def check_record_doi(record, update=False):
""" Checks that the DOI of a record is registered."""
recid = record.get('_deposit', {}).get('id')
click.secho('checking DOI for record {}'.format(recid))
doi_list = [DataCiteProvider.get(d.get('value'))
for d in record['_pid']
if d.get('type') == 'DOI']
for doi in doi_list:
if _datacite_doi_reference(doi.pid.pid_value) is None:
if doi.pid.status == PIDStatus.REGISTERED:
# the doi is not truly registered with datacite
click.secho(' {}: not registered with datacite'.format(
doi.pid.pid_value))
doi.pid.status = PIDStatus.RESERVED
click.secho(' {}: {}'.format(doi.pid.pid_value, doi.pid.status))
if doi.pid.status != PIDStatus.RESERVED:
continue
# RESERVED but not REGISTERED
if update:
recid = record.get('_deposit', {}).get('id')
url = make_record_url(recid)
doc = datacite_v31.serialize(doi.pid, record)
_datacite_register_doi(doi, url, doc)
db.session.commit()
click.secho(' registered just now', fg='green', bold=True)
else:
click.secho(' not registered', fg='red', bold=True)
def datacite_register(pid_value, record_uuid):
"""Mint the DOI with DataCite.
:param pid_value: Value of record PID, with pid_type='recid'.
:type pid_value: str
"""
try:
record = Record.get_record(record_uuid)
# Bail out if not a Zenodo DOI.
if not is_local_doi(record['doi']):
return
dcp = DataCiteProvider.get(record['doi'])
url = current_app.config['ZENODO_RECORDS_UI_LINKS_FORMAT'].format(
recid=pid_value)
doc = datacite_v31.serialize(dcp.pid, record)
if dcp.pid.status == PIDStatus.REGISTERED:
dcp.update(url, doc)
else:
dcp.register(url, doc)
db.session.commit()
except Exception as exc:
datacite_register.retry(exc=exc)
def register_doi(doi, url, xml, uuid):
"""
Given a data submission id, this method takes it's assigned DOI, creates the DataCite XML,
and registers the DOI.
:param data_submissions:
:param recid:
:return:
"""
log.info('{0} - {1}'.format(doi, url))
try:
provider = DataCiteProvider.get(doi, 'doi')
except PIDDoesNotExistError:
provider = create_doi(doi)
pidstore_obj = PersistentIdentifier.query.filter_by(pid_value=doi).first()
if pidstore_obj:
pidstore_obj.object_uuid = uuid
db.session.add(pidstore_obj)
db.session.commit()
try:
provider.register(url, xml)
except DataCiteUnauthorizedError:
log.error('Unable to mint DOI. No authorisation credentials provided.')
except PIDInvalidAction:
provider.update(url, xml)
except IntegrityError:
provider.update(url, xml)
except DataCiteError as dce:
log.error('Error registering {0} for URL {1}\n\n{2}'
.format(doi, url, dce))
def register_doi(doi, url, xml, uuid):
"""
Given a data submission id, this method takes it's assigned DOI, creates the DataCite XML,
and registers the DOI.
:param data_submissions:
:param recid:
:return:
"""
log.info('{0} - {1}'.format(doi, url))
try:
provider = DataCiteProvider.get(doi, 'doi')
except PIDDoesNotExistError:
provider = create_doi(doi)
pidstore_obj = PersistentIdentifier.query.filter_by(pid_value=doi).first()
if pidstore_obj:
pidstore_obj.object_uuid = uuid
db.session.add(pidstore_obj)
db.session.commit()
try:
provider.register(url, xml)
except DataCiteUnauthorizedError:
log.error('Unable to mint DOI. No authorisation credentials provided.')
except PIDInvalidAction:
provider.update(url, xml)
except IntegrityError:
provider.update(url, xml)
except DataCiteError as dce:
log.error('Error registering {0} for URL {1}\n\n{2}'
.format(doi, url, dce))
def check_record_doi(record, update=False):
""" Checks that the DOI of a record is registered."""
recid = record.get('_deposit', {}).get('id')
click.secho('checking DOI for record {}'.format(recid))
doi_list = [
DataCiteProvider.get(d.get('value')) for d in record['_pid']
if d.get('type') == 'DOI'
]
for doi in doi_list:
if _datacite_doi_reference(doi.pid.pid_value) is None:
if doi.pid.status == PIDStatus.REGISTERED:
# the doi is not truly registered with datacite
click.secho(' {}: not registered with datacite'.format(
doi.pid.pid_value))
doi.pid.status = PIDStatus.RESERVED
click.secho(' {}: {}'.format(doi.pid.pid_value, doi.pid.status))
if doi.pid.status != PIDStatus.RESERVED:
continue
# RESERVED but not REGISTERED
if update:
recid = record.get('_deposit', {}).get('id')
url = make_record_url(recid)
doc = datacite_v31.serialize(doi.pid, record)
_datacite_register_doi(doi, url, doc)
db.session.commit()
click.secho(' registered just now', fg='green', bold=True)
else:
click.secho(' not registered', fg='red', bold=True)
def datacite_register(self,
pid_value,
record_uuid,
max_retries=5,
countdown=5):
"""Mint the DOI with DataCite.
:param pid_value: Value of record PID, with pid_type='recid'.
:type pid_value: str
"""
try:
record = Record.get_record(record_uuid)
# Bail out if not a CDS DOI.
if not is_local_doi(record['doi']) or \
not current_app.config['DEPOSIT_DATACITE_MINTING_ENABLED']:
return
dcp = DataCiteProvider.get(record['doi'])
url = current_app.config['CDS_RECORDS_UI_LINKS_FORMAT'].format(
recid=pid_value)
doc = datacite_v31.serialize(dcp.pid, record)
if dcp.pid.status == PIDStatus.REGISTERED:
dcp.update(url, doc)
else:
dcp.register(url, doc)
db.session.commit()
except Exception as exc:
db.session.rollback()
raise self.retry(max_retries=max_retries, countdown=countdown, exc=exc)
def datacite_register(pid_value, record_uuid):
"""Mint DOI and Concept DOI with DataCite.
:param pid_value: Value of record PID, with pid_type='recid'.
:type pid_value: str
:param record_uuid: Record Metadata UUID.
:type record_uuid: str
"""
try:
record = Record.get_record(record_uuid)
# Bail out if not a Zenodo DOI.
if not is_local_doi(record['doi']):
return
dcp = DataCiteProvider.get(record['doi'])
doc = datacite_v41.serialize(dcp.pid, record)
url = current_app.config['ZENODO_RECORDS_UI_LINKS_FORMAT'].format(
recid=pid_value)
if dcp.pid.status == PIDStatus.REGISTERED:
dcp.update(url, doc)
else:
dcp.register(url, doc)
# If this is the latest record version, update/register the Concept DOI
# using the metadata of the record.
recid = PersistentIdentifier.get('recid', str(record['recid']))
pv = PIDVersioning(child=recid)
conceptdoi = record.get('conceptdoi')
if conceptdoi and pv.exists and pv.is_last_child:
conceptrecid = record.get('conceptrecid')
concept_dcp = DataCiteProvider.get(conceptdoi)
url = current_app.config['ZENODO_RECORDS_UI_LINKS_FORMAT'].format(
recid=conceptrecid)
doc = datacite_v41.serialize(concept_dcp.pid, record)
if concept_dcp.pid.status == PIDStatus.REGISTERED:
concept_dcp.update(url, doc)
else:
concept_dcp.register(url, doc)
db.session.commit()
except Exception as exc:
datacite_register.retry(exc=exc)
def datacite_register(pid_value, record_uuid):
"""Mint DOI and Concept DOI with DataCite.
:param pid_value: Value of record PID, with pid_type='recid'.
:type pid_value: str
:param record_uuid: Record Metadata UUID.
:type record_uuid: str
"""
try:
record = Record.get_record(record_uuid)
# Bail out if not a Zenodo DOI.
if not is_local_doi(record['doi']):
return
dcp = DataCiteProvider.get(record['doi'])
doc = datacite_v41.serialize(dcp.pid, record)
url = current_app.config['ZENODO_RECORDS_UI_LINKS_FORMAT'].format(
recid=pid_value)
if dcp.pid.status == PIDStatus.REGISTERED:
dcp.update(url, doc)
else:
dcp.register(url, doc)
# If this is the latest record version, update/register the Concept DOI
# using the metadata of the record.
recid = PersistentIdentifier.get('recid', str(record['recid']))
pv = PIDVersioning(child=recid)
conceptdoi = record.get('conceptdoi')
if conceptdoi and pv.exists and pv.is_last_child:
conceptrecid = record.get('conceptrecid')
concept_dcp = DataCiteProvider.get(conceptdoi)
url = current_app.config['ZENODO_RECORDS_UI_LINKS_FORMAT'].format(
recid=conceptrecid)
doc = datacite_v41.serialize(concept_dcp.pid, record)
if concept_dcp.pid.status == PIDStatus.REGISTERED:
concept_dcp.update(url, doc)
else:
concept_dcp.register(url, doc)
db.session.commit()
except Exception as exc:
datacite_register.retry(exc=exc)
def test_datacite_create_get(app, db):
"""Test datacite provider create/get."""
with app.app_context():
provider = DataCiteProvider.create('10.1234/a')
assert provider.pid.status == PIDStatus.NEW
assert provider.pid.pid_provider == 'datacite'
# Crete passing client kwarg to provider object creation
provider = DataCiteProvider.create('10.1234/b', client=MagicMock())
assert provider.pid.status == PIDStatus.NEW
assert provider.pid.pid_provider == 'datacite'
assert isinstance(provider.api, MagicMock)
provider = DataCiteProvider.get('10.1234/a')
assert provider.pid.status == PIDStatus.NEW
assert provider.pid.pid_provider == 'datacite'
provider = DataCiteProvider.get('10.1234/a', client=MagicMock())
assert isinstance(provider.api, MagicMock)
def create_doi(doi):
"""
:param doi: Creates a DOI using the data provider. If it already exists, we return back the existing provider.
:return: DataCiteProvider
"""
try:
return DataCiteProvider.create(doi)
except DataCiteUnauthorizedError:
log.error('Unable to mint DOI. No authorisation credentials provided.')
except Exception:
return DataCiteProvider.get(doi, 'doi')
def create_doi(doi):
"""
:param doi: Creates a DOI using the data provider. If it already exists, we return back the existing provider.
:return: DataCiteProvider
"""
try:
return DataCiteProvider.create(doi)
except DataCiteUnauthorizedError:
log.error('Unable to mint DOI. No authorisation credentials provided.')
except Exception:
return DataCiteProvider.get(doi, 'doi')
def datacite_inactivate(pid_value):
"""Mint the DOI with DataCite.
:param pid_value: Value of record PID, with pid_type='recid'.
:type pid_value: str
"""
try:
dcp = DataCiteProvider.get(pid_value)
dcp.delete()
db.session.commit()
except Exception as exc:
datacite_inactivate.retry(exc=exc)
def datacite_inactivate(pid_value):
"""Mint the DOI with DataCite.
:param pid_value: Value of record PID, with pid_type='recid'.
:type pid_value: str
"""
try:
dcp = DataCiteProvider.get(pid_value)
dcp.delete()
db.session.commit()
except Exception as exc:
datacite_inactivate.retry(exc=exc)
def register_doi(doi, url, xml, uuid):
"""
Given a data submission id, this method takes its assigned DOI, creates the DataCite XML,
and registers the DOI.
:param data_submissions:
:param recid:
:return:
"""
if current_app.config.get('NO_DOI_MINTING', False) or not doi:
return None
log.info('{0} - {1}'.format(doi, url))
print('Minting doi {}'.format(doi))
try:
provider = DataCiteProvider.get(doi, 'doi')
except PIDDoesNotExistError:
provider = create_doi(doi)
pidstore_obj = PersistentIdentifier.query.filter_by(pid_value=doi).first()
if pidstore_obj:
pidstore_obj.object_uuid = uuid
db.session.add(pidstore_obj)
db.session.commit()
try:
provider.register(url, xml)
except DataCiteUnauthorizedError:
log.error('Unable to mint DOI. No authorisation credentials provided.')
except (PIDInvalidAction, IntegrityError):
try:
provider.update(url, xml) # try again in case of temporary problem
except DataCiteError:
try:
provider.update(url, xml)
except DataCiteError as dce:
log.error('Error updating {0} for URL {1}\n\n{2}'.format(
doi, url, dce))
except DataCiteError:
try:
provider.register(url,
xml) # try again in case of temporary problem
except (PIDInvalidAction, IntegrityError):
try:
provider.update(url, xml)
except DataCiteError as dce:
log.error('Error updating {0} for URL {1}\n\n{2}'.format(
doi, url, dce))
except DataCiteError as dce:
log.error('Error registering {0} for URL {1}\n\n{2}'.format(
doi, url, dce))
def datacite_register(pid_value, record_uuid):
"""Mint the DOI with DataCite.
:param pid_value: Value of record PID, with pid_type='recid'.
:type pid_value: str
"""
record = Record.get_record(record_uuid)
dcp = DataCiteProvider.get(record['doi'])
url = current_app.config['ZENODO_RECORDS_UI_LINKS_FORMAT'].format(
recid=pid_value)
doc = datacite_v31.serialize(dcp.pid, record)
dcp.update(url, doc) if dcp.pid.status == PIDStatus.REGISTERED \
else dcp.register(url, doc)
db.session.commit()
def update_datacite_metadata(doi, object_uuid, job_id):
"""Update DataCite metadata of a single PersistentIdentifier.
:param doi: Value of doi PID, with pid_type='doi'. It could be a normal
DOI or a concept DOI.
:type doi: str
:param object_uuid: Record Metadata UUID.
:type object_uuid: str
:param job_id: id of the job to which this task belongs.
:type job_id: str
"""
task_details = current_cache.get('update_datacite:task_details')
if task_details is None or job_id != task_details['job_id']:
return
record = Record.get_record(object_uuid)
dcp = DataCiteProvider.get(doi)
if dcp.pid.status != PIDStatus.REGISTERED:
return
doc = datacite_v41.serialize(dcp.pid, record)
for validator in xsd41():
validator.assertValid(etree.XML(doc.encode('utf8')))
url = None
if doi == record.get('doi'):
url = current_app.config['ZENODO_RECORDS_UI_LINKS_FORMAT'].format(
recid=str(record['recid']))
elif doi == record.get('conceptdoi'):
url = current_app.config['ZENODO_RECORDS_UI_LINKS_FORMAT'].format(
recid=str(record['conceptrecid']))
result = dcp.update(url, doc)
if result is True:
dcp.pid.updated = datetime.utcnow()
db.session.commit()
def update_datacite_metadata(doi, object_uuid, job_id):
"""Update DataCite metadata of a single PersistentIdentifier.
:param doi: Value of doi PID, with pid_type='doi'. It could be a normal
DOI or a concept DOI.
:type doi: str
:param object_uuid: Record Metadata UUID.
:type object_uuid: str
:param job_id: id of the job to which this task belongs.
:type job_id: str
"""
task_details = current_cache.get('update_datacite:task_details')
if task_details is None or job_id != task_details['job_id']:
return
record = Record.get_record(object_uuid)
dcp = DataCiteProvider.get(doi)
if dcp.pid.status != PIDStatus.REGISTERED:
return
doc = datacite_v41.serialize(dcp.pid, record)
for validator in xsd41():
validator.assertValid(etree.XML(doc.encode('utf8')))
url = None
if doi == record.get('doi'):
url = current_app.config['ZENODO_RECORDS_UI_LINKS_FORMAT'].format(
recid=str(record['recid']))
elif doi == record.get('conceptdoi'):
url = current_app.config['ZENODO_RECORDS_UI_LINKS_FORMAT'].format(
recid=str(record['conceptrecid']))
result = dcp.update(url, doc)
if result is True:
dcp.pid.updated = datetime.utcnow()
db.session.commit()
def update_datacite_metadata(pid_value, object_uuid, job_id):
"""Update DataCite metadata of a single PersistentIdentifier."""
task_details = current_cache.get('update_datacite:task_details')
if task_details is None or job_id != task_details['job_id']:
return
record = Record.get_record(object_uuid)
dcp = DataCiteProvider.get(record['doi'])
doc = datacite_v41.serialize(dcp.pid, record)
for validator in xsd41():
validator.assertValid(etree.XML(doc.encode('utf8')))
url = current_app.config['ZENODO_RECORDS_UI_LINKS_FORMAT'].format(
recid=pid_value)
result = dcp.update(url, doc)
if result is True:
dcp.pid.updated = datetime.utcnow()
db.session.commit()
def select_doi(metadata, status):
doi_list = [DataCiteProvider.get(d.get('value'))
for d in metadata['_pid']
if d.get('type') == 'DOI']
return [d for d in doi_list
if d and d.pid and d.pid.status == status]
def select_doi(metadata, status):
doi_list = [DataCiteProvider.get(d.get('value'))
for d in metadata['_pid']
if d.get('type') == 'DOI']
return [d for d in doi_list
if d and d.pid and d.pid.status == status]