@manuscripts/transform 4.3.53 → 4.4.1

package/src/schema/migration/migrate.ts

@@ -0,0 +1,77 @@
+/*!
+ * © 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 { cloneDeep } from 'lodash'
+import semver from 'semver'
+
+import { JSONProsemirrorNode } from '../../types'
+import { schema } from '..'
+import { MigrationScript } from './migration-script'
+import migrationScripts from './migration-scripts'
+
+export default function migrate(
+  oldDoc: JSONProsemirrorNode,
+  migrationScript: MigrationScript['migrateNode']
+) {
+  function migrateNode(node: JSONProsemirrorNode) {
+    const migrated = migrationScript(node, oldDoc)
+    if (migrated.content) {
+      migrated.content = migrated.content.map((m) => migrateNode(m))
+    }
+    return migrated
+  }
+
+  return migrateNode(oldDoc)
+}
+
+export function migrateFor(oldDoc: JSONProsemirrorNode, baseVersion: string) {
+  const migrationScripts = ensureVersionAscOrder()
+  let migratedDoc = cloneDeep(oldDoc)
+
+  for (let i = 0; i < migrationScripts.length; i++) {
+    const script = migrationScripts[i]
+    if (semver.lt(script.fromVersion, baseVersion)) {
+      continue
+    }
+    console.log('Migrating doc with script to version ' + script.toVersion)
+    migratedDoc = migrate(migratedDoc, (node, oldDoc) =>
+      script.migrateNode(node, oldDoc)
+    )
+  }
+
+  return testDoc(migratedDoc, baseVersion)
+  // now find all versions that we have to migrate that do from version
+}
+
+const ensureVersionAscOrder = () =>
+  migrationScripts.sort((a, b) => semver.compare(a.toVersion, b.toVersion))
+
+function testDoc(doc: JSONProsemirrorNode, fromVersion: string) {
+  try {
+    // not that even if the doc doesn't really require a migration but the schema changed it still needs to go through migration process
+    // this is needed to make sure that DB version of it is in sync with FE so the updates can be correctly exchanged
+    const resultDoc = schema.nodeFromJSON(doc)
+
+    resultDoc.check()
+    return resultDoc
+  } catch (e) {
+    const error =
+      'Migration application from version ' +
+      fromVersion +
+      ' did not produce a valid document with ' +
+      e
+    throw new Error(error)
+  }
+}

package/src/schema/migration/migration-script.ts

@@ -0,0 +1,26 @@
+/*!
+ * © 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 { JSONProsemirrorNode } from '../../types'
+
+export interface MigrationScript {
+  fromVersion: string
+  toVersion: string
+  migrateNode: (
+    node: JSONProsemirrorNode,
+    doc: JSONProsemirrorNode
+  ) => JSONProsemirrorNode
+}

package/src/schema/migration/migration-scripts/1.2.5.ts

@@ -0,0 +1,44 @@
+/*!
+ * © 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 { JSONProsemirrorNode } from '../../../types'
+import { MigrationScript } from '../migration-script'
+
+// @NOTE - this is an example migration
+class Migration125 implements MigrationScript {
+  fromVersion = '1.2.3'
+  toVersion = '1.2.5'
+  // eslint-disable-next-line @typescript-eslint/no-unused-vars
+  migrateNode(node: JSONProsemirrorNode, doc: JSONProsemirrorNode) {
+    /*
+      NOTE - if schema is used in this function, it is imported from the current version of the package
+      in pratical terms it means that it's always the latest schema and you can't rely on that it will correspond the version in
+      which you created the migration script. That would also mean that you shouldn't rely on schema for migrations
+    */
+    if (node.type === 'paragraph') {
+      return {
+        ...node,
+        attrs: {
+          ...node.attrs,
+          someNewFanctAttribute: 'example-value',
+        },
+      }
+    }
+    return node
+  }
+}
+
+export default Migration125

package/src/schema/migration/migration-scripts/2.3.22.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 { JSONProsemirrorNode } from '../../../types'
+import { MigrationScript } from '../migration-script'
+
+class Migration2322 implements MigrationScript {
+  fromVersion = '2.3.21'
+  toVersion = '2.3.22'
+
+  migrateNode(node: JSONProsemirrorNode): JSONProsemirrorNode {
+    if (node.type === 'table_element' && Array.isArray(node.content)) {
+      let figcaptionNode = null
+      const remainingContent = []
+
+      for (const child of node.content) {
+        if (child.type === 'figcaption') {
+          figcaptionNode = child
+        } else {
+          remainingContent.push(child)
+        }
+      }
+
+      // Create the new content array
+      const newContent = figcaptionNode
+        ? [figcaptionNode, ...remainingContent]
+        : remainingContent
+
+      // Return the updated node with the new content order
+      return {
+        ...node,
+        content: newContent,
+      }
+    }
+
+    return node
+  }
+}
+
+export default Migration2322

package/src/schema/migration/migration-scripts/3.0.12.ts

@@ -0,0 +1,33 @@
+/*!
+ * © 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 { JSONProsemirrorNode } from '../../../types'
+import { MigrationScript } from '../migration-script'
+
+export class Migration3012 implements MigrationScript {
+  fromVersion = '3.0.12'
+  toVersion = '3.0.13'
+
+  migrateNode(node: JSONProsemirrorNode): JSONProsemirrorNode {
+    if (node.type === 'body') {
+      const content = node.content?.filter((n) => n.type !== 'toc_section')
+      return {
+        ...node,
+        content,
+      }
+    }
+    return node
+  }
+}

package/src/schema/migration/migration-scripts/3.0.21.ts

@@ -0,0 +1,50 @@
+/*!
+ * © 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 { JSONProsemirrorNode } from '../../../types'
+import { MigrationScript } from '../migration-script'
+
+class Migration3021 implements MigrationScript {
+  fromVersion = '3.0.20'
+  toVersion = '3.0.21'
+
+  private suffixMap = new Map([
+    ['competing-interests', 'coi-statement'],
+    ['acknowledgement', 'acknowledgements'],
+    ['introduction', 'intro'],
+    ['materials-method', 'methods'],
+    ['subsection', ''],
+  ])
+
+  migrateNode(node: JSONProsemirrorNode): JSONProsemirrorNode {
+    if (
+      node.type === 'section' &&
+      node.attrs.category.startsWith('MPSectionCategory:')
+    ) {
+      const [, suffix] = node.attrs.category.split(':', 2)
+      const newCategory = this.suffixMap.get(suffix) || suffix
+      return {
+        ...node,
+        attrs: {
+          ...node.attrs,
+          category: newCategory,
+        },
+      }
+    }
+    return node
+  }
+}
+
+export default Migration3021

package/src/schema/migration/migration-scripts/3.0.30.ts

@@ -0,0 +1,65 @@
+/*!
+ * © 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 { MigrationScript } from '../migration-script'
+
+class Migration3030 implements MigrationScript {
+  fromVersion = '3.0.29'
+  toVersion = '3.0.30'
+
+  private addTypeToFigures(node: JSONProsemirrorNode, type: string) {
+    if (!Array.isArray(node.content)) {
+      return node.content
+    }
+
+    return node.content.map((child) =>
+      child.type === 'figure'
+        ? { ...child, attrs: { ...child.attrs, type } }
+        : child
+    )
+  }
+
+  private migrateFigure(node: JSONProsemirrorNode): JSONProsemirrorNode {
+    const type = node.attrs.contentType || node.attrs.type || ''
+    if (node.attrs.contentType) {
+      delete node.attrs.contentType
+    }
+    return { ...node, attrs: { ...node.attrs, type } }
+  }
+
+  private migrateFigureElement(node: JSONProsemirrorNode): JSONProsemirrorNode {
+    const newContent = this.addTypeToFigures(node, node.attrs.type || '')
+    if (node.attrs.type) {
+      delete node.attrs.type
+    }
+    return { ...node, content: newContent, attrs: { ...node.attrs } }
+  }
+
+  migrateNode(node: JSONProsemirrorNode): JSONProsemirrorNode {
+    if (node.type === 'figure') {
+      return this.migrateFigure(node)
+    }
+
+    if (node.type === 'figure_element') {
+      return this.migrateFigureElement(node)
+    }
+
+    return node
+  }
+}
+
+export default Migration3030

package/src/schema/migration/migration-scripts/3.0.31.ts

@@ -0,0 +1,40 @@
+/*!
+ * © 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 { JSONProsemirrorNode } from '../../../types'
+import { MigrationScript } from '../migration-script'
+
+class Migration3031 implements MigrationScript {
+  fromVersion = '3.0.30'
+  toVersion = '3.0.31'
+
+  migrateNode(node: JSONProsemirrorNode): JSONProsemirrorNode {
+    if (node.type === 'table_header' || node.type === 'table_cell') {
+      return {
+        ...node,
+        content: [
+          {
+            type: 'text_block',
+            attrs: {},
+            content: node.content,
+          },
+        ],
+      }
+    }
+    return node
+  }
+}
+
+export default Migration3031

package/src/schema/migration/migration-scripts/3.0.41.ts

@@ -0,0 +1,37 @@
+/*!
+ * © 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 { JSONProsemirrorNode } from '../../../types'
+import { MigrationScript } from '../migration-script'
+
+class Migration3041 implements MigrationScript {
+  fromVersion = '3.0.40'
+  toVersion = '3.0.41'
+
+  migrateNode(node: JSONProsemirrorNode): JSONProsemirrorNode {
+    if (node.type === 'graphical_abstract_section') {
+      return {
+        ...node,
+        attrs: {
+          ...node.attrs,
+          category: 'abstract-graphical',
+        },
+      }
+    }
+    return node
+  }
+}
+
+export default Migration3041

package/src/schema/migration/migration-scripts/3.0.55.ts

@@ -0,0 +1,42 @@
+/*!
+ * © 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 { MigrationScript } from '../migration-script'
+
+class Migration3055 implements MigrationScript {
+  fromVersion = '3.0.54'
+  toVersion = '3.0.55'
+
+  migrateNode(node: JSONProsemirrorNode): JSONProsemirrorNode {
+    if (node.type === 'bibliography_item') {
+      const doi = node.attrs.doi
+      const containerTitle = node.attrs.containerTitle
+      delete node.attrs.doi
+      delete node.attrs.containerTitle
+      return {
+        ...node,
+        attrs: {
+          ...node.attrs,
+          DOI: doi,
+          'container-title': containerTitle,
+        },
+      }
+    }
+    return node
+  }
+}
+
+export default Migration3055

package/src/schema/migration/migration-scripts/3.0.56.ts

@@ -0,0 +1,114 @@
+/*!
+ * © 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 { generateNodeID } from '../../../transformer'
+import { JSONProsemirrorNode } from '../../../types'
+import { schema } from '../../index'
+import { MigrationScript } from '../migration-script'
+
+class Migration3056 implements MigrationScript {
+  fromVersion = '3.0.55'
+  toVersion = '3.0.56'
+
+  migrateNode(node: JSONProsemirrorNode): JSONProsemirrorNode {
+    const targetNodeTypes = [
+      'figure_element',
+      'table_element',
+      'image_element',
+      'figure',
+      'embed',
+    ]
+    const content = node.content
+
+    if (!targetNodeTypes.includes(node.type) || !content) {
+      return node
+    }
+
+    if (!content.some((node) => node.type === 'alt_text')) {
+      this.addAltText(node, content)
+    }
+
+    if (!content.some((node) => node.type === 'long_desc')) {
+      this.addLongDesc(content)
+    }
+
+    return node
+  }
+
+  private addAltText(
+    node: JSONProsemirrorNode,
+    content: JSONProsemirrorNode[]
+  ): void {
+    const altText = schema.nodes.alt_text
+      .create({
+        id: generateNodeID(schema.nodes.alt_text),
+      })
+      .toJSON()
+
+    switch (node.type) {
+      case 'image_element':
+        if (content.some((n) => n.type === 'long_desc')) {
+          const longDescIndex = content.findIndex((n) => n.type === 'long_desc')
+          content.splice(longDescIndex, 0, altText)
+        } else {
+          content.push(altText)
+        }
+        break
+
+      case 'figure_element':
+      case 'embed': {
+        const figCaption = content.findIndex((n) => n.type === 'figcaption')
+        if (figCaption !== -1) {
+          content.splice(figCaption + 1, 0, altText)
+        }
+        break
+      }
+
+      case 'table_element': {
+        const elementTypes = [
+          'table_element_footer',
+          'col_group',
+          'table',
+          'placeholder',
+        ]
+        for (const type of elementTypes) {
+          const index = content.findIndex((n) => n.type === type)
+          if (index !== -1) {
+            content.splice(index + 1, 0, altText)
+            break
+          }
+        }
+        break
+      }
+    }
+  }
+
+  private addLongDesc(content: JSONProsemirrorNode[]): void {
+    const altTextIndex = content.findIndex((n) => n.type === 'alt_text')
+    if (altTextIndex !== -1) {
+      content.splice(
+        altTextIndex + 1,
+        0,
+        schema.nodes.long_desc
+          .create({
+            id: generateNodeID(schema.nodes.long_desc),
+          })
+          .toJSON()
+      )
+    }
+  }
+}
+
+export default Migration3056

package/src/schema/migration/migration-scripts/4.2.13.ts

@@ -0,0 +1,37 @@
+/*!
+ * © 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 { schema } from '../..'
+import { MigrationScript } from '../migration-script'
+
+class Migration4213 implements MigrationScript {
+  fromVersion = '4.2.12'
+  toVersion = '4.2.13'
+
+  migrateNode(node: JSONProsemirrorNode): JSONProsemirrorNode {
+    if (node.type === 'trans_abstract') {
+      const content = node.content || []
+      const sectionTitleNode = schema.nodes.section_title.create()
+      return {
+        ...node,
+        content: [sectionTitleNode.toJSON(), ...content],
+      }
+    }
+    return node
+  }
+}
+
+export default Migration4213

package/src/schema/migration/migration-scripts/4.2.15.ts

@@ -0,0 +1,48 @@
+/*!
+ * © 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 { schema } from '../..'
+import { MigrationScript } from '../migration-script'
+
+class Migration4215 implements MigrationScript {
+  fromVersion = '4.2.14'
+  toVersion = '4.2.15'
+
+  migrateNode(node: JSONProsemirrorNode): JSONProsemirrorNode {
+    if (node.type !== schema.nodes.manuscript.name || !node.content) {
+      return node
+    }
+
+    const supplementsNode = node.content.find(
+      (child) => child.type === schema.nodes.supplements.name
+    )
+
+    if (supplementsNode) {
+      node.content = node.content.filter(
+        (child) => child.type !== schema.nodes.supplements.name
+      )
+
+      const backmatterIndex = node.content.findIndex(
+        (child) => child.type === schema.nodes.backmatter.name
+      )
+      node.content.splice(backmatterIndex + 1, 0, supplementsNode)
+    }
+
+    return node
+  }
+}
+
+export default Migration4215