1
+    tr.insert(pos, supplement)
+    return { node: supplements.node, pos }
+  }
+
+  // Section missing -> create new with supplement inside
+  const pos = findInsertionPosition(schema.nodes.supplements, doc)
+  const node = schema.nodes.supplements.createAndFill(
+    { id: generateNodeID(schema.nodes.supplements) },
+    [
+      schema.nodes.section_title.create(undefined, schema.text('Supplements')),
+      supplement,
+    ]
+  ) as SupplementsNode
+
+  tr.insert(pos, node)
+  return {
+    node,
+    pos,
+  }
+}
+
+export const insertAttachmentsNode = (tr: ManuscriptTransaction) => {
+  const attachmentsNodes = findChildrenByType(tr.doc, schema.nodes.attachments)
+  if (attachmentsNodes.length) {
+    return {
+      node: attachmentsNodes[0].node,
+      pos: attachmentsNodes[0].pos,
+    }
+  }
+  const pos = findInsertionPosition(schema.nodes.attachments, tr.doc)
+  const node = schema.nodes.attachments.create({
+    id: generateNodeID(schema.nodes.attachments),
+  })
+  tr.insert(pos, node)
+  return { node, pos }
+}
+
+export const insertFootnotesSection = (tr: ManuscriptTransaction) => {
+  const doc = tr.doc
+  const section = findChildrenByType(doc, schema.nodes.footnotes_section)[0]
+  if (section) {
+    return section
+  }
+
+  const backmatter = findChildrenByType(doc, schema.nodes.backmatter, true)
+
+  const backmatterNode = backmatter[0].node
+  const backmatterPos = backmatter[0].pos
+
+  // Find the last child node in the backmatter (references section)
+  const lastChild =
+    backmatterNode.content.childCount > 0
+      ? backmatterNode.content.child(backmatterNode.content.childCount - 1)
+      : null
+
+  const insertPos =
+    lastChild && lastChild.type === schema.nodes.bibliography_section
+      ? backmatterPos + backmatterNode.content.size - lastChild.nodeSize // Insert before last child (refernces section)
+      : backmatterPos + backmatterNode.content.size // Insert at the end of backmatter
+
+  const pos = tr.mapping.map(insertPos)
+
+  const node = schema.nodes.footnotes_section.create({}, [
+    schema.nodes.section_title.create({}, schema.text('Footnotes')),
+  ])
+  tr.insert(pos, node)
+  return {
+    node,
+    pos,
+  }
+}
+
+export const findAbstractsNode = (doc: ManuscriptNode) => {
+  // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+  return findChildrenByType(doc, schema.nodes.abstracts)[0]!
+}
+
+export const findBody = (doc: ManuscriptNode) => {
+  // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+  return findChildrenByType(doc, schema.nodes.body)[0]!
+}
+
+export const findBackmatter = (doc: ManuscriptNode) => {
+  // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+  return findChildrenByType(doc, schema.nodes.backmatter)[0]!
+}
+
+export const findBibliographySection = (doc: ManuscriptNode) => {
+  return findChildrenByType(doc, schema.nodes.bibliography_section)[0]
+}
+
+export const findFootnotesSection = (doc: ManuscriptNode) => {
+  return findChildrenByType(doc, schema.nodes.footnotes_section)[0]
+}
+
+export const findGraphicalAbstractFigureElement = (doc: ManuscriptNode) => {
+  const ga = findChildrenByType(doc, schema.nodes.graphical_abstract_section)[0]
+  if (!ga) {
+    return
+  }
+  const element = findChildrenByType(ga.node, schema.nodes.figure_element)[0]
+  if (!element) {
+    return
+  }
+  return {
+    node: element.node,
+    pos: ga.pos + element.pos + 1,
+  }
+}
+
+export const findNodeByID = (doc: ManuscriptNode, id: string) => {
+  const children = findChildren(doc, (n) => n.attrs.id === id)
+  return children[0]
+}

package/src/lib/dompurify.ts

@@ -0,0 +1,28 @@
+/*!
+ * © 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.
+ */
+
+import purify, { Config } from 'dompurify'
+
+type Sanitize = (
+  dirty: string,
+  config?: Pick<Config, 'USE_PROFILES' | 'ALLOWED_TAGS'>
+) => DocumentFragment
+
+export const sanitize: Sanitize = (dirty, config) =>
+  purify.sanitize(dirty, {
+    RETURN_DOM_FRAGMENT: true,
+    ...config,
+  })

package/src/lib/files.ts

@@ -0,0 +1,180 @@
+/*!
+ * © 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 { ManuscriptNode, schema } from '@manuscripts/transform'
+import { findChildrenByType } from 'prosemirror-utils'
+
+import { isHidden } from './track-changes-utils'
+
+export type FileAttachment = {
+  id: string
+  name: string
+  link?: string
+  createdDate?: Date
+}
+
+export type NodeFile = {
+  node: ManuscriptNode
+  pos: number
+  file: FileAttachment
+}
+
+export type ElementFiles = {
+  node: ManuscriptNode
+  pos: number
+  files: NodeFile[]
+}
+
+export type ManuscriptFiles = {
+  figures: ElementFiles[]
+  supplements: NodeFile[]
+  attachments: NodeFile[]
+  linkedFiles: NodeFile[]
+  others: FileAttachment[]
+}
+
+const MISSING_FILE: FileAttachment = {
+  id: '',
+  name: '',
+}
+
+export type Upload = (
+  file: File,
+  OnProgress?: (percentage: number) => void
+) => Promise<FileAttachment>
+
+export type Download = (file: FileAttachment) => void
+
+export type PreviewLink = (file: FileAttachment) => string | undefined
+
+export type FileManagement = {
+  upload: Upload
+  download: Download
+  previewLink: PreviewLink
+}
+
+const figureTypes = [
+  schema.nodes.figure_element,
+  schema.nodes.image_element,
+  schema.nodes.hero_image,
+  schema.nodes.embed,
+]
+
+export function memoGroupFiles() {
+  let prevFiles: FileAttachment[] = []
+  let prevDoc: ManuscriptNode | undefined = undefined
+  let result: ManuscriptFiles | undefined
+
+  return function (doc: ManuscriptNode, files: FileAttachment[]) {
+    if (result && prevDoc === doc && prevFiles === files) {
+      return result
+    }
+    prevDoc = doc
+    prevFiles = files
+    return groupFiles(doc, files)
+  }
+}
+
+export const groupFiles = (
+  doc: ManuscriptNode,
+  files: FileAttachment[]
+): ManuscriptFiles => {
+  const fileMap = new Map(files.map((f) => [f.id, f]))
+  const figures: ElementFiles[] = []
+  const supplements: NodeFile[] = []
+  const linkedFiles: NodeFile[] = []
+  const attachments: NodeFile[] = []
+
+  const getFile = (href: string) => {
+    const file = fileMap.get(href)
+    if (file) {
+      fileMap.delete(href)
+      return file
+    } else {
+      return MISSING_FILE
+    }
+  }
+
+  const getFigureElementFiles = (node: ManuscriptNode, pos: number) => {
+    const figureFiles = []
+
+    if (node.type === schema.nodes.embed) {
+      if (node.attrs.href) {
+        figureFiles.push({
+          node,
+          pos,
+          file: getFile(node.attrs.href),
+        })
+      }
+    } else {
+      for (const figure of findChildrenByType(node, schema.nodes.figure)) {
+        if (isHidden(figure.node)) {
+          continue
+        }
+        figureFiles.push({
+          node: figure.node,
+          pos: pos + figure.pos + 1,
+          file: getFile(figure.node.attrs.src),
+        })
+      }
+    }
+
+    return {
+      node,
+      pos,
+      files: figureFiles,
+    }
+  }
+
+  doc.descendants((node, pos) => {
+    if (isHidden(node)) {
+      return
+    }
+    if (figureTypes.includes(node.type)) {
+      figures.push(getFigureElementFiles(node, pos))
+    }
+    if (node.type === schema.nodes.image_element) {
+      if (node.attrs.extLink) {
+        linkedFiles.push({
+          node,
+          pos,
+          file: getFile(node.attrs.extLink),
+        })
+      }
+    }
+    if (node.type === schema.nodes.supplement) {
+      supplements.push({
+        node,
+        pos,
+        file: getFile(node.attrs.href),
+      })
+    }
+    if (node.type === schema.nodes.attachment) {
+      attachments.push({
+        node,
+        pos,
+        file: getFile(node.attrs.href),
+      })
+    }
+  })
+
+  return {
+    figures,
+    supplements,
+    attachments,
+    linkedFiles,
+    others: [...fileMap.values()],
+  }
+}

package/src/lib/footnotes.ts

@@ -0,0 +1,83 @@
+/*!
+ * © 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 {
+  FootnoteNode,
+  generateNodeID,
+  ManuscriptEditorState,
+  ManuscriptNode,
+  schema,
+} from '@manuscripts/transform'
+import { Selection } from 'prosemirror-state'
+import {
+  ContentNodeWithPos,
+  findParentNodeOfType,
+  findParentNodeOfTypeClosestToPos,
+} from 'prosemirror-utils'
+
+import { footnotesKey } from '../plugins/footnotes'
+
+export const findFootnotesContainerNode = (
+  doc: ManuscriptNode,
+  pos: number
+) => {
+  const $pos = doc.resolve(pos)
+  return (
+    findParentNodeOfTypeClosestToPos($pos, schema.nodes.table_element) || {
+      node: doc,
+      pos: 0,
+    }
+  )
+}
+
+export const findParentFootnote: (selection: Selection) => ContentNodeWithPos | undefined = findParentNodeOfType([
+  schema.nodes.footnote,
+  schema.nodes.general_table_footnote,
+])
+
+export const getFootnotesElementState = (
+  state: ManuscriptEditorState,
+  id: string
+) => {
+  const fns = footnotesKey.getState(state)
+  if (!fns) {
+    return
+  }
+  const elementID = fns.footnotesElementIDs.get(id)
+  if (!elementID) {
+    return
+  }
+  return fns.footnotesElements.get(elementID)
+}
+
+export const getFootnoteLabel = (
+  state: ManuscriptEditorState,
+  footnote: FootnoteNode
+) => {
+  const id = footnote.attrs.id
+  const fns = getFootnotesElementState(state, id)
+  return fns?.labels.get(id) || ''
+}
+
+export const createFootnote = () => {
+  return schema.nodes.footnote.createAndFill(
+    {
+      id: generateNodeID(schema.nodes.footnote),
+      kind: 'footnote',
+    },
+    [schema.nodes.paragraph.create({})]
+  ) as FootnoteNode
+}