@manuscripts/transform 4.3.53 → 4.4.1

package/src/schema/migration/migration-scripts/4.3.23.ts

@@ -0,0 +1,55 @@
+/*!
+ * © 2026 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 { JSONProsemirrorNode } from '../../../types'
+import { MigrationScript } from '../migration-script'
+
+class Migration4323 implements MigrationScript {
+  fromVersion = '4.3.22'
+  toVersion = '4.3.23'
+
+  migrateNode(node: JSONProsemirrorNode): JSONProsemirrorNode {
+    if (node.type === 'contributor') {
+      if (node.attrs.affiliations) {
+        node.attrs.affiliationIDs = node.attrs.affiliations
+        delete node.attrs.affiliations
+      }
+      if (Array.isArray(node.attrs.corresp)) {
+        node.attrs.correspIDs = node.attrs.corresp.map((c) => c.correspID)
+        delete node.attrs.corresp
+      }
+      if (Array.isArray(node.attrs.footnote)) {
+        node.attrs.footnoteIDs = node.attrs.footnote.map((f) => f.noteID)
+        delete node.attrs.footnote
+      }
+      node.attrs.given = node.attrs.bibliographicName.given
+      node.attrs.family = node.attrs.bibliographicName.family
+      node.attrs.suffix = node.attrs.bibliographicName.suffix
+      node.attrs.ORCID = node.attrs.ORCIDIdentifier
+      delete node.attrs.bibliographicName
+      delete node.attrs.userID
+      delete node.attrs.ORCIDIdentifier
+    }
+    if (node.type === 'comment') {
+      const contribution = node.attrs.contributions[0]
+      node.attrs.userID = contribution.profileID
+      node.attrs.timestamp = contribution.timestamp
+      delete node.attrs.contributions
+    }
+    return node
+  }
+}
+
+export default Migration4323

package/src/schema/migration/migration-scripts/4.3.34.ts

@@ -0,0 +1,132 @@
+/*!
+ * © 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 { JSONProsemirrorNode } from '../../../types'
+import { Nodes, schema } from '../../index'
+import { MigrationScript } from '../migration-script'
+
+interface Config {
+  title?: 'required' | 'optional'
+  caption?: 'required' | 'optional'
+  location: { pos?: 'start' | 'end'; before?: Nodes }
+}
+
+const CONFIG: Record<string, Config> = {
+  figure_element: { caption: 'required', location: { before: 'alt_text' } },
+  table_element: { title: 'required', location: { pos: 'start' } },
+  image_element: { caption: 'required', location: { before: 'alt_text' } },
+  listing_element: {
+    title: 'required',
+    caption: 'required',
+    location: { pos: 'end' },
+  },
+  supplement: {
+    title: 'required',
+    caption: 'required',
+    location: { pos: 'start' },
+  },
+  embed: { title: 'required', caption: 'required', location: { pos: 'start' } },
+  box_element: {
+    title: 'optional',
+    caption: 'optional',
+    location: { pos: 'start' },
+  },
+}
+
+const getCaptionNode = (nodes: JSONProsemirrorNode[], isRequired: boolean) => {
+  if (nodes.length === 0) {
+    return isRequired
+      ? {
+          type: 'caption',
+          content: [{ type: 'text_block', attrs: {} }],
+          attrs: {},
+        }
+      : undefined
+  }
+
+  return nodes.reduce<JSONProsemirrorNode>(
+    (caption, { content }) => ({
+      ...caption,
+      content: [
+        ...(caption.content || []),
+        { type: 'text_block', content, attrs: {} },
+      ],
+    }),
+    { type: 'caption', content: [], attrs: {} }
+  )
+}
+
+class Migration4334 implements MigrationScript {
+  fromVersion = '4.3.33'
+  toVersion = '4.3.34'
+
+  migrateNode(node: JSONProsemirrorNode): JSONProsemirrorNode {
+    const config = CONFIG[node.type]
+    if (!node.content || !config) {
+      return node
+    }
+
+    const figCaption = node.content.find((n) => n.type === 'figcaption')
+    const foundTitle = (figCaption?.content || []).find(
+      (n) => n.type === 'caption_title'
+    )
+    const captionNodes = (figCaption?.content || []).filter(
+      (node) => node.type === 'caption')
+    const foundCaption = getCaptionNode(
+      captionNodes,
+      config.caption === 'required'
+    )
+
+    const cleanContent = node.content.filter((n) => n.type !== 'figcaption')
+
+    const placeholderTitle = schema.nodes.caption_title.create().toJSON()
+    const placeholderCaption = schema.nodes.caption.create().toJSON()
+
+    const captionGroup: JSONProsemirrorNode[] = []
+
+    if (
+      config.title === 'required' ||
+      (config.title === 'optional' && foundTitle)
+    ) {
+      captionGroup.push(foundTitle || placeholderTitle)
+    }
+
+    if (
+      config.caption === 'required' ||
+      (config.caption === 'optional' && foundCaption)
+    ) {
+      captionGroup.push(foundCaption || placeholderCaption)
+    }
+
+    if (config.location.pos === 'start') {
+      cleanContent.unshift(...captionGroup)
+    } else if (config.location.pos === 'end') {
+      cleanContent.push(...captionGroup)
+    } else if (config.location.before) {
+      const idx = cleanContent.findIndex(
+        (n) => n.type === config.location.before
+      )
+      cleanContent.splice(
+        idx === -1 ? cleanContent.length : idx,
+        0,
+        ...captionGroup
+      )
+    }
+
+    return { ...node, content: cleanContent }
+  }
+}
+
+export default Migration4334

package/src/schema/migration/migration-scripts/4.3.35.ts

@@ -0,0 +1,41 @@
+/*!
+ * © 2026 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 { JSONProsemirrorNode } from '../../../types'
+import { MigrationScript } from '../migration-script'
+
+class Migration4335 implements MigrationScript {
+  fromVersion = '4.3.34'
+  toVersion = '4.3.35'
+
+  migrateNode(node: JSONProsemirrorNode): JSONProsemirrorNode {
+    if (
+      node.type === 'pullquote_element' ||
+      node.type === 'blockquote_element'
+    ) {
+      return {
+        ...node,
+        content: (node.content ?? []).map((child) =>
+          child.type === 'paragraph'
+            ? { ...child, type: 'text_block' }
+            : child
+        ),
+      }
+    }
+    return node
+  }
+}
+
+export default Migration4335

package/src/schema/migration/migration-scripts/index.ts

@@ -0,0 +1,49 @@
+/*!
+ * © 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 Migration125 from './1.2.5'
+import Migration2322 from './2.3.22'
+import { Migration3012 } from './3.0.12'
+import Migration3021 from './3.0.21'
+import Migration3030 from './3.0.30'
+import Migration3031 from './3.0.31'
+import Migration3041 from './3.0.41'
+import Migration3055 from './3.0.55'
+import Migration3056 from './3.0.56'
+import Migration4213 from './4.2.13'
+import Migration4215 from './4.2.15'
+import Migration4323 from './4.3.23'
+import Migration4334 from './4.3.34'
+import Migration4335 from './4.3.35'
+
+const migrations = [
+  new Migration125(),
+  new Migration2322(),
+  new Migration3012(),
+  new Migration3021(),
+  new Migration3030(),
+  new Migration3031(),
+  new Migration3041(),
+  new Migration3055(),
+  new Migration3056(),
+  new Migration4213(),
+  new Migration4215(),
+  new Migration4323(),
+  new Migration4334(),
+  new Migration4335(),
+]
+
+export default migrations

package/src/schema/nodes/abstracts.ts

@@ -0,0 +1,29 @@
+/*!
+ * © 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 { NodeSpec } from 'prosemirror-model'
+
+// This node has no representation in json-schema
+// It exists for the purpose of styling in the UI
+
+export const abstracts: NodeSpec = {
+  content: 'sections* (trans_abstract | trans_graphical_abstract)*',
+  attrs: {
+    id: { default: '' },
+  },
+  group: 'block',
+  toDOM: () => ['div', { class: 'abstracts' }, 0],
+}

package/src/schema/nodes/affiliation.ts

@@ -0,0 +1,88 @@
+/*!
+ * © 2023 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 { NodeSpec } from 'prosemirror-model'
+
+import { ManuscriptNode } from '../types'
+
+export interface Email {
+  href: string
+  text: string
+}
+
+interface Attrs {
+  id: string
+  institution: string
+  department: string
+  addressLine1: string
+  addressLine2: string
+  addressLine3: string
+  postCode: string
+  country: string
+  county: string
+  city: string
+  email: Email
+  priority: number
+}
+
+export interface AffiliationNode extends ManuscriptNode {
+  attrs: Attrs
+}
+
+export const affiliation: NodeSpec = {
+  content: 'inline*',
+  atom: true,
+  attrs: {
+    id: { default: '' },
+    institution: { default: '' },
+    department: { default: '' },
+    addressLine1: { default: '' },
+    addressLine2: { default: '' },
+    addressLine3: { default: '' },
+    postCode: { default: '' },
+    country: { default: '' },
+    county: { default: '' },
+    city: { default: '' },
+    priority: { default: undefined },
+    email: { default: undefined },
+    dataTracked: { default: null },
+  },
+  group: 'block',
+  parseDOM: [
+    {
+      tag: 'div.affiliation',
+      getAttrs: (node) => {
+        const dom = node as HTMLSpanElement
+        return {
+          id: dom.getAttribute('id'),
+        }
+      },
+    },
+  ],
+  toDOM: (node) => {
+    const affiliationNode = node as AffiliationNode
+    return [
+      'div',
+      {
+        class: 'affiliation',
+        id: affiliationNode.attrs.id,
+      },
+    ]
+  },
+}
+
+export const isAffiliationNode = (
+  node: ManuscriptNode
+): node is AffiliationNode => node.type === node.type.schema.nodes.affiliation

package/src/schema/nodes/affiliations.ts

@@ -0,0 +1,30 @@
+/*!
+ * © 2023 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 { NodeSpec } from 'prosemirror-model'
+
+// This node has no representation in json-schema
+// It exists for the purpose of styling in the UI
+
+export const affiliations: NodeSpec = {
+  content: 'affiliation*',
+  attrs: {
+    id: { default: '' },
+  },
+  group: 'block',
+  selectable: false,
+  toDOM: () => ['div', { class: 'affiliations' }, 0],
+}

package/src/schema/nodes/alt_text.ts

@@ -0,0 +1,36 @@
+/*!
+ * © 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 type { NodeSpec } from 'prosemirror-model'
+
+import type { ManuscriptNode } from '../types'
+
+export interface AltTextAttrs {
+  id: string
+}
+
+export interface AltTextNode extends ManuscriptNode {
+  attrs: AltTextAttrs
+}
+
+export const altText: NodeSpec = {
+  content: 'text*',
+  attrs: {
+    id: { default: '' },
+  },
+  parseDOM: [{ tag: 'div' }],
+  toDOM: () => ['div', 0],
+}

package/src/schema/nodes/alt_title.ts

@@ -0,0 +1,40 @@
+/*!
+ * © 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 { NodeSpec } from 'prosemirror-model'
+
+import { ManuscriptNode } from '../types'
+
+export interface AltTitleAttrs {
+  id: string
+  type: string
+}
+
+export interface AltTitleNode extends ManuscriptNode {
+  attrs: AltTitleAttrs
+}
+
+export const altTitle: NodeSpec = {
+  content: '(text | highlight_marker)*',
+  attrs: {
+    id: { default: '' },
+    type: { default: '' },
+    dataTracked: { default: null },
+  },
+  group: 'block element',
+  parseDOM: [{ tag: 'div' }],
+  toDOM: () => ['div', 0],
+}

package/src/schema/nodes/alt_titles_section.ts

@@ -0,0 +1,58 @@
+/*!
+ * © 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 { NodeSpec } from 'prosemirror-model'
+
+import { ManuscriptNode } from '../types'
+
+export interface AltTitlesSectionAttrs {
+  id: string
+}
+
+export interface AltTitlesSectionNode extends ManuscriptNode {
+  attrs: AltTitlesSectionAttrs
+}
+
+export const altTitlesSection: NodeSpec = {
+  content: 'alt_title*',
+  attrs: {
+    id: { default: '' },
+  },
+  group: 'block sections',
+  selectable: false,
+  parseDOM: [
+    {
+      tag: 'section.alt-titles',
+    },
+  ],
+  toDOM: (node) => {
+    const altTitlesSectionNode = node as AltTitlesSectionNode
+
+    return [
+      'section',
+      {
+        id: altTitlesSectionNode.attrs.id,
+        class: 'alt-titles',
+      },
+      0,
+    ]
+  },
+}
+
+export const isAltTitlesSectionNode = (
+  node: ManuscriptNode
+): node is AltTitlesSectionNode =>
+  node.type === node.type.schema.nodes.alt_titles_section

package/src/schema/nodes/attachment.ts

@@ -0,0 +1,46 @@
+/*!
+ * © 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 { NodeSpec } from 'prosemirror-model'
+
+import { ManuscriptNode } from '../types'
+export interface AttachmentAttrs {
+  id: string
+  href: string
+  type: string
+}
+
+export interface AttachmentNode extends ManuscriptNode {
+  attrs: AttachmentAttrs
+}
+export const attachment: NodeSpec = {
+  attrs: {
+    id: { default: '' },
+    type: { default: '' },
+    href: { default: '' },
+  },
+  toDOM: (node) => {
+    return [
+      'div',
+      {
+        class: 'attachment',
+        id: node.attrs.id,
+      },
+    ]
+  },
+}
+export const isAttachmentNode = (
+  node: ManuscriptNode
+): node is AttachmentNode => node.type === node.type.schema.nodes.attachment

package/src/schema/nodes/attachments.ts

@@ -0,0 +1,45 @@
+/*!
+ * © 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 { NodeSpec } from 'prosemirror-model'
+
+import { ManuscriptNode } from '../types'
+export interface AttachmentsAttrs {
+  id: string
+}
+
+export interface AttachmentsNode extends ManuscriptNode {
+  attrs: AttachmentsAttrs
+}
+export const attachments: NodeSpec = {
+  content: 'attachment*',
+  attrs: {
+    id: { default: '' },
+  },
+  toDOM: (node) => {
+    return [
+      'div',
+      {
+        class: 'attachments',
+        id: node.attrs.id,
+      },
+    ]
+  },
+}
+
+export const isAttachmentsNode = (
+  node: ManuscriptNode
+): node is AttachmentsNode => node.type === node.type.schema.nodes.attachments

package/src/schema/nodes/attribution.ts

@@ -0,0 +1,38 @@
+/*!
+ * © 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 { NodeSpec } from 'prosemirror-model'
+
+import { ManuscriptNode } from '../types'
+
+export interface AttributionNode extends ManuscriptNode {
+  attrs: Record<string, unknown>
+}
+
+export const attribution: NodeSpec = {
+  content: '(text | link | highlight_marker)*',
+  attrs: { dataTracked: { default: null } },
+  group: 'block',
+  isolating: true,
+  selectable: false,
+  parseDOM: [
+    {
+      tag: 'footer',
+      context: 'blockquote_element/|pullquote_element/',
+    },
+  ],
+  toDOM: () => ['footer', 0],
+}