Document toolboxDocument toolbox

DOI API Update (2018)

Owned by Nick Grosenbacher
Last updated: Jul 17, 2018
6 min read

Background & Motivation

See Meredith Slota (Unlicensed)'s 1-pager and the epic issue:

  PLFM-4063 - Getting issue details... STATUS

In summary, we

  1. Must transition to a new DOI provider
  2. Can enhance usability by allowing clients to set and update descriptive metadata stored by the DOI provider.
  3. Can redesign how we handle DOI creation to better fit with existing software design paradigms in Synapse (including changing our API, handling asynchronous workers differently, etc.)

Current API 

We should strongly consider deprecating these calls in favor of the new API, see below section 'API Additions' 

URL
HTTP Type
Description
Response Object
/entity/{id}/doiPUTCreates a DOI for the specified entity. The DOI will associated with the most recent version where applicable.Doi
/entity/{id}/version/{versionNumber}/doiPUTCreates a new DOI for the specified entity version.Doi
/entity/{id}/doiGETGets the DOI status for the specified entity.Doi
/entity/{id}/version/{versionNumber}/doiGETGets the DOI status for the specified entity version.Doi

Proposed Changes

Object changes:
  • Creation of new Doi (v2) data transfer object that implements new interface DataciteMetadata and new class DoiAssociation
    • DataciteMetadata
      • Separates DOI metadata (that is stored by DataCite) from Synapse-associated metadata
      • The client never uses this object, but it clearly delineates metadata that DataCite stores and metadata Synapse stores (in DoiAssociation)
    • DoiAssociation
      • Stores data that describes a Synapse object's association with a DOI object (like the object ID, type, version, etag, etc.)
      • Client can request this object to quickly get a DOI without relying on DataCite service availability to collect additional metadata.
      • We can return the DOI URI and URL to the client (currently, the URI is "guessed" by the client)
    • By using Doi (v2):
      • The client can supply and update metadata
      • We have the option to extend support to additional metadata fields
      • We decouple our API URI from /entity/{id}
      • We have the option to extend support to mint DOIs for non-entity objects in Synapse
  • Creation of DoiRequest object to retrieve a DOI and all of its metadata

The new fields in object is a direct mapping of the most recent version (v4.1) of DataCite's metadata schema, simplified to contain only required fields and a small amount of optional fields that we curate. This ensures that we don't need to deprecate our API if we wish to support more of their optional metadata fields. If we do wish to support new optional metadata fields, we can easily extend our object.

Similarly, this is likely to simplify future transitions if DataCite deprecates the schema that we configure to use.

DataCite-imposed constraints for implementing clients to consider:

  • There cannot be more than 8000-10000 creators
  • Publication year must be in 'YYYY' format (regex: /[\d]{4}/)
  • There must be at least one creator
    • Each creator must have a creatorName that is at least 1 character long
    • nameIdentifier is not required, but if an identifier is provided, the scheme must also be provided
  • There must be at least one title
    • The title should be at least one character long
  • There must be a resourceTypeGeneral
    • One of the following
      • Audiovisual
      • Collection
      • Data Paper
      • Dataset
      • Event
      • Image
      • Interactive Resource
      • Model
      • Physical Object
      • Service
      • Software
      • Sound
      • Text
      • Workflow
      • Other

API Additions

URLHTTP VerbDescriptionRequest ObjectResponse ObjectNotes
/doi/async/startPOST

Asynchronously create or update a DOI. If the DOI does not exist, start a DOI creation job that will attempt to register a DOI with the DOI provider with the supplied metadata. If the DOI does exist, then it will simply update the DOI with the supplied metadata.

Note: The caller must have the ACCESS_TYPE.UPDATE permission on the Entity to make this call.

Doi 

(application/json)

AsyncJobId

Shift the work to an asynchronous worker queue (as we have been doing with other asynchronous services).

We combine the create and update calls because they require the same information and are both idempotent.

The Doi object must contain all fields required to mint or update a DOI with DataCite.

/doi/async/get/{asyncToken}GET

Asynchronously get the results of a DOI transaction started with POST /doi/async/start

Note: When the result is not ready yet, this method will return a status code of 202 (ACCEPTED) and the response body will be a AsynchronousJobStatus object.

None

AsynchronousJobStatus

Doi

Get the status of the asynchronous job. If complete, returns the Doi object created by the job.
/doiGET

Get a Doi object (including associated metadata) for the object referred to in DoiRequest, if the Doi object exists.

None (supply required path parameters id, objectType, and optional objectVersion)

Doi

This call relies on availability of DataCite's API to return the metadata, as we do not store it.

/doi/associationGETGet a DoiAssociation object that contains the DOI of an object referred to in DOI.None (supply required path parameters id, objectType, and optional objectVersion)DoiAssociation

By making this call, a client can get the DOI of an object without certain metadata that relies on availability of DataCite's API.

/doi/locateGETRedirect to a specific object in the web portal, or a "Not found" page if the object cannot be located.None (supply required path parameters id, objectType, and optional objectVersion)Redirect

This redirects a URL that we supply to DataCite to the current URL of an associated object.

This allows us to register a more "permanent" URL with DataCite in case the URL to an object changes. For example, http://synapse.org/#!Synapse:syn123 may change and become http://sage.gov/syn123. This service can be updated to support that and as a result, the DOI does not break.

Internal design notes

API Choice

DataCite has two APIs that we can use. They have a standard "MDS" API that they recommend for users, and they have a new (but also seemingly temporary) "EZ" API that is designed for orgs like us who are transitioning from EZID.

For the sake of not having to do more work later, we are opting to not use DataCite's temporary EZ API that is designed to mock the EZID API.

Instead, we will be using their standard MDS API, as we would need to transition to it eventually anyways.

CRUD Workflows

With the MDS API the basic workflow to create a DOI is to

  1. (POST) Register metadata (including the DOI symbol e.g. 10.####/syn01234)
  2. (PUT) Register the DOI symbol and tie it to a URL (synapse.org/#!Synapse:syn01234)

Simply updating the metadata requires just step 1. Both of the above calls are idempotent, so we can combine create and update calls and simply treat the implementation as a create. This would simplify the implementation, though an unnecessary outgoing PUT call would made when existing DOIs are updated.

Retrieval and Translation of Metadata

DataCite requires that new DOIs have associated metadata that adheres to a schema that they revise occasionally. The current version of their schema is v4.1 (Oct 2017). Metadata that we have registered through EZID is adherent to v2.2 (June 2011), v3, and v4. It is unclear if/when DataCite will deprecate v2.2 and no longer accept it. In another attempt to future-proof our DOI minting service, we will only submit metadata adherent to v4.1.

As a result of this, we must be able to retrieve metadata adherent to schemas 2.2+ in order for the client to update it. We can create a translator tool to convert data from these schemas to an intermediate object (see new fields in Doi above) that can hold the appropriate metadata. This object can be translated into the most recent version of the schema. The client can retrieve and submit this object by interfacing with our API 

Work to do

Outside of our control

DataCite has now approved us to transition to their service, so we should coordinate to transition as soon as possible.

Platform

  • Create, test, and implement a DataCite Java client that simplifies creating/updating DOIs and their metadata.
    • Agree on API
    • This can be done without coordination if we preserve existing behavior, but it would be much easier if we create this client intending to only support proposed and agreed-upon behavior.
    • Implementation can use test credentials until we are ready to switch to DataCite in prod
  • Create and route new API changes

Clients

  • Support asynchronous API + metadata submission
    • Can begin as soon as we agree upon the API
    • Can implement as soon as it is tested and implemented on backend

UX

  • User-facing design of DOI minting process and metadata submission
  • What to show users when reaching
    • embargo/restricted pages?
    • tombstone pages (deleted content)?

Mockups

Mockup of what the DOI minting form could look like. This form could be presented when a user clicks "Mint DOI for this Project/File" (as they currently do)

More mockups may be added later

Points of Discussion

  • General feedback
  • Proposed alterations
  • Transition steps
  • Displaying metadata/contact information on deleted/restricted pages
    • Tombstone pages
    • Embargo pages
    • Perhaps we could show this on a 'Not Found' page when referred by the /doi/locate API?

Optional fields we can consider supporting:

 Creator sub-fields
  • Name type (organizational or personal)
  • Given Name; Family Name
  • Name Identifiers like ORCID and ISNI
  • Affiliation
  • Title sub-field: title type (one of: alternative title, subtitle, translated title)
 Contributor - The institution or person responsible for collecting, managing, distributing, or otherwise contributing to the development of the resource.
  • Contributor type - mandatory. One of:
    • ContactPerson
    • DataCollector
    • DataCurator
    • DataManager
    • Distributor
    • Editor
    • HostingInstitution
    • Producer
    • ProjectLeader
    • ProjectManager
    • ProjectMember
    • RegistrationAgency
    • RegistrationAuthority
    • RelatedPerson
    • Researcher
    • ResearchGroup
    • RightsHolder
    • Sponsor
    • Supervisor
    • WorkPackageLeader
    • Other
  • Contributor name (mandatory)
  • Name type (organizational/personal)
  • Given name; family name
  • Name identifiers
  • Affiliation
  • Subject - Subject, keyword, classification code, or key phrase describing the resource.
 Date
  • Mandatory dateType. One of:
    • Accepted
    • Available
    • Copyrighted
    • Collected
    • Created
    • Issued
    • Submitted
    • Updated
    • Valid
    • Other
  • Date information
  • Language
  • AlternateIdentifier. This may be used for local identifiers
    • alternateIdentifierType - mandatory
 RelatedIdentifier


 RelatedIdentifierType - mandatory. One of:
  • ARK
  • arXiv
  • bibcode
  • DOI
  • EAN13
  • EISSN
  • Handle
  • IGSN
  • ISBN
  • ISSN
  • ISTC
  • LISSN
  • LSID
  • PMID
  • PURL
  • UPC
  • URL
  • URN
 RelationType - mandatory. One of:
  • IsCitedBy
  • Cites
  • IsSupplementTo
  • IsSupplementedBy
  • IsContinuedBy
  • Continues
  • IsDescribedBy
  • Describes
  • HasMetadata
  • IsMetadataFor
  • HasVersion
  • IsVersionOf
  • IsNewVersionOf
  • IsPreviousVersionOf
  • IsPartOf
  • HasPart
  • IsReferencedBy
  • References
  • IsDocumentedBy
  • Documents
  • IsCompiledBy
  • Compiles
  • IsVariantFormOf
  • IsOriginalFormOf
  • IsIdenticalTo
  • IsReviewedBy
  • Reviews
  • IsDerivedFrom
  • IsSourceOf
  • IsRequiredBy
  • Requires
  • Size
  • Format
  • Version
  • Rights (include embargo information if applicable)
  • Description
    • Description Type (mandatory). One of:
      • Abstract
      • Methods
      • SeriesInformation
      • TableOfContents
      • TechnicalInfo
      • Other
  • GeoLocation (and many subfields)
  • Funding Reference
    • Funder Name
    • Funder Identifier
    • Funder Identifier Type
    • Award Number
    • Award Title