@openneuro/server 4.47.6 → 5.0.0-alpha.0

package/src/types/datacite/datacite-v4.5.ts

@@ -0,0 +1,281 @@
+/* eslint-disable */
+/**
+ * This file was automatically generated by json-schema-to-typescript.
+ * DO NOT MODIFY IT BY HAND. Instead, modify the source JSONSchema file,
+ * and run json-schema-to-typescript to regenerate this file.
+ */
+
+export type ResourceTypeGeneral =
+  | "Audiovisual"
+  | "Book"
+  | "BookChapter"
+  | "Collection"
+  | "ComputationalNotebook"
+  | "ConferencePaper"
+  | "ConferenceProceeding"
+  | "DataPaper"
+  | "Dataset"
+  | "Dissertation"
+  | "Event"
+  | "Image"
+  | "Instrument"
+  | "InteractiveResource"
+  | "Journal"
+  | "JournalArticle"
+  | "Model"
+  | "OutputManagementPlan"
+  | "PeerReview"
+  | "PhysicalObject"
+  | "Preprint"
+  | "Report"
+  | "Service"
+  | "Software"
+  | "Sound"
+  | "Standard"
+  | "StudyRegistration"
+  | "Text"
+  | "Workflow"
+  | "Other"
+export type Creator = Person
+export type NameType = "Organizational" | "Personal"
+export type NameIdentifiers = {
+  nameIdentifier: string
+  nameIdentifierScheme: string
+  schemeUri?: string
+}[]
+export type Affiliation = {
+  name: string
+  affiliationIdentifier?: string
+  affiliationIdentifierScheme?: string
+  schemeUri?: string
+}[]
+export type TitleType =
+  | "AlternativeTitle"
+  | "Subtitle"
+  | "TranslatedTitle"
+  | "Other"
+export type PublicationYear = string
+export type Contributor = Person & {
+  contributorType: ContributorType
+  [k: string]: unknown
+}
+export type ContributorType =
+  | "ContactPerson"
+  | "DataCollector"
+  | "DataCurator"
+  | "DataManager"
+  | "Distributor"
+  | "Editor"
+  | "HostingInstitution"
+  | "Producer"
+  | "ProjectLeader"
+  | "ProjectManager"
+  | "ProjectMember"
+  | "RegistrationAgency"
+  | "RegistrationAuthority"
+  | "RelatedPerson"
+  | "Researcher"
+  | "ResearchGroup"
+  | "RightsHolder"
+  | "Sponsor"
+  | "Supervisor"
+  | "WorkPackageLeader"
+  | "Other"
+export type Date = {
+  [k: string]: unknown
+}
+export type Date1 = string
+export type DateType =
+  | "Accepted"
+  | "Available"
+  | "Copyrighted"
+  | "Collected"
+  | "Created"
+  | "Issued"
+  | "Submitted"
+  | "Updated"
+  | "Valid"
+  | "Withdrawn"
+  | "Other"
+export type RelationType =
+  | "IsCitedBy"
+  | "Cites"
+  | "IsCollectedBy"
+  | "Collects"
+  | "IsSupplementTo"
+  | "IsSupplementedBy"
+  | "IsContinuedBy"
+  | "Continues"
+  | "IsDescribedBy"
+  | "Describes"
+  | "HasMetadata"
+  | "IsMetadataFor"
+  | "HasVersion"
+  | "IsVersionOf"
+  | "IsNewVersionOf"
+  | "IsPartOf"
+  | "IsPreviousVersionOf"
+  | "IsPublishedIn"
+  | "HasPart"
+  | "IsReferencedBy"
+  | "References"
+  | "IsDocumentedBy"
+  | "Documents"
+  | "IsCompiledBy"
+  | "Compiles"
+  | "IsVariantFormOf"
+  | "IsOriginalFormOf"
+  | "IsIdenticalTo"
+  | "IsReviewedBy"
+  | "Reviews"
+  | "IsDerivedFrom"
+  | "IsSourceOf"
+  | "IsRequiredBy"
+  | "Requires"
+  | "IsObsoletedBy"
+  | "Obsoletes"
+export type DescriptionType =
+  | "Abstract"
+  | "Methods"
+  | "SeriesInformation"
+  | "TableOfContents"
+  | "TechnicalInfo"
+  | "Other"
+export type Longitude = number
+export type Latitude = number
+export type FunderIdentifierType =
+  | "ISNI"
+  | "GRID"
+  | "Crossref Funder ID"
+  | "ROR"
+  | "Other"
+
+/**
+ * JSON representation of the DataCite v4.5 schema.
+ */
+export interface DataCiteV45 {
+  doi?: string
+  prefix?: string
+  suffix?: string
+  event?: "hide" | "register" | "publish"
+  url?: string
+  types: {
+    resourceType?: string
+    resourceTypeGeneral: ResourceTypeGeneral
+  }
+  /**
+   * @minItems 1
+   */
+  creators: [Creator, ...Creator[]]
+  /**
+   * @minItems 1
+   */
+  titles: [
+    {
+      title: string
+      titleType?: TitleType
+      lang?: string
+    },
+    ...{
+      title: string
+      titleType?: TitleType
+      lang?: string
+    }[],
+  ]
+  publisher: {
+    name: string
+    publisherIdentifier?: string
+    publisherIdentifierScheme?: string
+    schemeUri?: string
+    lang?: string
+  }
+  publicationYear: PublicationYear
+  subjects?: {
+    subject: string
+    subjectScheme?: string
+    schemeUri?: string
+    valueUri?: string
+    classificationCode?: string
+    lang?: string
+  }[]
+  contributors?: Contributor[]
+  dates?: {
+    date: Date & Date1
+    dateType: DateType
+    dateInformation?: string
+  }[]
+  language?: string
+  alternateIdentifiers?: {
+    alternateIdentifier: string
+    alternateIdentifierType: string
+  }[]
+  relatedIdentifiers?: RelatedObject[]
+  relatedItems?: RelatedObject[]
+  sizes?: string[]
+  formats?: string[]
+  version?: string
+  rightsList?: {
+    rights?: string
+    rightsUri?: string
+    rightsIdentifier?: string
+    rightsIdentifierScheme?: string
+    schemeUri?: string
+    lang?: string
+  }[]
+  descriptions?: {
+    description: string
+    descriptionType: DescriptionType
+    lang?: string
+  }[]
+  geoLocations?: {
+    geoLocationPlace?: string
+    geoLocationPoint?: GeoLocationPoint
+    geoLocationBox?: {
+      westBoundLongitude: Longitude
+      eastBoundLongitude: Longitude
+      southBoundLatitude: Latitude
+      northBoundLatitude: Latitude
+    }
+    geoLocationPolygon?: {
+      polygonPoint?: GeoLocationPoint
+      inPolygonPoint?: GeoLocationPoint
+    }[]
+  }[]
+  fundingReferences?: {
+    funderName: string
+    funderIdentifier?: string
+    funderIdentifierType?: FunderIdentifierType
+    awardNumber?: string
+    awardUri?: string
+    awardTitle?: string
+  }[]
+  schemaVersion: "http://datacite.org/schema/kernel-4"
+  container?: {
+    type?: string
+    title?: string
+    firstPage?: string
+    [k: string]: unknown
+  }
+}
+export interface Person {
+  name: string
+  nameType?: NameType
+  givenName?: string
+  familyName?: string
+  nameIdentifiers?: NameIdentifiers
+  affiliation?: Affiliation
+  lang?: string
+  [k: string]: unknown
+}
+export interface RelatedObject {
+  relationType: RelationType
+  relatedMetadataScheme?: string
+  schemeUri?: string
+  schemeType?: string
+  resourceTypeGeneral?: ResourceTypeGeneral
+  [k: string]: unknown
+}
+export interface GeoLocationPoint {
+  pointLongitude: Longitude
+  pointLatitude: Latitude
+}

package/src/types/datacite.ts

@@ -1,29 +1,44 @@
 /**
- * Interfaces for working with datacite.yml metadata.
- * Both contributors and creators
+ * DataCite types.
+ *
+ * Schema-derived types are re-exported from the generated datacite-v4.5 module.
+ * Only app-specific types that don't exist in the DataCite schema are defined here.
  */
 
-/**
- * Unique identifier for a person or organization.
- */
-export interface NameIdentifier {
-  nameIdentifier: string
-  nameIdentifierScheme: string
-  schemeUri?: string
-}
+export type {
+  Affiliation,
+  ContributorType,
+  Creator,
+  DescriptionType,
+  NameIdentifiers,
+  NameType,
+  Person,
+  PublicationYear,
+  ResourceTypeGeneral,
+  TitleType,
+} from "./datacite/datacite-v4.5"
+
+export type { Contributor as DataciteContributor } from "./datacite/datacite-v4.5"
+
+import type { Creator, DataCiteV45, TitleType } from "./datacite/datacite-v4.5"
 
 /**
- * An interface for an organizational or institutional affiliation.
+ * Re-export the versioned schema type under a version-agnostic name.
+ *
+ * Titles and creators are omitted and we separately check minItems:1
  */
-export interface Affiliation {
-  name: string
-  schemeUri?: string
-  affiliationIdentifier?: string
-  affiliationIdentifierScheme?: string
+export type DataCite = Omit<DataCiteV45, "creators" | "titles"> & {
+  creators: Creator[]
+  titles: {
+    title: string
+    titleType?: TitleType
+    lang?: string
+  }[]
 }
 
 /**
- * Contributor object (normalized form used internally in app).
+ * Internal app contributor type with fields not in the DataCite schema
+ * (orcid shorthand, display order, linked user ID).
  */
 export interface Contributor {
   name: string
@@ -36,62 +51,37 @@ export interface Contributor {
 }
 
 /**
- * Base interface shared by both creators and contributors in datacite.yml
- */
-export interface RawDataciteBaseContributor {
-  name: string
-  nameType: "Personal" | "Organizational"
-  givenName?: string
-  familyName?: string
-  nameIdentifiers?: NameIdentifier[]
-  affiliation?: Affiliation[]
-}
-
-/**
- * Raw Creator object as it appears in datacite.yml creators array.
- * Does NOT have contributorType.
- */
-export type RawDataciteCreator = RawDataciteBaseContributor
-
-/**
- * Raw Contributor object as it appears in datacite.yml contributors array.
- * Adds contributorType, which is required.
+ * DOI states tracked in our database (response-only, not in the DataCite request schema).
  */
-export interface RawDataciteContributor extends RawDataciteBaseContributor {
-  contributorType: string
-}
+export type DoiState = "draft" | "registered" | "findable"
 
-/**
- * An interface for the resource types.
- */
-export interface RawDataciteTypes {
-  resourceType?: string
-  resourceTypeGeneral: string
+export interface DatasetWithDescription {
+  dataset_description?: {
+    Description?: string
+  }
 }
 
 /**
- * The main attributes section of the datacite.yml file.
- */
-export interface RawDataciteAttributes {
-  contributors?: RawDataciteContributor[]
-  creators?: RawDataciteCreator[]
-  types: RawDataciteTypes
-  descriptions?: {
-    description: string
-    descriptionType: string
-  }[]
-}
-/**
- * The top-level interface for the entire datacite.yml file structure.
+ * The datacite.yml file structure stored in dataset repositories.
+ * Uses a subset of DataCiteV45 fields wrapped in a JSON:API-like envelope.
  */
 export interface RawDataciteYml {
   data: {
-    attributes: RawDataciteAttributes
+    attributes: Partial<
+      Pick<
+        DataCite,
+        "contributors" | "creators" | "types" | "descriptions"
+      >
+    >
   }
 }
 
-export interface DatasetWithDescription {
-  dataset_description?: {
-    Description?: string
+/**
+ * JSON:API request envelope for the DataCite REST API.
+ */
+export interface DataciteDoiRequest {
+  data: {
+    type: "dois"
+    attributes: DataCite
   }
 }

package/src/utils/datacite-mapper.ts

@@ -1,11 +1,15 @@
-import type { Contributor, RawDataciteContributor } from "../types/datacite"
+import type {
+  Contributor,
+  ContributorType,
+  DataciteContributor,
+} from "../types/datacite"
 
 export const mapToRawContributor = (
   c: Contributor,
-): RawDataciteContributor => ({
+): DataciteContributor => ({
   name: c.name,
   nameType: "Personal",
-  contributorType: c.contributorType || "Researcher",
+  contributorType: (c.contributorType || "Researcher") as ContributorType,
   givenName: c.givenName,
   familyName: c.familyName,
   nameIdentifiers: c.orcid

package/src/utils/datacite-utils.ts

@@ -7,7 +7,9 @@ import { commitFiles } from "../datalad/dataset"
 import { getDatasetWorker } from "../libs/datalad-service"
 import type {
   Contributor,
-  RawDataciteContributor,
+  ContributorType,
+  Creator,
+  DataciteContributor,
   RawDataciteYml,
 } from "../types/datacite"
 import { validateOrcid } from "../utils/orcid-utils"
@@ -131,11 +133,11 @@ export const saveDataciteYmlToRepo = async (
 }
 
 /**
- * Converts RawDataciteContributor -> internal Contributor type.
+ * Converts DataciteContributor -> internal Contributor type.
  * Optionally attaches a `userId` if the contributor exists as a site user.
  */
 export const normalizeRawContributors = async (
-  raw: RawDataciteContributor[] | undefined,
+  raw: DataciteContributor[] | undefined,
 ): Promise<Contributor[]> => {
   if (!Array.isArray(raw)) return []
 
@@ -183,14 +185,14 @@ export const updateContributors = async (
       dataciteData = await emptyDataciteYml({ datasetId, revision })
     }
 
-    // Map contributors to RawDataciteContributor format
-    const rawContributors: RawDataciteContributor[] = newContributors.map((
+    // Map contributors to DataciteContributor format
+    const rawContributors: DataciteContributor[] = newContributors.map((
       c,
     ) => ({
       name: c.name,
       givenName: c.givenName,
       familyName: c.familyName,
-      contributorType: c.contributorType || "Researcher",
+      contributorType: (c.contributorType || "Researcher") as ContributorType,
       nameType: "Personal" as const,
       nameIdentifiers: c.orcid
         ? [{ nameIdentifier: c.orcid, nameIdentifierScheme: "ORCID" }]
@@ -223,7 +225,7 @@ export const updateContributorsUtil = async (
   //
   // 1. Build contributors (full form, includes `order`)
   //
-  const contributorsCopy: RawDataciteContributor[] = newContributors.map((
+  const contributorsCopy: DataciteContributor[] = newContributors.map((
     c,
     index,
   ) => ({
@@ -240,7 +242,7 @@ export const updateContributorsUtil = async (
         schemeUri: "https://orcid.org",
       }]
       : [],
-    contributorType: c.contributorType || "Researcher",
+    contributorType: (c.contributorType || "Researcher") as ContributorType,
     order: index + 1,
   }))
 
@@ -249,13 +251,8 @@ export const updateContributorsUtil = async (
   //
   // 2. Build creators (strictly filtered / no empty fields / no order)
   //
-  type RawDataciteCreator = Omit<
-    RawDataciteContributor,
-    "contributorType" | "order"
-  >
-
-  const creators: RawDataciteCreator[] = contributorsCopy.map((c) => {
-    const creator: RawDataciteCreator = {
+  const creators: Creator[] = contributorsCopy.map((c) => {
+    const creator: Creator = {
       name: c.name,
       nameType: "Personal",
     }

package/src/libs/doi/__tests__/__snapshots__/doi.spec.ts.snap

@@ -1,17 +0,0 @@
-// Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
-
-exports[`DOI minting utils > template() > accepts expected arguments 1`] = `
-"<?xml version="1.0" encoding="UTF-8"?>
-<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
-  <identifier identifierType="DOI">12345</identifier>
-  <creators>
-  <creator><creatorName>A. User</creatorName></creator><creator><creatorName>B. User</creatorName></creator>
-  </creators>
-  <titles>
-    <title xml:lang="en-us">Test Dataset</title>
-  </titles>
-  <publisher>Openneuro</publisher>
-  <publicationYear>1999</publicationYear>
-  <resourceType resourceTypeGeneral="Dataset">fMRI</resourceType>
-</resource>"
-`;