Other Integrations

Whole Tale Integration Proposal

Whole Tale (http://www.wholetale.org) is a platform for the creation, publication, and re-execution of reproducible computational artifacts. Researchers can create new tales that contain the code, data, workflow, and information about the computational environment required to reproduce their analysis. Tales have basic metadata including authors, title, keywords, description, and related identifiers (cited derived from). Tales can be published to archival repositories including DataONE network members and Zenodo.

Whole Tale is an integration partner for the PresQT project. As part of the integration testing process, we explored two different use cases:

• Publish Tales from the WT platform to Zenodo and CurateND using the PresQT APIs

• Import an OSF project into WT using the PresQT APIs

BagIt Serialization

Tales are exported as BDBag-compatible bags with the following structure:

5e696df5f1c291f11ae9e1a8/
  README.md               <-- Top-level readme (Tag file)
  bagit.txt
  bag-info.txt
  fetch.txt               <-- Fetch file
  manifest-md5.txt
  manifest-sha256.txt
  run-local.sh            <-- Script to run Tale locally (Tag file)
  tagmanifest-md5.txt
  tagmanifest-sha256.txt
  data/
    workspace/            <-- Tale workspace (user code, data, etc)
      environment.yml
      index.ipynb
    LICENSE               <-- Tale license (Tag file)
  metadata/               <-- Tale metadata (Tag directory)
      environment.json
      manifest.json

The Tale bag is not currently compatible with PresQT, since PresQT currently requires a single top-level folder in the payload representing the project. The folder name is used as the dataset title when publishing to a target. Since the Tale bag has a separate structure, one option is to double-bag. In the following example, the above Tale is zipped and bagged:

presqt_bag/
  bagit.txt
  bag-info.txt
  manifest-md5.txt
  manifest-sha256.txt
  tagmanifest-md5.txt
  tagmanifest-sha256.txt
  data/
    Mapping Estimated Water Usage/
      5e7e10163632f4f0c84c51a8.zip

Publishing to Zenodo

The following figures illustrate the Tale as published to Zenodo using the WT internal integration and using PresQT.

The first images illustrates a tale published to Zenodo using the WT internal integration. The title, author, and description are all provided by the user during tale creation. The WT platform adds a note with a custom link allowing the user to import and re-execute the tale in the WT system. WT also supports related identifiers, license, and keywork metadata. The tale is published as a zipped bag.

Tale published to Zenodo via WT

The second image illustrates a tale published to Zenodo using the PresQT integration. The user is directed to the draft dataset creation form where they are required to manually enter relevant metadata.

Tale published to Zenodo via PresQT

Metadata Support

To support our current Zenodo integration using the PresQT system would require the ability to specify additional metadata during dataset creation. We use the following fields:

• Title

• Creator/Authors (first name, last name, ORCID)

• Publication date/date

• Description

• Subject/keywords

• Rights/license

• Related identifiers (Cites, Derived From)

• References

• Notes

The notes field is important as it provides a way for us to embed a link in the record that allows users to easily re-import and run the published tale.

For more information, see https://github.com/whole-tale/serialization-format/

Whole Tale Integration Implementation

An ‘extra_metadata’ field has been added to the PRESQT_FTS_METADATA.json. To get these extra metadata fields to the new resource being created, the uploaded resources must have a PRESQT_FTS_METADATA.json file at the highest level.

The following is an example:

{
    "allKeywords": [],
    "actions": [],
    "extra_metadata": {
        "title": "str",
        "creators": [
            {
                "first_name": "Example",
                "last_name": "User",
                "ORCID": "0931234123"
            }
        ],
        "publication_date": "2021-02-19",
        "description": "This is it.",
        "

        s": [],
        "license": "MIT",
        "related_identifiers": [],
        "references": "Nothing here.",
        "notes": "Nope."
    }
}