def get_revisions(endpoint, pid_value):
"""Get revisions of given record"""
try:
Transaction = transaction_class(RecordMetadata)
pid_type = PidStoreBase.get_pid_type_from_endpoint(endpoint)
record = InspireRecord.get_record_by_pid_value(pid_value,
pid_type,
original_record=True)
if not check_permissions_for_private_collection_read(
record.get("_collections", [])):
return jsonify(message="Unauthorized", code=403), 403
revisions = []
for revision in reversed(record.revisions):
transaction_id = revision.model.transaction_id
user = Transaction.query.filter(
Transaction.id == transaction_id).one().user
if user:
user_email = user.email
else:
user_email = "system"
revisions.append({
"updated": revision.updated,
"revision_id": revision.revision_id,
"user_email": user_email,
"transaction_id": transaction_id,
"rec_uuid": record.id,
})
return jsonify(revisions)
except Exception:
raise EditorGetRevisionError
def authorlist_text():
"""Run authorlist on a piece of text."""
try:
parsed_authors = authorlist(request.json["text"])
return jsonify(parsed_authors)
except Exception as err:
return jsonify(status=400, message=" / ".join(err.args)), 400
def put(self, pid_value):
"""Updates existing record in db"""
data = self.load_data_from_request()
try:
pid, _ = pid_value.data
record = JobsRecord.get_record_by_pid_value(pid.pid_value)
if not self.user_can_edit(record):
return (
jsonify(
{"message": "You are not allowed to edit this Job opening"}
),
403,
)
except PIDDoesNotExistError:
abort(404)
self.raise_if_user_can_not_modify_status(data, record)
builder = self.get_builder_with_updated_record(data, record)
data = self.get_valid_record_data_from_builder(builder)
record.update(data)
db.session.commit()
if not is_superuser_or_cataloger_logged_in():
self.create_ticket(record, "rt/update_job.html")
return jsonify({"pid_value": record["control_number"]})
def upload():
"""Upload file to S3."""
if "file" not in request.files:
return jsonify(success=False, message="File key is missing."), 400
file_data = request.files["file"]
filename = file_data.filename
mime_type = file_data.mimetype
_, extension = splitext(filename)
if extension not in current_app.config["EDITOR_UPLOAD_ALLOWED_EXTENSIONS"]:
return (
jsonify(
success=False, message=f"File extension '{extension}' is not supported."
),
400,
)
key = hash_data(file_data.read())
bucket = current_app.config.get("S3_EDITOR_BUCKET")
file_data.seek(0)
current_s3_instance.upload_file(
file_data, key, filename, mime_type, current_app.config["S3_FILE_ACL"], bucket
)
file_url = current_s3_instance.get_s3_url(key, bucket)
return jsonify({"path": file_url}), 200
def refextract_url():
"""Run refextract on a URL."""
if current_app.config.get("FEATURE_FLAG_ENABLE_REFEXTRACT_SERVICE"):
headers = {
"Content-Type": "application/json",
"Accept": "application/json"
}
data = {
"journal_kb_data": create_journal_dict(),
"url": request.json["url"]
}
response = requests.post(
f"{current_app.config['REFEXTRACT_SERVICE_URL']}/extract_references_from_url",
headers=headers,
data=orjson.dumps(data),
)
if response.status_code != 200:
return jsonify({"message": "Can not extract references"}, 500)
extracted_references = response.json()["extracted_references"]
else:
extracted_references = extract_references_from_url(
request.json["url"],
override_kbs_files={"journals": create_journal_dict()},
reference_format="{title},{volume},{page}",
)
deduplicated_extracted_references = dedupe_list(extracted_references)
references = map_refextract_to_schema(deduplicated_extracted_references)
match_result = match_references(references)
return jsonify(match_result.get("matched_references"))
def literature_export_to_cds(args):
literature_recids = args["literature_recids"]
try:
export_papers_to_cds(literature_recids)
except Exception:
LOGGER.exception("Cannot start 'export_to_cds' task.")
return jsonify({"message": "Internal Error"}), 500
return jsonify({"message": "Success"}), 200
def literature_assign_conferences_view(args):
conference_recid = args["conference_recid"]
literature_recids = args["literature_recids"]
try:
assign_paper_to_conference.delay(literature_recids, conference_recid)
except Exception:
LOGGER.exception("Cannot start 'assign_paper_to_conference' task.")
return jsonify({"message": "Internal Error"}), 500
return jsonify({"message": "Success"}), 200
def local_login():
body = request.get_json()
email = body["email"]
password = body["password"]
user = User.query.filter_by(email=email).one_or_none()
if user and verify_password(password, user.password):
login_user(user)
data_current_user = get_current_user_data()
return jsonify(data_current_user), 200
return jsonify({"message": "Email or password is incorrect"}), 422
def sign_up_user():
try:
current_oauthclient.signup_handlers["orcid"]["view"]()
except IntegrityError:
# invenio-oauthclient doesn't handle properly the case of duplicate
# emails, and it's raising a sqlalchemy ``IntegrityError``.
return jsonify({"message": "Email already exists.", "code": 400}), 400
except Exception:
return jsonify({"message": "Cannot create user.", "code": 400}), 400
else:
data_current_user = get_current_user_data()
return jsonify(data_current_user), 200
def author_assign_view():
body = request.get_json()
to_author_recid = body.get("to_author_recid")
from_author_recid = body["from_author_recid"]
literature_recids = body["literature_recids"]
if to_author_recid is None:
stub_author_id = assign_to_new_stub_author(from_author_recid, literature_recids)
else:
assign_to_author(from_author_recid, to_author_recid, literature_recids)
db.session.commit()
if to_author_recid is None:
return jsonify({"stub_author_id": stub_author_id}), 200
return jsonify({"message": "Success"}), 200
def get(self, pid_value):
try:
record = AuthorsRecord.get_record_by_pid_value(pid_value)
if not can_user_edit_author_record(record):
return (
jsonify({"message": "You are not allowed to edit this author"}),
403,
)
except PIDDoesNotExistError:
abort(404)
serialized_record = author_v1.dump(record)
return jsonify({"data": serialized_record})
def remove_editor_lock(endpoint, pid_value):
version_id = request.headers["ETag"]
record = request.json
if not check_permissions_for_private_collection_read_write(
record.get("_collections", [])):
return jsonify(message="Unauthorized", code=403), 403
version_from_etag = re.findall(r"\d+", version_id)
if not version_from_etag:
return jsonify(message="Incorrect Etag passed", code=400), 400
version_id = int(version_from_etag[0]) + 1
editor_soft_lock = EditorSoftLock(recid=pid_value,
record_version=version_id,
user_email=current_user.email)
editor_soft_lock.remove_lock()
return jsonify(success=True)
def set_orcid_push_setting():
orcid_account = get_current_user_remote_orcid_account()
data = request.json
allow_push = data["value"]
orcid_account.extra_data["allow_push"] = allow_push
db.session.add(orcid_account)
db.session.commit()
if allow_push is True:
orcid = orcid_account.extra_data["orcid"]
tokens = orcid_account.remote_tokens
if len(tokens) != 1:
raise ValueError(
f"One token per remote account is expected, but found {len(tokens)} for {orcid}"
)
push_account_literature_to_orcid.apply_async(
kwargs={
"orcid": orcid,
"token": tokens[0].access_token
})
return jsonify({"message": "Successfully changed orcid push setting"}), 200
def get_tickets_for_record(endpoint, pid_value):
"""View to get rt ticket belongs to given record"""
tickets_for_record = tickets.get_tickets_by_recid(pid_value)
simplified_tickets = [
_simplify_ticket_response(ticket) for ticket in tickets_for_record
]
return jsonify(simplified_tickets)
def get_record_and_schema(endpoint, pid_value):
pid_type = PidStoreBase.get_pid_type_from_endpoint(endpoint)
record = InspireRecord.get_record_by_pid_value(pid_value,
pid_type,
original_record=True)
if not check_permissions_for_private_collection_read(
record.get("_collections", [])):
return jsonify(message="Unauthorized", code=403), 403
editor_soft_lock_service = EditorSoftLock(
recid=record["control_number"],
record_version=record.model.version_id,
user_email=current_user.email,
)
editor_lock_payload = editor_soft_lock_service.prepare_editor_lock_api_payload(
)
editor_soft_lock_service.add_lock()
json = {
"record": {
"metadata": record
},
"schema": load_schema(record["$schema"]),
}
json.update(editor_lock_payload)
response = make_response(json)
set_headers_for_record_caching_and_concurrency(response, record)
return response
def delete(self, args):
record_uuid = args.get("record_uuid")
source = args.get("source")
result = WorkflowsRecordSources.query.filter_by(
record_uuid=str(record_uuid), source=source.lower()).one_or_none()
if not result:
return (
jsonify({
"message":
"No record found for given record_uuid and source!"
}),
404,
)
db.session.delete(result)
db.session.commit()
return jsonify({"message": "Record succesfully deleted"}), 200
def query_parser():
try:
query = request.values.get("q", "", type=str)
result = parse_query(query)
return jsonify(result)
except Exception:
abort(400)
def post(self):
"""Adds new experiment record"""
data = self.load_data_from_request()
record = ExperimentsRecord(data=data).create(data)
db.session.commit()
return (jsonify({"control_number": record["control_number"]}), 201)
def author_assign_view(args):
to_author_recid = args.get("to_author_recid")
from_author_recid = args["from_author_recid"]
literature_recids = args.get("literature_recids", [])
claimed_literature_recids = args.get("papers_ids_already_claimed")
not_allowed_to_be_claimed_literature_recids = args.get(
"papers_ids_not_matching_name"
)
if not any(
[
literature_recids,
claimed_literature_recids,
not_allowed_to_be_claimed_literature_recids,
]
):
return (
jsonify(
success=False,
message="None of required fields was passed",
),
400,
)
if claimed_literature_recids:
from_author_record = AuthorsRecord.get_record_by_pid_value(from_author_recid)
if from_author_record.get("stub"):
literature_recids = literature_recids + claimed_literature_recids
claimed_literature_recids = []
if claimed_literature_recids or not_allowed_to_be_claimed_literature_recids:
create_rt_ticket_for_claiming_action.delay(
from_author_recid,
to_author_recid,
claimed_literature_recids,
not_allowed_to_be_claimed_literature_recids,
)
return jsonify({"message": "Success", "created_rt_ticket": True}), 200
if to_author_recid is None:
stub_author_id = assign_to_new_stub_author(from_author_recid, literature_recids)
else:
assign_to_author(from_author_recid, to_author_recid, literature_recids)
db.session.commit()
if to_author_recid is None:
return jsonify({"stub_author_id": stub_author_id}), 200
return jsonify({"message": "Success"}), 200
def post(self):
"""Adds new Institution"""
data = self.load_data_from_request()
record = InstitutionsRecord(data=data).create(data)
db.session.commit()
return jsonify({"control_number": record["control_number"]}), 201
def get(self, pid_value):
try:
record = SeminarsRecord.get_record_by_pid_value(pid_value)
except PIDDoesNotExistError:
abort(404)
serialized_record = seminar_serializer_v1.dump(record)
return jsonify({"data": serialized_record})
def revert_to_revision(endpoint, pid_value):
"""Revert given record to given revision"""
try:
pid_type = PidStoreBase.get_pid_type_from_endpoint(endpoint)
record = InspireRecord.get_record_by_pid_value(pid_value,
pid_type,
original_record=True)
if not check_permissions_for_private_collection_read_write(
record.get("_collections", [])):
return jsonify(message="Unauthorized", code=403), 403
revision_id = request.json["revision_id"]
record.revert(revision_id)
db.session.commit()
return jsonify(success=True)
except Exception:
raise EditorRevertToRevisionError
def post(self):
"""Adds new job record"""
data = self.load_data_from_request()
builder = self.get_builder_with_new_record(data)
data = self.get_valid_record_data_from_builder(builder)
record = JobsRecord.create(data)
db.session.commit()
self.create_ticket(record, "rt/new_job.html")
return jsonify({"pid_value": record["control_number"]}), 201
def refextract_url():
"""Run refextract on a URL."""
extracted_references = extract_references_from_url(
request.json["url"],
override_kbs_files={"journals": create_journal_dict()},
reference_format="{title},{volume},{page}",
)
references = map_refextract_to_schema(extracted_references)
match_result = match_references(references)
return jsonify(match_result.get("matched_references"))
def put(self, pid_value):
try:
record = SeminarsRecord.get_record_by_pid_value(pid_value)
if not can_user_edit_record(record):
return (
jsonify({"message": "You are not allowed to edit this seminar"}),
403,
)
except PIDDoesNotExistError:
abort(404)
data = self.load_data_from_request()
updated_record_data = self.get_updated_record_data(data, record)
record.update(updated_record_data)
db.session.commit()
if not is_superuser_or_cataloger_logged_in():
self.create_ticket(record, "rt/update_seminar.html")
return jsonify({"pid_value": record["control_number"]})
def put(self, pid_value):
try:
record = AuthorsRecord.get_record_by_pid_value(pid_value)
# check if we need to check the orcid in the acquisition source or the one in ids
if not can_user_edit_author_record(record):
return (
jsonify({"message": "You are not allowed to edit this author"}),
403,
)
except PIDDoesNotExistError:
abort(404)
data = self.load_data_from_request()
self.update_author_record(data, record)
db.session.commit()
if current_app.config.get("FEATURE_FLAG_ENABLE_WORKFLOW_ON_AUTHOR_UPDATE"):
self.start_workflow_for_submission(record)
return jsonify({"pid_value": record["control_number"]})
def query_parser():
if not current_app.config.get("FEATURE_FLAG_ENABLE_QUERY_PARSER_ENDPOINT", True):
abort(404)
try:
query = request.values.get("q", "", type=str)
result = parse_query(query)
return jsonify(result)
except Exception:
abort(400)
def create_rt_ticket(endpoint, pid_value):
"""View to create an rt ticket"""
json = request.json
ticket_id = tickets.create_ticket(
json["queue"],
current_user.email,
json.get("description"),
json.get("subject"),
pid_value,
Owner=json.get("owner"),
)
if ticket_id != -1:
return jsonify(
success=True,
data={
"id": str(ticket_id),
"link": tickets.get_rt_link_for_ticket(ticket_id),
},
)
else:
return jsonify(success=False), 500
def disambiguate():
data = request.get_json()
request_data = DisambiguateSignaturesSchema().load(data)
if request_data.errors:
LOGGER.info("Validation error.", user=data, errors=request_data.errors)
return (
jsonify({
"message": "Validation Error.",
"errors": request_data.errors
}),
400,
)
clusters = request_data.data["clusters"]
if not current_app.config["FEATURE_FLAG_ENABLE_DISAMBIGUATION"]:
LOGGER.info("Disambiguation is disabled.")
return jsonify({"message": "Disambiguation feature is disabled."}), 200
disambiguation_task = disambiguate_signatures.apply_async(
kwargs={"clusters": clusters}, queue="disambiguation")
LOGGER.info("Disambiguation task started.",
task_uuid=disambiguation_task.id)
return jsonify({"message": "Disambiguation started."}), 200
def import_article_view(identifier):
try:
article = import_article(identifier)
return jsonify({"data": literature_v1.dump(article)})
except ExistingArticleError as e:
message, recid = e.args
return jsonify(message=str(message), recid=str(recid)), 409
except ImportArticleNotFoundError as e:
LOGGER.exception("Exception in import_article_view", exception=e)
return jsonify(message=str(e)), 404
except ImportParsingError as e:
LOGGER.exception("Exception in import_article_view", exception=e)
return jsonify(message="The article has an invalid format."), 500
except UnknownImportIdentifierError:
return jsonify(
message=f"{identifier} is not a recognized identifier."), 400
except RequestException as e:
LOGGER.exception("Exception in import_article_view", exception=e)
return (
jsonify(
message=
"There was an error when importing metadata. Please try again later or fill the form manually."
),
502,
)