@manuscripts/transform 4.3.53 → 4.4.0

package/src/jats/types.ts

@@ -0,0 +1,16 @@
+/*!
+ * © 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.
+ */
+export type IDGenerator = (element: Element) => Promise<string | null>

package/src/lib/__tests__/footnotes.test.ts

@@ -0,0 +1,36 @@
+/*!
+ * © 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 {
+  generateAlphaFootnoteLabel,
+  generateNumericFootnoteLabel,
+} from '../footnotes'
+
+describe('Footnotes alpha label generation', () => {
+  it('should start from "a"', () => {
+    const label = generateAlphaFootnoteLabel(0)
+    expect(label).toBe('a')
+  })
+  it('should generate 2 characters for large indexes', () => {
+    const label = generateAlphaFootnoteLabel(26)
+    expect(label).toBe('aa')
+  })
+})
+describe('Footnotes numeric label generation', () => {
+  it('should start from "1"', () => {
+    const label = generateNumericFootnoteLabel(0)
+    expect(label).toBe('1')
+  })
+})

package/src/lib/citeproc.ts

@@ -0,0 +1,30 @@
+/*!
+ * © 2025 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 * as Citeproc from 'citeproc'
+
+import { CitationAttrs } from '../schema'
+
+export const buildCiteprocCitation = (
+  citation: CitationAttrs
+): Citeproc.Citation => ({
+  citationID: citation.id,
+  citationItems: citation.rids.map((rid) => ({
+    id: rid,
+  })),
+  properties: {
+    noteIndex: 0,
+  },
+})

package/src/lib/credit-roles.ts

@@ -0,0 +1,91 @@
+/*!
+ * © 2025 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.
+ */
+
+export enum CreditVocabTerm {
+  Conceptualization = 'Conceptualization',
+  DataCuration = 'Data curation',
+  FormalAnalysis = 'Formal analysis',
+  FundingAcquisition = 'Funding acquisition',
+  Investigation = 'Investigation',
+  Methodology = 'Methodology',
+  ProjectAdministration = 'Project administration',
+  Resources = 'Resources',
+  Software = 'Software',
+  Supervision = 'Supervision',
+  Validation = 'Validation',
+  Visualization = 'Visualization',
+  WritingOriginalDraft = 'Writing – original draft',
+  WritingReviewEditing = 'Writing – review & editing',
+}
+
+export const CreditRoleUrls = new Map([
+  [
+    CreditVocabTerm.Conceptualization,
+    'https://credit.niso.org/contributor-roles/conceptualization/',
+  ],
+  [
+    CreditVocabTerm.DataCuration,
+    'https://credit.niso.org/contributor-roles/data-curation/',
+  ],
+  [
+    CreditVocabTerm.FormalAnalysis,
+    'https://credit.niso.org/contributor-roles/formal-analysis/',
+  ],
+  [
+    CreditVocabTerm.FundingAcquisition,
+    'https://credit.niso.org/contributor-roles/funding-acquisition/',
+  ],
+  [
+    CreditVocabTerm.Investigation,
+    'https://credit.niso.org/contributor-roles/investigation/',
+  ],
+  [
+    CreditVocabTerm.Methodology,
+    'https://credit.niso.org/contributor-roles/methodology/',
+  ],
+  [
+    CreditVocabTerm.ProjectAdministration,
+    'https://credit.niso.org/contributor-roles/project-administration/',
+  ],
+  [
+    CreditVocabTerm.Resources,
+    'https://credit.niso.org/contributor-roles/resources/',
+  ],
+  [
+    CreditVocabTerm.Software,
+    'https://credit.niso.org/contributor-roles/software/',
+  ],
+  [
+    CreditVocabTerm.Supervision,
+    'https://credit.niso.org/contributor-roles/supervision/',
+  ],
+  [
+    CreditVocabTerm.Validation,
+    'https://credit.niso.org/contributor-roles/validation/',
+  ],
+  [
+    CreditVocabTerm.Visualization,
+    'https://credit.niso.org/contributor-roles/visualization/',
+  ],
+  [
+    CreditVocabTerm.WritingOriginalDraft,
+    'https://credit.niso.org/contributor-roles/writing-original-draft/',
+  ],
+  [
+    CreditVocabTerm.WritingReviewEditing,
+    'https://credit.niso.org/contributor-roles/writing-review-editing/',
+  ],
+])

package/src/lib/deafults.ts

@@ -0,0 +1,17 @@
+/*!
+ * © 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.
+ */
+
+export const defaultTitle = 'Untitled Manuscript'

package/src/lib/footnotes.ts

@@ -0,0 +1,85 @@
+/*!
+ * © 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 {
+  isFootnotesElementNode,
+  isTableElementFooter,
+  ManuscriptNode,
+} from '../schema'
+
+export const generateFootnoteLabels = (doc: ManuscriptNode) => {
+  const labels = new Map()
+  doc.descendants((node, pos, parent) => {
+    if (isFootnotesElementNode(node) && parent) {
+      const generator = footnoteLabelGenerator(parent)
+      for (let i = 0; i < node.childCount; i++) {
+        const footnote = node.child(i)
+        const label = generator(i)
+        labels.set(footnote.attrs.id, label)
+      }
+      return false
+    }
+  })
+  return labels
+}
+
+export const footnoteLabelGenerator = (parent: ManuscriptNode) => {
+  if (isTableElementFooter(parent)) {
+    return generateNumericFootnoteLabel
+  } else {
+    return generateAlphaFootnoteLabel
+  }
+}
+
+export const generateNumericFootnoteLabel = (index: number) => String(index + 1)
+
+export const generateAlphaFootnoteLabel = (index: number) => {
+  const unicodeInterval = [97, 123]
+  const places = unicodeInterval[1] - unicodeInterval[0]
+
+  function getClassCount(n: number, order: number) {
+    return n * Math.pow(places, order - 1)
+  }
+
+  let indices: number[] | null = null
+
+  for (;;) {
+    let current = index
+    let position = 1
+    while (current >= places) {
+      current = current / places
+      position++
+    }
+    const newIndex = Math.floor(current)
+    indices = indices ? indices : new Array(position).fill(0)
+    indices.splice(indices.length - position, 1, newIndex)
+
+    index -= getClassCount(newIndex, position)
+
+    if (position === 1) {
+      break
+    }
+  }
+  return (indices || [])
+    .map((v, i, array) => {
+      // offseting to start with zero for the second and later classes
+      // @TODO: find better solution instead of this indexing offset
+      if (array.length > 1 && i !== array.length - 1) {
+        return String.fromCodePoint(v + unicodeInterval[0] - 1)
+      }
+      return String.fromCodePoint(v + unicodeInterval[0])
+    })
+    .join('')
+}

package/src/lib/html.ts

@@ -0,0 +1,56 @@
+/*!
+ * © 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.
+ */
+
+function decodeHTMLEntities(text: string) {
+  // those entities that pertain to XML are supported and don't need to be replaced (e.g.: &amp, &quote etc)
+  const entities = [
+    ['#x27', "'"],
+    ['#x2F', '/'],
+    ['#39', "'"],
+    ['#47', '/'],
+    ['nbsp', ' '],
+  ]
+
+  for (let i = 0; i < entities.length; i++) {
+    text = text.replace(
+      new RegExp('&' + entities[i][0] + ';', 'g'),
+      entities[i][1]
+    )
+  }
+
+  return text
+}
+
+export const nodeFromHTML = (html: string) => {
+  html = html.trim()
+
+  if (!html.length) {
+    return null
+  }
+
+  const template = document.createElement('template')
+
+  template.innerHTML = html
+  template.innerHTML = decodeHTMLEntities(template.innerHTML)
+  return template.content.firstChild
+}
+
+export const textFromHTML = (html: string) => {
+  const template = document.createElement('template')
+
+  template.innerHTML = html
+  return template.content.textContent
+}

package/src/lib/section-categories.ts

@@ -0,0 +1,27 @@
+/*!
+ * © 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 { SectionCategory, SectionGroup } from '../schema'
+
+export const getGroupCategories = (
+  sections: Map<string, SectionCategory> | SectionCategory[],
+  group: SectionGroup
+): SectionCategory[] => {
+  const sectionsArray = Array.isArray(sections)
+    ? sections
+    : Array.from(sections.values())
+  return sectionsArray.filter((section) => section.group === group)
+}

package/src/lib/utils.ts

@@ -0,0 +1,145 @@
+/*!
+ * © 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 { Node as ProsemirrorNode, ResolvedPos } from 'prosemirror-model'
+
+import { htmlFromJatsNode } from '../jats/importer/jats-parser-utils'
+import {
+  CreditRole,
+  isBibliographySectionNode,
+  isGraphicalAbstractSectionNode,
+  ManuscriptEditorState,
+  ManuscriptNode,
+} from '../schema'
+import { CreditRoleUrls, CreditVocabTerm } from './credit-roles'
+
+export function* iterateChildren(
+  node: ManuscriptNode,
+  recurse = false
+): Iterable<ManuscriptNode> {
+  for (let i = 0; i < node.childCount; i++) {
+    const child = node.child(i)
+    yield child
+
+    if (recurse) {
+      for (const grandchild of iterateChildren(child, true)) {
+        yield grandchild
+      }
+    }
+  }
+}
+
+export const findNodePositions = (
+  state: ManuscriptEditorState,
+  predicate: (node: ManuscriptNode) => boolean
+) => {
+  const found: number[] = []
+  state.doc.descendants((node, nodePos) => {
+    if (predicate(node as ManuscriptNode)) {
+      found.push(nodePos)
+    }
+    return true
+  })
+  return found
+}
+
+export const isInGraphicalAbstractSection = ($pos: ResolvedPos): boolean => {
+  for (let i = $pos.depth; i > 0; i--) {
+    const node = $pos.node(i)
+    if (isGraphicalAbstractSectionNode(node)) {
+      return true
+    }
+  }
+  return false
+}
+
+export const isInBibliographySection = ($pos: ResolvedPos): boolean => {
+  for (let i = $pos.depth; i > 0; i--) {
+    const node = $pos.node(i)
+    if (isBibliographySectionNode(node)) {
+      return true
+    }
+  }
+  return false
+}
+
+export const findParentNodeClosestToPos = (
+  $pos: ResolvedPos,
+  predicate: (node: ProsemirrorNode) => boolean
+) => {
+  for (let i = $pos.depth; i > 0; i--) {
+    const node = $pos.node(i)
+    if (predicate(node)) {
+      return {
+        pos: i > 0 ? $pos.before(i) : 0,
+        start: $pos.start(i),
+        depth: i,
+        node,
+      }
+    }
+  }
+}
+
+export const getTrimmedTextContent = (
+  node: Element | Document | null,
+  selector?: string
+) => {
+  if (!node) {
+    return undefined
+  }
+  return selector
+    ? node.querySelector(selector)?.textContent?.trim()
+    : node.textContent?.trim()
+}
+
+export const getHTMLContent = (node: Element, querySelector: string) => {
+  return htmlFromJatsNode(node.querySelector(querySelector))
+}
+
+export const dateToTimestamp = (dateElement: Element) => {
+  const selectors = ['year', 'month', 'day']
+  const values: Array<number> = []
+  for (const selector of selectors) {
+    const value = getTrimmedTextContent(dateElement, selector)
+    if (!value || isNaN(+value)) {
+      return
+    }
+    values.push(+value)
+  }
+
+  // timestamp stored in seconds in manuscript schema
+  return Date.UTC(values[0], values[1] - 1, values[2]) / 1000 // ms => s
+}
+
+export function getCreditRole(elem: Element) {
+  const sources = elem.querySelectorAll(
+    'role[vocab="CRediT"][vocab-identifier="http://credit.niso.org/"][vocab-term][vocab-term-identifier]'
+  )
+  const results: CreditRole[] = []
+  sources.forEach((source) => {
+    if (
+      source &&
+      CreditRoleUrls.has(source.getAttribute('vocab-term') as CreditVocabTerm)
+    ) {
+      const result: CreditRole = {
+        vocabTerm: source.getAttribute('vocab-term') as CreditVocabTerm,
+      }
+      results.push(result)
+    }
+  })
+
+  return results
+}

package/src/lib/xml.ts

@@ -0,0 +1,28 @@
+/*!
+ * © 2025 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.
+ */
+
+export const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink'
+export const XML_NAMESPACE = 'http://www.w3.org/XML/1998/namespace'
+
+export function sanitizeXmlString(str: string): string {
+  return (
+    str
+      // Escape bare ampersands (not part of valid entities)
+      .replace(/&(?!(?:amp|lt|gt|quot|apos|#[0-9]+|#x[0-9a-fA-F]+);)/g, '&')
+      // Escape < that doesn't start a valid tag
+      .replace(/<(?![a-zA-Z_\/!?])/g, '&lt;')
+  )
+}