DataCite

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Python API wrapper for the DataCite Metadata Store API and DataCite XML generation.

Installation

The datacite package is on PyPI so all you need is:

$ pip install datacite

Usage

Below is full usage example of the DataCite MDS client API wrapper. Please see the DataCite MDS API documentation for further information on the API.

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from datacite import DataCiteMDSClient, schema42

# If you want to generate XML for earlier versions, you need to use either the
# schema31, schema40 or schema41 instead.

data = {
    'identifier': {
        'identifierType': 'DOI',
        'identifier': '10.1234/foo.bar',
    },
    'creators': [
        {'name': 'Smith, John'},
    ],
    'titles': [
        {'title': 'Minimal Test Case', }
    ],
    'publisher': 'Invenio Software',
    'publicationYear': '2015',
    'types': {
        'resourceType': 'Dataset',
        'resourceTypeGeneral': 'Dataset'
    },
    'schemaVersion': 'http://datacite.org/schema/kernel-4',
}

# Validate dictionary
assert schema42.validate(data)

# Generate DataCite XML from dictionary.
doc = schema42.tostring(data)

# Initialize the MDS client.
d = DataCiteMDSClient(
    username='MYDC.MYACCOUNT',
    password='mypassword',
    prefix='10.5072',
)

# Set metadata for DOI
d.metadata_post(doc)

# Mint new DOI
d.doi_post('10.5072/test-doi', 'http://example.org/test-doi')

# Get DOI location
location = d.doi_get("10.5072/test-doi")

# Set alternate URL for content type (available through content negotiation)
d.media_post(
    "10.5072/test-doi",
    {"application/json": "http://example.org/test-doi/json/",
     "application/xml": "http://example.org/test-doi/xml/"}
)

# Get alternate URLs
mapping = d.media_get("10.5072/test-doi")
assert mapping["application/json"] == "http://example.org/test-doi/json/"

# Get metadata for DOI
doc = d.metadata_get("10.5072/test-doi")

# Make DOI inactive
d.metadata_delete("10.5072/test-doi")

Metadata Store API

Python API wrapper for the DataCite Metadata Store API.

class datacite.DataCiteMDSClient(username=None, password=None, url=None, prefix=None, test_mode=False, api_ver='2', timeout=None)[source]

DataCite MDS API client wrapper.

doi_get(doi)[source]

Get the URL where the resource pointed by the DOI is located.

Parameters:doi – DOI name of the resource.
doi_post(new_doi, location)[source]

Mint new DOI.

Parameters:
  • new_doi – DOI name for the new resource.
  • location – URL where the resource is located.
Returns:

“CREATED” or “HANDLE_ALREADY_EXISTS”.

media_get(doi)[source]

Get list of pairs of media type and URLs associated with a DOI.

Parameters:doi – DOI name of the resource.
media_post(doi, media)[source]

Add/update media type/urls pairs to a DOI.

Standard domain restrictions check will be performed.

Parameters:media – Dictionary of (mime-type, URL) key/value pairs.
Returns:“OK”
metadata_delete(doi)[source]

Mark as ‘inactive’ the metadata set of a DOI resource.

Parameters:doi – DOI name of the resource.
Returns:“OK”
metadata_get(doi)[source]

Get the XML metadata associated to a DOI name.

Parameters:doi – DOI name of the resource.
metadata_post(metadata)[source]

Set new metadata for an existing DOI.

Metadata should follow the DataCite Metadata Schema: http://schema.datacite.org/

Parameters:metadata – XML format of the metadata.
Returns:“CREATED” or “HANDLE_ALREADY_EXISTS”

Errors

Errors for the DataCite API.

MDS error responses will be converted into an exception from this module. Connection issues raises datacite.errors.HttpError while DataCite MDS error responses raises a subclass of datacite.errors.DataCiteError.

exception datacite.errors.DataCiteBadRequestError[source]

Bad request error.

Bad requests can include e.g. invalid XML, wrong domain, wrong prefix. Request body must be exactly two lines: DOI and URL One or more of the specified mime-types or urls are invalid (e.g. non supported mimetype, not allowed url domain, etc.)

exception datacite.errors.DataCiteError[source]

Exception raised when the server returns a known HTTP error code.

Known HTTP error codes include:

  • 204 No Content
  • 400 Bad Request
  • 401 Unauthorized
  • 403 Forbidden
  • 404 Not Found
  • 410 Gone (deleted)
static factory(err_code, *args)[source]

Create exceptions through a Factory based on the HTTP error code.

exception datacite.errors.DataCiteForbiddenError[source]

Login problem, dataset belongs to another party or quota exceeded.

exception datacite.errors.DataCiteGoneError[source]

Requested dataset was marked inactive (using DELETE method).

exception datacite.errors.DataCiteNoContentError[source]

DOI is known to MDS, but not resolvable.

This might be due to handle’s latency.

exception datacite.errors.DataCiteNotFoundError[source]

DOI does not exist in the database.

exception datacite.errors.DataCitePreconditionError[source]

Metadata must be uploaded first.

exception datacite.errors.DataCiteRequestError[source]

A DataCite request error. You made an invalid request.

Base class for all 4XX-related HTTP error codes as well as 204.

exception datacite.errors.DataCiteServerError[source]

An internal server error happened on the DataCite end. Try later.

Base class for all 5XX-related HTTP error codes.

exception datacite.errors.DataCiteUnauthorizedError[source]

Bad username or password.

exception datacite.errors.HttpError[source]

Exception raised when a connection problem happens.

DataCite v3.1 XML generation

DataCite v3.1 JSON to XML transformations.

datacite.schema31.dump_etree(data)[source]

Convert JSON dictionary to DataCite v3.1 XML as ElementTree.

datacite.schema31.tostring(data, **kwargs)[source]

Convert JSON dictionary to DataCite v3.1 XML as string.

datacite.schema31.validate(data)[source]

Validate DataCite v3.1 JSON dictionary.

DataCite v4.0 XML generation

DataCite v4.0 JSON to XML transformations.

datacite.schema40.dump_etree(data)[source]

Convert JSON dictionary to DataCite v4.0 XML as ElementTree.

datacite.schema40.tostring(data, **kwargs)[source]

Convert JSON dictionary to DataCite v4.0 XML as string.

datacite.schema40.validate(data)[source]

Validate DataCite v4.0 JSON dictionary.

DataCite v4.1 XML generation

DataCite v4.1 JSON to XML transformations.

datacite.schema41.dump_etree(data)[source]

Convert JSON dictionary to DataCite v4.1 XML as ElementTree.

datacite.schema41.tostring(data, **kwargs)[source]

Convert JSON dictionary to DataCite v4.1 XML as string.

datacite.schema41.validate(data)[source]

Validate DataCite v4.1 JSON dictionary.

DataCite v4.2 XML generation

DataCite v4.2 JSON to XML transformations.

datacite.schema42.dump_etree(data)[source]

Convert JSON dictionary to DataCite v4.2 XML as ElementTree.

datacite.schema42.tostring(data, **kwargs)[source]

Convert JSON dictionary to DataCite v4.2 XML as string.

datacite.schema42.validate(data)[source]

Validate DataCite v4.2 JSON dictionary.

Changes

Version v1.0.1 (released 2018-03-08):

  • Fixes schema location url for DataCite v4.1

Version v1.0.0 (released 2018-02-28):

  • Adds full support for DataCite Metadata Schema v4.1 XML generation.

Version v0.3.0 (released 2016-11-18):

  • Adds full support for DataCite Metadata Schema v4.0 XML generation.
  • Adds the message from the server in the error exceptions.

Version v0.2.2 (released 2016-09-23):

  • Fixes issue with generated order of nameIdentifier and affiliation tags.

Version v0.2.1 (released 2016-03-29):

  • Fixes issue with JSON schemas not being included when installing from PyPI.

Version v0.2.0 (released 2016-03-21):

  • Adds DataCite XML generation support.

Version 0.1 (released 2015-02-25):

  • Initial public release.

Contributing

Bug reports, feature requests, and other contributions are welcome. If you find a demonstrable problem that is caused by the code of this library, please:

  1. Search for already reported problems.
  2. Check if the issue has been fixed or is still reproducible on the latest master branch.
  3. Create an issue with a test case.

If you create a feature branch, you can run the tests to ensure everything is operating correctly:

$ python setup.py test

License

DataCite is free software; you can redistribute it and/or modify it under the terms of the Revised BSD License quoted below.

Copyright (C) 2015-2018 CERN. Copyright (C) 2018 Center for Open Science.

All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  • Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
  • Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
  • Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Note

In applying this license, CERN does not waive the privileges and immunities granted to it by virtue of its status as an Intergovernmental Organization or submit itself to any jurisdiction.

Authors

DataCite is developed for use in Invenio digital library software.

Contact us at info@inveniosoftware.org

Contributors