def post(pid=None):
"""Save the file and associate it to the deposit record."""
deposit = DepositRecord.get_record_by_pid(pid)
if not deposit:
abort(400)
if 'key' not in request.args or 'type' not in request.args:
abort(400)
# Type must be either "main" or "additional"
if request.args['type'] not in ['main', 'additional']:
abort(400)
key = request.args['key']
# Store document
deposit.files[key] = BytesIO(request.get_data())
deposit.files[key]['label'] = re.search(r'(.*)\..*$', key).group(1)
deposit.files[key]['category'] = request.args['type']
deposit.files[key]['type'] = 'file'
deposit.commit()
db.session.commit()
return make_response(jsonify(deposit.files[key].dumps()))
def deposit(app, db, user, pdf_file, bucket_location, deposit_json,
embargo_date):
"""Deposit fixture."""
json = copy.deepcopy(deposit_json)
json['user'] = {
'$ref': 'https://sonar.ch/api/users/{pid}'.format(pid=user['pid'])
}
deposit = DepositRecord.create(json, dbcommit=True, with_bucket=True)
with open(pdf_file, 'rb') as file:
content = file.read()
deposit.files['main.pdf'] = BytesIO(content)
deposit.files['main.pdf']['label'] = 'Main file'
deposit.files['main.pdf']['category'] = 'main'
deposit.files['main.pdf']['type'] = 'file'
deposit.files['main.pdf']['embargo'] = True
deposit.files['main.pdf']['embargoDate'] = embargo_date.isoformat()
deposit.files['main.pdf']['exceptInOrganisation'] = True
deposit.files['additional.pdf'] = BytesIO(content)
deposit.files['additional.pdf']['label'] = 'Additional file 1'
deposit.files['additional.pdf']['category'] = 'additional'
deposit.files['additional.pdf']['type'] = 'file'
deposit.files['additional.pdf']['embargo'] = False
deposit.files['additional.pdf']['exceptInOrganisation'] = False
deposit.commit()
deposit.reindex()
db.session.commit()
return deposit
def put(pid=None, key=None):
"""Update metadata linked to file."""
deposit = DepositRecord.get_record_by_pid(pid)
if not deposit:
abort(400)
json = request.get_json()
if key not in deposit.files:
abort(400)
for item in json.items():
deposit.files[key][item[0]] = item[1]
if not deposit.files[key].get('embargoDate'):
deposit.files[key].data.pop('embargoDate')
try:
deposit.commit()
db.session.commit()
except Exception:
abort(400)
return make_response(jsonify(deposit.files[key].dumps()))
def read(cls, user, record):
"""Read permission check.
:param user: Logged user.
:param recor: Record to check.
:returns: True is action can be done.
"""
# At least for submitters logged users.
if not current_user_record or not current_user_record.is_submitter:
return False
# Superuser is allowd
if current_user_record.is_superuser:
return True
deposit = DepositRecord.get_record_by_pid(record['pid'])
deposit = deposit.replace_refs()
# Moderators are allowed only for their organisation's deposits.
if current_user_record.is_moderator:
return current_organisation['pid'] == deposit['user'][
'organisation']['pid']
# Submitters have only access to their own deposits.
return current_user_record['pid'] == deposit['user']['pid']
def publish(pid=None):
"""Publish a deposit or send a message for review."""
deposit = DepositRecord.get_record_by_pid(pid)
if not deposit or deposit[
'step'] != DepositRecord.STEP_DIFFUSION or deposit[
'status'] not in [
DepositRecord.STATUS_IN_PROGRESS,
DepositRecord.STATUS_ASK_FOR_CHANGES
]:
abort(400)
user = UserRecord.get_record_by_ref_link(deposit['user']['$ref'])
# Deposit can be validated directly
if user.is_granted(UserRecord.ROLE_MODERATOR):
deposit['status'] = DepositRecord.STATUS_VALIDATED
# Create document based on deposit
deposit.create_document()
else:
deposit['status'] = DepositRecord.STATUS_TO_VALIDATE
subdivision = SubdivisionRecord.get_record_by_ref_link(
user['subdivision']['$ref']) if user.get('subdivision') else None
moderators_emails = user.get_moderators_emails(
subdivision['pid'] if subdivision else None)
email_subject = _('Deposit to validate')
if subdivision:
email_subject += f' ({get_language_value(subdivision["name"])})'
if moderators_emails:
# Send an email to validators
send_email(
moderators_emails, email_subject, 'deposits/email/validation',
{
'deposit': deposit,
'user': user,
'link': current_app.config.get('SONAR_APP_ANGULAR_URL')
}, False)
deposit.log_action(user, 'submit')
deposit.commit()
deposit.reindex()
db.session.commit()
return make_response()
def test_user_resolver(app, organisation, roles):
"""Test user resolver."""
UserRecord.create({
'pid': '1',
'full_name': 'Jules Brochu',
'email': '*****@*****.**',
'roles': ['user'],
'organisation': {
'$ref': 'https://sonar.ch/api/organisations/org'
}
})
record = DepositRecord.create(
{'user': {
'$ref': 'https://sonar.ch/api/users/1'
}}, with_bucket=False)
assert record.replace_refs().get('user')['email'] == '*****@*****.**'
def read(cls, user, record):
"""Read permission check.
:param user: Current user record.
:param record: Record to check.
:returns: True is action can be done.
"""
# At least for submitters logged users.
if not user or not user.is_submitter:
return False
if user.is_superuser:
return True
deposit = DepositRecord.get_record_by_pid(record['pid'])
deposit = deposit.replace_refs()
# Admin is allowed only for same organisation's records
if user.is_admin:
return current_organisation['pid'] == deposit['user'][
'organisation']['pid']
# Special rules for moderators
if user.is_moderator:
user = user.replace_refs()
# Deposit does not belong to user's organisation
if current_organisation['pid'] != deposit['user']['organisation'][
'pid']:
return False
# Moderator has no subdivision, he can read the deposit
if not user.get('subdivision'):
return True
# User has a subdivision, he can only read his own deposits and
# deposits from the same subdivision
return user['pid'] == deposit['user'][
'pid'] or deposit.has_subdivision(
user.get('subdivision', {}).get('pid'))
# Submitters have only access to their own deposits.
return user['pid'] == deposit['user']['pid']
def _make_deposit(role='submitter', organisation=None):
user = make_user(role, organisation)
deposit_json['user'] = {
'$ref': 'https://sonar.ch/api/users/{pid}'.format(pid=user['pid'])
}
deposit_json.pop('pid', None)
record = DepositRecord.create(deposit_json,
dbcommit=True,
with_bucket=True)
with open(pdf_file, 'rb') as file:
content = file.read()
record.files['main.pdf'] = BytesIO(content)
record.files['main.pdf']['label'] = 'Main file'
record.files['main.pdf']['category'] = 'main'
record.files['main.pdf']['type'] = 'file'
record.files['main.pdf']['embargo'] = True
record.files['main.pdf']['embargoDate'] = embargo_date.isoformat()
record.files['main.pdf']['exceptInOrganisation'] = True
record.files['additional.pdf'] = BytesIO(content)
record.files['additional.pdf']['label'] = 'Additional file 1'
record.files['additional.pdf']['category'] = 'additional'
record.files['additional.pdf']['type'] = 'file'
record.files['additional.pdf']['embargo'] = False
record.files['additional.pdf']['exceptInOrganisation'] = False
record.commit()
record.reindex()
db.session.commit()
return record
def extract_metadata(pid=None):
"""Publish a deposit or send a message for review."""
deposit = DepositRecord.get_record_by_pid(pid)
if not deposit:
abort(400)
main_file = [
file for file in deposit.files
if file['category'] == 'main' and file.mimetype == 'application/pdf'
]
if not main_file:
abort(500)
# Get file content
with main_file[0].file.storage().open() as pdf_file:
content = pdf_file.read()
# Extract data from pdf
pdf_extractor = PDFExtractor()
pdf_metadata = format_extracted_data(pdf_extractor.process_raw(content))
return make_response(jsonify(pdf_metadata))
def get_deposit(cls, parent_record):
"""Get the deposit from the parent record."""
return DepositRecord.get_record_by_pid(parent_record.get('pid'))
def get(pid=None):
"""Get list of files associated with bucket."""
deposit = DepositRecord.get_record_by_pid(pid)
return make_response(jsonify(deposit.files.dumps()))
def review(pid=None):
"""Review a deposit and change the deposit status depending on action."""
deposit = DepositRecord.get_record_by_pid(pid)
if not deposit or deposit['status'] != DepositRecord.STATUS_TO_VALIDATE:
abort(400)
payload = request.get_json()
if not payload:
abort(400)
if 'action' not in payload or 'user' not in payload or payload[
'action'] not in [
DepositRecord.REVIEW_ACTION_APPROVE,
DepositRecord.REVIEW_ACTION_REJECT,
DepositRecord.REVIEW_ACTION_ASK_FOR_CHANGES
]:
abort(400)
user = UserRecord.get_record_by_ref_link(payload['user']['$ref'])
if not user or not user.is_moderator:
abort(403)
subject = None
status = None
if payload['action'] == DepositRecord.REVIEW_ACTION_APPROVE:
subject = _('Deposit approval')
status = DepositRecord.STATUS_VALIDATED
# Create document based on deposit
deposit.create_document()
elif payload['action'] == DepositRecord.REVIEW_ACTION_REJECT:
subject = _('Deposit rejection')
status = DepositRecord.STATUS_REJECTED
else:
subject = _('Ask for changes on deposit')
status = DepositRecord.STATUS_ASK_FOR_CHANGES
deposit['status'] = status
# Log action
deposit.log_action(payload['user'], payload['action'], payload['comment'])
# Load user who creates the deposit
deposit_user = UserRecord.get_record_by_ref_link(deposit['user']['$ref'])
send_email(
[deposit_user['email']], subject,
'deposits/email/{action}'.format(action=payload['action']), {
'deposit': deposit,
'deposit_user': deposit_user,
'user': user,
'date': datetime.now().strftime('%d.%m.%Y %H:%M:%S'),
'comment': payload['comment'],
'link': current_app.config.get('SONAR_APP_ANGULAR_URL')
}, False)
deposit.commit()
deposit.reindex()
db.session.commit()
return make_response(jsonify(deposit))