def set_data_review_status():
recid = int(request.form['publication_recid'])
data_id = int(request.form['data_recid'])
status = request.form['status']
version = int(request.form['version'])
if user_allowed_to_perform_action(recid):
record_sql = DataReview.query.filter_by(data_recid=data_id,
version=version)
try:
record = record_sql.first()
except NoResultFound:
record = create_data_review(data_id, recid, version)
record_sql.update({"status": status}, synchronize_session='fetch')
try:
db.session.commit()
except Exception:
db.session.rollback()
return jsonify(
{"recid": record.publication_recid, "data_id": record.data_recid,
"status": record.status})
return jsonify(
{"recid": recid, "data_id": data_id, 'message': 'You are not authorised to update the review status for '
'this data record.'})
def set_data_review_status():
recid = int(request.form["publication_recid"])
data_id = int(request.form["data_recid"])
status = request.form["status"]
version = int(request.form["version"])
if user_allowed_to_perform_action(recid):
record_sql = DataReview.query.filter_by(data_recid=data_id, version=version)
try:
record = record_sql.one()
except NoResultFound:
record = create_data_review(data_id, recid, version)
record_sql.update({"status": status}, synchronize_session="fetch")
try:
db.session.commit()
except Exception:
db.session.rollback()
return jsonify({"recid": record.publication_recid, "data_id": record.data_recid, "status": record.status})
return jsonify(
{
"recid": recid,
"data_id": data_id,
"message": "You are not authorised to update the review status for " "this data record.",
}
)
def add_data_review_messsage(publication_recid, data_recid):
"""
Adds a new review message for a data submission.
:param publication_recid:
:param data_recid:
"""
trace = []
message = encode_string(request.form.get('message', ''))
version = request.form['version']
userid = current_user.get_id()
try:
datareview_query = DataReview.query.filter_by(data_recid=data_recid,
version=version)
# if the data review is not already created, create one.
try:
data_review_record = datareview_query.one()
trace.append("adding data review record")
except:
data_review_record = create_data_review(data_recid,
publication_recid)
trace.append("created a new data review record")
data_review_message = Message(user=userid, message=message)
data_review_record.messages.append(data_review_message)
db.session.commit()
current_user_obj = get_user_from_id(userid)
update_action_for_submission_participant(publication_recid, userid,
'reviewer')
send_new_review_message_email(data_review_record, data_review_message,
current_user_obj)
return json.dumps(
{
"publication_recid": data_review_record.publication_recid,
"data_recid": data_review_record.data_recid,
"status": data_review_record.status,
"message": decode_string(data_review_message.message),
"post_time": data_review_message.creation_date,
'user': current_user_obj.email
},
default=default_time)
except Exception as e:
db.session.rollback()
raise e
def set_data_review_status():
recid = int(request.form['publication_recid'])
status = request.form['status']
version = int(request.form['version'])
all_tables = request.form.get('all_tables')
if user_allowed_to_perform_action(recid):
if all_tables:
data_ids = db.session.query(DataSubmission.id) \
.filter_by(publication_recid=recid, version=version).distinct()
else:
data_ids = [int(request.form['data_recid'])]
for data_id in data_ids:
record_sql = DataReview.query.filter_by(data_recid=data_id,
version=version)
record = record_sql.first()
if not record:
record = create_data_review(data_id, recid, version)
record_sql.update({"status": status}, synchronize_session='fetch')
try:
db.session.commit()
success = True
except Exception:
db.session.rollback()
success = False
if all_tables:
return jsonify({"recid": recid, "success": success})
else:
return jsonify({
"recid": record.publication_recid,
"data_id": record.data_recid,
"status": record.status
})
return jsonify({
"recid":
recid,
'message':
'You are not authorised to update the review status for '
'this data record.'
})
def assign_or_create_review_status(data_table_metadata, publication_recid,
version):
"""
If a review already exists, it will be attached to the current data record.
If a review does not exist for a data table, it will be created.
:param data_table_metadata: the metadata describing the main table.
:param publication_recid: publication record id
:param version:
"""
data_review_query = DataReview.query.filter_by(
publication_recid=publication_recid, version=version)
# this method should also create all the DataReviews for data_tables that
# are not currently present to avoid
# only creating data reviews when the review is clicked explicitly.
assigned_tables = []
if data_review_query.count() > 0:
data_review_records = data_review_query.all()
for data_review in data_review_records:
if data_review.data_recid in data_table_metadata:
data_table_metadata[
data_review.data_recid]["review_flag"] = data_review.status
data_table_metadata[data_review.data_recid]["review_status"] = \
RECORD_PLAIN_TEXT[data_review.status]
data_table_metadata[data_review.data_recid]["messages"] = len(
data_review.messages) > 0
assigned_tables.append(data_review.data_recid)
# now create the missing data reviews
for data_table_id in data_table_metadata:
if data_table_id not in assigned_tables:
data_record = create_data_review(data_table_id,
publication_recid,
version=version)
data_table_metadata[data_table_id][
"review_flag"] = data_record.status
data_table_metadata[data_table_id]["review_status"] = \
RECORD_PLAIN_TEXT[data_record.status]
def add_data_review_messsage(publication_recid, data_recid):
# need to set up a session and query for the data review.
trace = []
message = request.form["message"]
version = request.form["version"]
userid = current_user.get_id()
datareview_query = DataReview.query.filter_by(data_recid=data_recid, version=version)
# if the data review is not already created, create one.
try:
data_review_record = datareview_query.one()
trace.append("adding data review record")
except:
data_review_record = create_data_review(data_recid, publication_recid)
trace.append("created a new data review record")
data_review_message = Message(user=userid, message=message)
data_review_record.messages.append(data_review_message)
db.session.commit()
current_user_obj = get_user_from_id(userid)
update_action_for_submission_participant(publication_recid, userid, "reviewer")
send_new_review_message_email(data_review_record, data_review_message, current_user_obj)
return json.dumps(
{
"publication_recid": data_review_record.publication_recid,
"data_recid": data_review_record.data_recid,
"status": data_review_record.status,
"message": data_review_message.message,
"post_time": data_review_message.creation_date,
"user": current_user_obj.email,
},
default=default_time,
)
def assign_or_create_review_status(data_table_metadata, publication_recid,
version):
"""
If a review already exists, it will be attached to the current data record.
If a review does not exist for a data table, it will be created.
:param data_table_metadata: the metadata describing the main table.
:param publication_recid: publication record id
"""
data_review_query = DataReview.query.filter_by(
publication_recid=publication_recid, version=version)
# this method should also create all the DataReviews for data_tables that
# are not currently present to avoid
# only creating data reviews when the review is clicked explicitly.
assigned_tables = []
if data_review_query.count() > 0:
data_review_records = data_review_query.all()
for data_review in data_review_records:
if data_review.data_recid in data_table_metadata:
data_table_metadata[data_review.data_recid][
"review_flag"] = data_review.status
data_table_metadata[data_review.data_recid]["review_status"] = \
RECORD_PLAIN_TEXT[data_review.status]
data_table_metadata[data_review.data_recid]["messages"] = len(
data_review.messages) > 0
assigned_tables.append(data_review.data_recid)
# now create the missing data reviews
for data_table_id in data_table_metadata:
if data_table_id not in assigned_tables:
data_record = create_data_review(
data_table_id, publication_recid, version=version)
data_table_metadata[data_table_id][
"review_flag"] = data_record.status
data_table_metadata[data_table_id]["review_status"] = \
RECORD_PLAIN_TEXT[data_record.status]
def get_table_details(recid, data_recid, version):
"""
:param recid:
:param data_recid:
:param version:
:return:
"""
datasub_query = DataSubmission.query.filter_by(id=data_recid, version=version)
table_contents = {}
if datasub_query.count() > 0:
datasub_record = datasub_query.one()
data_query = db.session.query(DataResource).filter(DataResource.id == datasub_record.data_file)
if data_query.count() > 0:
data_record = data_query.one()
file_location = data_record.file_location
try:
table_contents = yaml.load(file(file_location), Loader=yaml.CSafeLoader)
except:
table_contents = yaml.load(file(file_location))
table_contents["name"] = datasub_record.name
table_contents["title"] = datasub_record.description
table_contents["keywords"] = datasub_record.keywords
table_contents["doi"] = datasub_record.doi
# we create a map of files mainly to accommodate the use of thumbnails for images where possible.
tmp_assoc_files = {}
for associated_data_file in datasub_record.resources:
alt_location = associated_data_file.file_location
location_parts = alt_location.split("/")
key = location_parts[-1].replace("thumb_", "")
if key not in tmp_assoc_files:
tmp_assoc_files[key] = {}
if "thumb_" in alt_location:
tmp_assoc_files[key]["preview_location"] = "/record/resource/{0}?view=true".format(
associated_data_file.id
)
else:
tmp_assoc_files[key].update(
{
"description": associated_data_file.file_description,
"type": associated_data_file.file_type,
"id": associated_data_file.id,
"alt_location": alt_location,
}
)
# add associated files to the table contents
table_contents["associated_files"] = tmp_assoc_files.values()
table_contents["review"] = {}
data_review_record = create_data_review(data_recid, recid, version)
table_contents["review"]["review_flag"] = data_review_record.status
table_contents["review"]["messages"] = len(data_review_record.messages) > 0
# translate the table_contents to an easy to render format of the qualifiers (with colspan),
# x and y headers (should not require a colspan)
# values, that also encompass the errors
return jsonify(generate_table_structure(table_contents))
def get_table_details(recid, data_recid, version):
"""
Get the table details.
:param recid:
:param data_recid:
:param version:
:return:
"""
datasub_query = DataSubmission.query.filter_by(id=data_recid,
version=version)
table_contents = {}
if datasub_query.count() > 0:
datasub_record = datasub_query.one()
data_query = db.session.query(DataResource).filter(
DataResource.id == datasub_record.data_file)
if data_query.count() > 0:
data_record = data_query.one()
file_location = data_record.file_location
attempts = 0
while True:
try:
with open(file_location, 'r') as table_file:
table_contents = yaml.load(table_file, Loader=Loader)
except:
attempts += 1
# allow multiple attempts to read file in case of temporary disk problems
if (table_contents and table_contents is not None) or attempts > 5:
break
table_contents["name"] = datasub_record.name
table_contents["title"] = datasub_record.description
table_contents["keywords"] = datasub_record.keywords
table_contents["doi"] = datasub_record.doi
table_contents["location"] = datasub_record.location_in_publication
# we create a map of files mainly to accommodate the use of thumbnails for images where possible.
tmp_assoc_files = {}
for associated_data_file in datasub_record.resources:
alt_location = associated_data_file.file_location
location_parts = alt_location.split('/')
key = location_parts[-1].replace("thumb_", "")
if key not in tmp_assoc_files:
tmp_assoc_files[key] = {}
if "thumb_" in alt_location and associated_data_file.file_type.lower() in IMAGE_TYPES:
tmp_assoc_files[key]['preview_location'] = '/record/resource/{0}?view=true'.format(
associated_data_file.id)
else:
tmp_assoc_files[key].update({'description': associated_data_file.file_description,
'type': associated_data_file.file_type,
'id': associated_data_file.id,
'alt_location': alt_location})
# add associated files to the table contents
table_contents['associated_files'] = list(tmp_assoc_files.values())
table_contents["review"] = {}
data_review_record = create_data_review(data_recid, recid, version)
table_contents["review"]["review_flag"] = data_review_record.status if data_review_record else "todo"
table_contents["review"]["messages"] = len(data_review_record.messages) > 0 if data_review_record else False
# translate the table_contents to an easy to render format of the qualifiers (with colspan),
# x and y headers (should not require a colspan)
# values, that also encompass the errors
return jsonify(generate_table_structure(table_contents))
