inspirehep.modules.orcid package

Submodules

inspirehep.modules.orcid.builder module

Builds an ORCID work record.

class inspirehep.modules.orcid.builder.OrcidBuilder

Bases: object

Class used to build ORCID-compatible work records in JSON.

add_arxiv(value, relationship=None)

Add arXiv identifier to the record.

Parameters:

• value (string) – the identifier itself
• relationship (string) – either “part-of” or “self”, optional, see OrcidBuilder._make_external_id_field

add_citation(_type, value)

Add a citation string.

Parameters:

• _type (string) – citation type, one of: https://git.io/vdKXv#L313-L321
• value (string) – citation string for the provided citation type

add_contributor(credit_name, role='author', orcid=None, email=None)

Adds a contributor entry to the record.

Parameters:

• credit_name (string) – contributor’s name
• orcid (string) – ORCID identifier string
• role (string) – role, see OrcidBuilder._make_contributor_field
• email (string) – contributor’s email address

add_country(country_code)

Set country if the ORCID record.

Parameters:country_code (string) – ISO ALPHA-2 country code

add_doi(value, relationship=None)

Add DOI to the record.

Parameters:

• value (string) – the identifier itself
• relationship (string) – either “part-of” or “self”, optional, see OrcidBuilder._make_external_id_field

add_external_id(type, value, url=None, relationship=None)

Add external identifier to the record.

Parameters:

• type (string) – type of external ID (doi, etc.)
• value (string) – the identifier itself
• url (string) – URL for the resource
• relationship (string) – either “part-of” or “self”, optional, see OrcidBuilder._make_external_id_field

add_journal_title(journal_title)

Set title of the publication containing the record.

Parameters:journal_title (string) –

Title of publication containing the record.

After ORCID v2.0 schema (https://git.io/vdKXv#L268-L280): “The title of the publication or group under which the work was published. - If a journal, include the journal title of the work. - If a book chapter, use the book title. - If a translation or a manual, use the series title. - If a dictionary entry, use the dictionary title. - If a conference poster, abstract or paper, use the conference name.”

add_publication_date(partial_date)

Set publication date field.

Parameters:partial_date (inspire_utils.date.PartialDate) – publication date

add_recid(value, url, relationship=None)

Add Inspire recid to the record.

Parameters:

• value (string) – the recid.
• url (string) – url to the Inspire record.
• relationship (string) – either “part-of” or “self”, optional, see OrcidBuilder._make_external_id_field

add_title(title, subtitle=None, translated_title=None)

Set a title of the work, and optionaly a subtitle.

Parameters:

• title (string) – title of the work
• subtitle (string) – subtitle of the work
• translated_title (Tuple[string, string]) – tuple consiting of the translated title and its language code

add_type(work_type)

Add a work type.

Parameters:work_type (string) – type of work, see: https://git.io/vdKXv#L118-L155

add_url(url)

Add a url.

Parameters:url (string) – alternative url of the record

get_xml()

Get an XML record.

Returns:ORCID work record compatible with API v2.0 Return type:lxml.etree._Element

set_put_code(put_code)

Set the put-code of an ORCID record, to update existing one.

Parameters:put_code (string | integer) – a number, being a put code

set_visibility(visibility)

Set visibility setting on ORCID.

Can only be set during record creation.

Parameters:visibility (string) – one of (private, limited, registered-only, public), see https://git.io/vdKXt#L904-L937

inspirehep.modules.orcid.cache module

class inspirehep.modules.orcid.cache.OrcidCache(orcid, recid)

Bases: object

delete_work_putcode

Delete the putcode for the given (orcid, recid).

has_work_content_changed

True if the work content has changed compared to the cached version.

Parameters:inspire_record (InspireRecord) – InspireRecord instance. If provided, the hash for the record content is re-computed.

read_work_putcode

Read the putcode for the given (orcid, recid).

redis

write_work_putcode

Write the putcode and the hash for the given (orcid, recid).

Parameters:

• putcode (string) – the putcode used to push the record to ORCID.
• inspire_record (InspireRecord) – InspireRecord instance. If provided, the hash for the record content is re-computed.

Raises:

ValueError – when the putcode is empty.

inspirehep.modules.orcid.converter module

Handle conversion from INSPIRE records to ORCID.

class inspirehep.modules.orcid.converter.ExternalIdentifier(type, value)

Bases: tuple

type

Alias for field number 0

value

Alias for field number 1

class inspirehep.modules.orcid.converter.OrcidConverter(record, url_pattern, put_code=None, visibility=None)

Bases: object

Coverter for the Orcid format.

INSPIRE_DOCTYPE_TO_ORCID_TYPE = {'note': 'other', 'proceedings': 'edited-book', 'book': 'book', 'book chapter': 'book-chapter', 'thesis': 'dissertation', 'conference paper': 'conference-paper', 'report': 'report', 'article': 'journal-article', 'activity report': 'report'}

INSPIRE_TO_ORCID_ROLES_MAP = {'supervisor': None, 'editor': 'editor', 'author': 'author'}

added_external_identifiers

arxiv_eprint

Get arXiv ID of a record.

bibtex_citation

book_series_title

Get record’s book series title.

conference_country

Get conference record country.

conference_title

Get record’s conference title.

doi

Get DOI of a record.

get_xml

Create an ORCID XML representation of the record.

Parameters:do_add_bibtex_citation (bool) – True to add BibTeX-serialized record Returns:ORCID XML work record Return type:lxml.etree._Element

journal_title

Get record’s journal title.

orcid_for_inspire_author(author)

ORCID identifier for an INSPIRE author field.

Parameters:author (dict) – an author field from INSPIRE literature record Returns:ORCID identifier of an author, if available Return type:string

orcid_role_for_inspire_author(author)

ORCID role for an INSPIRE author field.

Parameters:author (dict) – an author field from INSPIRE literature record Returns:ORCID role of a person Return type:string

orcid_work_type

Get record’s ORCID work type.

publication_date

(Partial) date of publication.

Returns:publication date Return type:partial_date (inspire_utils.date.PartialDate)

recid

Get INSPIRE record ID.

subtitle

Get record subtitle.

title

Get record title.

title_translation

Translated title.

Returns:translated title and the language code of the translation, if available Return type:Tuple[string, string]

inspirehep.modules.orcid.domain_models module

class inspirehep.modules.orcid.domain_models.OrcidPusher(orcid, recid, oauth_token, do_fail_if_duplicated_identifier=False, record_db_version=None)

Bases: object

push

inspirehep.modules.orcid.exceptions module

exception inspirehep.modules.orcid.exceptions.BaseOrcidPusherException(*args, **kwargs)

Bases: exceptions.Exception

exception inspirehep.modules.orcid.exceptions.DuplicatedExternalIdentifierPusherException(*args, **kwargs)

Bases: inspirehep.modules.orcid.exceptions.BaseOrcidPusherException

The underneath Orcid service client response raised DuplicatedExternalIdentifierPusherException. We checked for the clashing work, pushed it and repeated the original operation which failed again.

exception inspirehep.modules.orcid.exceptions.InputDataInvalidException(*args, **kwargs)

Bases: inspirehep.modules.orcid.exceptions.BaseOrcidPusherException

The underneath Orcid service client response included an error related to input data like TokenInvalidException, OrcidNotFoundException, PutcodeNotFoundPutException. Note: that re-trying would not help in this case.

exception inspirehep.modules.orcid.exceptions.PutcodeNotFoundInCacheAfterCachingAllPutcodes(*args, **kwargs)

Bases: inspirehep.modules.orcid.exceptions.BaseOrcidPusherException

No putcode was found in cache after having cached all author putcodes.

exception inspirehep.modules.orcid.exceptions.PutcodeNotFoundInOrcidException(*args, **kwargs)

Bases: inspirehep.modules.orcid.exceptions.BaseOrcidPusherException

No putcode was found in ORCID API.

exception inspirehep.modules.orcid.exceptions.RecordNotFoundException(*args, **kwargs)

Bases: inspirehep.modules.orcid.exceptions.BaseOrcidPusherException

exception inspirehep.modules.orcid.exceptions.StaleRecordDBVersionException(*args, **kwargs)

Bases: inspirehep.modules.orcid.exceptions.BaseOrcidPusherException

inspirehep.modules.orcid.ext module

Search extension.

class inspirehep.modules.orcid.ext.InspireOrcid(app=None)

Bases: object

init_app(app)

init_config(app)

inspirehep.modules.orcid.putcode_getter module

class inspirehep.modules.orcid.putcode_getter.OrcidPutcodeGetter(orcid, oauth_token)

Bases: object

get_all_inspire_putcodes_and_recids_iter()

Query ORCID api and get all the Inspire putcodes for the given ORCID.

get_putcodes_and_recids_by_identifiers_iter(identifiers)

Yield putcode and recid for each work matched by the external identifiers. Note: external identifiers of type ‘other-id’ are skipped.

Parameters:identifiers (List[inspirehep.modules.orcid.converter.ExternalIdentifier]) – list af all external identifiers added after the xml conversion.

inspirehep.modules.orcid.tasks module

Manage ORCID OAUTH token migration from INSPIRE legacy instance.

exception inspirehep.modules.orcid.tasks.RemoteTokenOrcidMismatch(user, orcids)

Bases: exceptions.Exception

(task)inspirehep.modules.orcid.tasks.import_legacy_orcid_tokens

Celery task to import OAUTH ORCID tokens from legacy. Note: bind=True for compatibility with @time_execution.

inspirehep.modules.orcid.tasks.legacy_orcid_arrays()

Generator to fetch token data from redis.

Note: this function consumes the queue populated by the legacy tasklet: inspire/bibtasklets/bst_orcidsync.py

Yields:list – user data in the form of [orcid, token, email, name]

(task)inspirehep.modules.orcid.tasks.orcid_push

Celery task to push a record to ORCID.

Parameters:

• self (celery.Task) – the task
• orcid (String) – an orcid identifier.
• rec_id (Int) – inspire record’s id to push to ORCID.
• oauth_token (String) – orcid token.
• kwargs_to_pusher (Dict) – extra kwargs to pass to the pusher object.

inspirehep.modules.orcid.utils module

ORCID utils.

class inspirehep.modules.orcid.utils.RetryMixin(*args, **kwargs)

Bases: celery.app.task.Task

request

retry(*args, **kwargs)

inspirehep.modules.orcid.utils.account_setup(remote, token, resp)

Perform additional setup after user have been logged in.

This is a modified version of invenio_oauthclient.contrib.orcid.account_setup that stores additional metadata.

Parameters:

• remote – The remote application.
• token – The token value.
• resp – The response.

inspirehep.modules.orcid.utils.apply_celery_task_with_retry(task_func, args=None, kwargs=None, max_retries=5, countdown=10, time_limit=None)

When executing a (bind=True) task synchronously (with mytask.apply() or just calling it as a function mytask()) the self.retry() does not work, but the original exception is raised (without any retry) so you “lose” the exception management logic written in the task code.

This function overcome such limitation. Example:

# Celery task: @shared_task(bind=True) def normalize_name_task(self, first_name, last_name, nick_name=’‘):

try:

result = ... network call ...

except RequestException as exc:

exception = None

raise self.retry(max_retries=3, countdown=5, exc=exception)

return result

# Call the task sync with retry: result = apply_celery_task_with_retry(

normalize_name_task, args=(‘John’, ‘Doe’), kwargs=dict(nick_name=’Dee’), max_retries=2, countdown=5*60, time_limit=2*60*60

)

Note: it assumes that @shared_task is the first (the one on top) decorator for the Celery task.

Parameters:

• task_func – Celery task function to be run.
• args – the positional arguments to pass on to the task.
• kwargs – the keyword arguments to pass on to the task.
• max_retries – maximum number of retries before raising MaxRetriesExceededError.
• countdown –

  hard time limit for each attempt. If the last attempt It can be a callable, eg:

  backoff = lambda retry_count: 2 ** (retry_count + 1) apply_celery_task_with_retry(..., countdown=backoff)

• time_limit – hard time limit for each single attempt in seconds. If the last attempt fails because of the time limit, raises TimeLimitExceeded.

Returns: what the task_func returns.

inspirehep.modules.orcid.utils.get_literature_recids_for_orcid(orcid)

Return the Literature recids that were claimed by an ORCiD.

We record the fact that the Author record X has claimed the Literature record Y by storing in Y an author object with a $ref pointing to X and the key curated_relation set to True. Therefore this method first searches the DB for the Author records for the one containing the given ORCiD, and then uses its recid to search in ES for the Literature records that satisfy the above property.

Parameters:orcid (str) – the ORCiD. Returns:the recids of the Literature records that were claimed by that ORCiD. Return type:list(int)

inspirehep.modules.orcid.utils.get_orcids_for_push(record)

Obtain the ORCIDs associated to the list of authors in the Literature record.

The ORCIDs are looked up both in the ids of the authors and in the Author records that have claimed the paper.

Parameters:record (dict) – metadata from a Literature record Returns:all ORCIDs associated to these authors Return type:Iterator[str]

inspirehep.modules.orcid.utils.get_push_access_tokens(orcids)

Get the remote tokens for the given ORCIDs.

Parameters:orcids (List[str]) – ORCIDs to get the tokens for. Returns:pairs of (ORCID, access_token), for ORCIDs having a token. These are similar to named tuples, in that the values can be retrieved by index or by attribute, respectively id and access_token. Return type:sqlalchemy.util._collections.result

inspirehep.modules.orcid.utils.log_service_response(logger, response, extra_message=None)

Module contents

ORCID integration module.