def create(self, validated_data):
node = Node.load(validated_data.pop('node', None))
if not node:
raise exceptions.NotFound('Unable to find Node with specified id.')
auth = get_user_auth(self.context['request'])
if not node.has_permission(auth.user, permissions.ADMIN):
raise exceptions.PermissionDenied
primary_file = validated_data.pop('primary_file', None)
if not primary_file:
raise exceptions.ValidationError(detail='You must specify a valid primary_file to create a preprint.')
provider = validated_data.pop('provider', None)
if not provider:
raise exceptions.ValidationError(detail='You must specify a valid provider to create a preprint.')
if PreprintService.find(Q('node', 'eq', node) & Q('provider', 'eq', provider)).count():
conflict = PreprintService.find_one(Q('node', 'eq', node) & Q('provider', 'eq', provider))
raise Conflict('Only one preprint per provider can be submitted for a node. Check `meta[existing_resource_id]`.', meta={'existing_resource_id': conflict._id})
preprint = PreprintService(node=node, provider=provider)
self.set_field(preprint.set_primary_file, primary_file, auth, save=True)
preprint.node._has_abandoned_preprint = True
preprint.node.save()
return self.update(preprint, validated_data)
def migrate(dry_run=True):
node_logs = list(
NodeLog.find(
Q("action", "in", [NodeLog.PREPRINT_FILE_UPDATED, NodeLog.PREPRINT_INITIATED])
& Q("params.preprint", "exists", False)
)
)
logger.info("Preparing to migrate {} NodeLogs".format(len(node_logs)))
count = 0
for log in node_logs:
preprint = None
node_id = log.params.get("node")
try:
preprint = PreprintService.find_one(Q("node", "eq", node_id))
except NoResultsFound:
logger.error("Skipping {}, preprint not found for node: {}".format(log._id, node_id))
continue
logger.info("Migrating log - {} - to add params.preprint: {}, ".format(log._id, preprint._id))
log.params["preprint"] = preprint._id
log.save()
count += 1
logger.info("Migrated {} logs".format(count))
def on_preprint_updated(preprint_id):
# WARNING: Only perform Read-Only operations in an asynchronous task, until Repeatable Read/Serializable
# transactions are implemented in View and Task application layers.
from website.models import PreprintService
preprint = PreprintService.load(preprint_id)
if settings.SHARE_URL:
if not preprint.provider.access_token:
raise ValueError(
'No access_token for {}. Unable to send {} to SHARE.'.format(
preprint.provider, preprint))
resp = requests.post(
'{}api/v2/normalizeddata/'.format(settings.SHARE_URL),
json={
'data': {
'type': 'NormalizedData',
'attributes': {
'tasks': [],
'raw': None,
'data': {
'@graph': format_preprint(preprint)
}
}
}
},
headers={
'Authorization':
'Bearer {}'.format(preprint.provider.access_token),
'Content-Type': 'application/vnd.api+json'
})
logger.debug(resp.content)
resp.raise_for_status()
def migrate(dry_run=True):
node_logs = list(NodeLog.find(
Q('action', 'in', [NodeLog.PREPRINT_FILE_UPDATED, NodeLog.PREPRINT_INITIATED]) &
Q('params.preprint', 'exists', False)
))
logger.info('Preparing to migrate {} NodeLogs'.format(len(node_logs)))
count = 0
for log in node_logs:
preprint = None
node_id = log.params.get('node')
try:
preprint = PreprintService.find_one(Q('node', 'eq', node_id))
except NoResultsFound:
logger.error('Skipping {}, preprint not found for node: {}'.format(log._id, node_id))
continue
logger.info(
'Migrating log - {} - to add params.preprint: {}, '.format(log._id, preprint._id)
)
log.params['preprint'] = preprint._id
log.save()
count += 1
logger.info('Migrated {} logs'.format(count))
def create(self, validated_data):
node = Node.load(validated_data.pop('node', None))
if not node:
raise exceptions.NotFound('Unable to find Node with specified id.')
elif node.is_deleted:
raise exceptions.ValidationError(
'Cannot create a preprint from a deleted node.')
auth = get_user_auth(self.context['request'])
if not node.has_permission(auth.user, permissions.ADMIN):
raise exceptions.PermissionDenied
primary_file = validated_data.pop('primary_file', None)
if not primary_file:
raise exceptions.ValidationError(
detail=
'You must specify a valid primary_file to create a preprint.')
provider = validated_data.pop('provider', None)
if not provider:
raise exceptions.ValidationError(
detail='You must specify a valid provider to create a preprint.'
)
if PreprintService.find(
Q('node', 'eq', node) & Q('provider', 'eq', provider)).count():
conflict = PreprintService.find_one(
Q('node', 'eq', node) & Q('provider', 'eq', provider))
raise Conflict(
'Only one preprint per provider can be submitted for a node. Check `meta[existing_resource_id]`.',
meta={'existing_resource_id': conflict._id})
preprint = PreprintService(node=node, provider=provider)
self.set_field(preprint.set_primary_file,
primary_file,
auth,
save=True)
preprint.node._has_abandoned_preprint = True
preprint.node.save()
return self.update(preprint, validated_data)
def main(dry):
if dry:
logging.warn('DRY mode running')
now = datetime.utcnow()
initiated_logs = NodeLog.find(
Q('action', 'eq', NodeLog.PREPRINT_INITIATED) & Q('date', 'lt', now))
for log in initiated_logs:
try:
preprint = PreprintService.find_one(Q('node', 'eq', log.node))
log.params.update({
'preprint': {
'id': preprint._id
},
'service': {
'name': preprint.provider.name
}
})
logging.info(
'Updating log {} from node {}, with preprint id: {}'.format(
log._id, log.node.title, preprint._id))
if not dry:
log.save()
except NoResultsFound:
pass
updated_logs = NodeLog.find(
Q('action', 'eq', NodeLog.PREPRINT_FILE_UPDATED)
& Q('date', 'lt', now))
for log in updated_logs:
try:
preprint = PreprintService.find_one(Q('node', 'eq', log.node))
log.params.update({'preprint': {'id': preprint._id}})
logging.info(
'Updating log {} from node {}, with preprint id: {}'.format(
log._id, log.node.title, preprint._id))
if not dry:
log.save()
except NoResultsFound:
pass
def on_preprint_updated(preprint_id):
# WARNING: Only perform Read-Only operations in an asynchronous task, until Repeatable Read/Serializable
# transactions are implemented in View and Task application layers.
from website.models import PreprintService
preprint = PreprintService.load(preprint_id)
if settings.SHARE_URL and settings.SHARE_API_TOKEN:
resp = requests.post('{}api/v2/normalizeddata/'.format(settings.SHARE_URL), json={
'created_at': datetime.datetime.utcnow().isoformat(),
'normalized_data': {
'@graph': format_preprint(preprint)
},
}, headers={'Authorization': 'Bearer {}'.format(settings.SHARE_API_TOKEN)})
logger.debug(resp.content)
resp.raise_for_status()
def main(dry):
if dry:
logging.warn('DRY mode running')
now = datetime.utcnow()
initiated_logs = NodeLog.find(Q('action', 'eq', NodeLog.PREPRINT_INITIATED) & Q('date', 'lt', now))
for log in initiated_logs:
try:
preprint = PreprintService.find_one(Q('node', 'eq', log.node))
log.params.update({
'preprint': {
'id': preprint._id
},
'service': {
'name': preprint.provider.name
}
})
logging.info('Updating log {} from node {}, with preprint id: {}'.format(log._id, log.node.title, preprint._id))
if not dry:
log.save()
except NoResultsFound:
pass
updated_logs = NodeLog.find(Q('action', 'eq', NodeLog.PREPRINT_FILE_UPDATED) & Q('date', 'lt', now))
for log in updated_logs:
try:
preprint = PreprintService.find_one(Q('node', 'eq', log.node))
log.params.update({
'preprint': {
'id': preprint._id
}
})
logging.info('Updating log {} from node {}, with preprint id: {}'.format(log._id, log.node.title, preprint._id))
if not dry:
log.save()
except NoResultsFound:
pass
def find_preprint_provider(node):
"""
Given a node, find the preprint and the service provider.
:param node: the node to which a contributer or preprint author is added
:return: the email template
"""
try:
preprint = PreprintService.find_one(Q('node', 'eq', node._id))
provider = preprint.provider
if provider._id == 'osf':
return 'osf', provider.name
else:
return 'branded', provider.name
# TODO: fine-grained exception handling
except Exception:
return None, None
def find_preprint_provider(node):
"""
Given a node, find the preprint and the service provider.
:param node: the node to which a contributer or preprint author is added
:return: the email template
"""
try:
preprint = PreprintService.find_one(Q('node', 'eq', node._id))
provider = preprint.provider
if provider._id == 'osf':
return 'osf', provider.name
else:
return 'branded', provider.name
# TODO: fine-grained exception handling
except Exception:
return None, None
def on_preprint_updated(preprint_id):
# WARNING: Only perform Read-Only operations in an asynchronous task, until Repeatable Read/Serializable
# transactions are implemented in View and Task application layers.
from website.models import PreprintService
preprint = PreprintService.load(preprint_id)
if settings.SHARE_URL:
if not preprint.provider.access_token:
raise ValueError('No access_token for {}. Unable to send {} to SHARE.'.format(preprint.provider, preprint))
resp = requests.post('{}api/v2/normalizeddata/'.format(settings.SHARE_URL), json={
'data': {
'type': 'NormalizedData',
'attributes': {
'tasks': [],
'raw': None,
'data': {'@graph': format_preprint(preprint)}
}
}
}, headers={'Authorization': 'Bearer {}'.format(preprint.provider.access_token), 'Content-Type': 'application/vnd.api+json'})
logger.debug(resp.content)
resp.raise_for_status()
def on_preprint_updated(preprint_id):
# WARNING: Only perform Read-Only operations in an asynchronous task, until Repeatable Read/Serializable
# transactions are implemented in View and Task application layers.
from website.models import PreprintService
preprint = PreprintService.load(preprint_id)
if settings.SHARE_URL and settings.SHARE_API_TOKEN:
resp = requests.post('{}api/v2/normalizeddata/'.format(
settings.SHARE_URL),
json={
'created_at':
datetime.datetime.utcnow().isoformat(),
'normalized_data': {
'@graph': format_preprint(preprint)
},
},
headers={
'Authorization':
'Bearer {}'.format(settings.SHARE_API_TOKEN)
})
logger.debug(resp.content)
resp.raise_for_status()
def validate_map_completeness():
logger.info('Validating completeness of PLOS->BePress mapping')
assert set([s['text'] for p in PreprintService.find() for hier in p.get_subjects() for s in hier]).issubset(set(PLOS_TO_BP_MAP.keys())),\
'Subjects not found in map: {}'.format(
set([s['text'] for p in PreprintService.find() for hier in p.get_subjects() for s in hier]) - set(PLOS_TO_BP_MAP.keys())
)
def get_queryset(self):
query = self.get_query_from_request()
return PreprintService.find(query)
def perform_destroy(self, instance):
if instance.is_published:
raise Conflict('Published preprints cannot be deleted.')
PreprintService.remove_one(instance)
def validate_map_completeness():
logger.info('Validating completeness of PLOS->BePress mapping')
assert set([s['text'] for p in PreprintService.find() for hier in p.get_subjects() for s in hier]).issubset(set(PLOS_TO_BP_MAP.keys())),\
'Subjects not found in map: {}'.format(
set([s['text'] for p in PreprintService.find() for hier in p.get_subjects() for s in hier]) - set(PLOS_TO_BP_MAP.keys())
)
def perform_destroy(self, instance):
if instance.is_published:
raise Conflict('Published preprints cannot be deleted.')
PreprintService.remove_one(instance)