def get_node(cls, info: ResolveInfo, id):
db = get_session(info)
row = db.query(cls._meta.db_model)\
.filter(and_(
cls._meta.db_model.is_deleted != True,
cls._meta.db_model.id == id,
))\
.first()
return cls._meta.model.parse_obj(versioned_row_to_dict(row, row.current))
def resolve_all_users(
root,
info: ResolveInfo,
# Search parameters
archived: Optional[bool] = None,
# Paging parameters
page: Optional[int] = None,
per_page: Optional[int] = None,
# Currently unused
before: Optional[str] = None,
after: Optional[str] = None,
first: Optional[int] = None,
last: Optional[int] = None,
):
enforcer = get_enforcer_from_request(info.context['request'])
current_user = get_current_user_from_request(info.context['request'])
if current_user is None:
raise HTTPException(401, "Unauthorized")
db = get_session(info)
pagination_dict = crud_get_users(
item_to_dict=lambda user: add_ids(versioned_row_to_dict(user, user.current), user_id=user.id),
enforcer=enforcer,
db=db,
current_user=current_user,
archived=archived,
page=page,
per_page=per_page,
)
return UserConnection(
page=pagination_dict.get('page', None),
pageCount=pagination_dict.get('pageCount', None),
edges=[
UserConnection.Edge(
node=UserModel.parse_obj(r),
cursor=f"{pagination_dict.get('page', 1)}.{i}",
)
for i, r
in enumerate(pagination_dict['users'])
],
page_info=relay.PageInfo(
has_next_page=pagination_dict.get('page', 1) < pagination_dict.get('pageCount', 1),
has_previous_page=pagination_dict.get('page', 1) > pagination_dict.get('pageCount', 1),
start_cursor="1.0",
end_cursor=f"1.{len(pagination_dict['users'])}" if pagination_dict.get('pageCount', None) is None else f"{pagination_dict['pageCount']}.{len(pagination_dict['users'])}",
),
)
def resolve_owner(root, info):
enforcer = get_enforcer_from_request(info.context['request'])
current_user = get_current_user_from_request(info.context['request'])
if current_user is None:
raise HTTPException(401, "Unauthorized")
db = get_session(info)
return UserModel.parse_obj(
crud_get_user(
item_to_dict=lambda user: add_ids(versioned_row_to_dict(user, user.current), user_id=user.id),
enforcer=enforcer,
db=db,
current_user=current_user,
user_id=root.created_by,
),
)
def resolve_samples(
root,
info: ResolveInfo,
# Paging parameters
page: Optional[int] = None,
per_page: Optional[int] = None,
):
enforcer = get_enforcer_from_request(info.context['request'])
current_user = get_current_user_from_request(info.context['request'])
if current_user is None:
raise HTTPException(401, "Unauthorized")
db = get_session(info)
pagination_dict = crud_get_run_samples(
item_to_dict=lambda sample: versioned_row_to_dict(sample, sample.current),
enforcer=enforcer,
db=db,
current_user=current_user,
run_id=root.run_id,
page=page,
per_page=per_page,
)
return SampleConnection(
page=pagination_dict.get('page', None),
pageCount=pagination_dict.get('pageCount', None),
edges=[
SampleConnection.Edge(
node=SampleResult.parse_obj(r),
cursor=f"{pagination_dict.get('page', 1)}.{i}",
)
for i, r
in enumerate(pagination_dict['samples'])
],
page_info=relay.PageInfo(
has_next_page=pagination_dict.get('page', 1) < pagination_dict.get('pageCount', 1),
has_previous_page=pagination_dict.get('page', 1) > pagination_dict.get('pageCount', 1),
start_cursor="1.0",
end_cursor=f"1.{len(pagination_dict['samples'])}" if pagination_dict.get('pageCount', None) is None else f"{pagination_dict['pageCount']}.{len(pagination_dict['samples'])}",
),
)
def resolve_protocol(root, info):
current_user = get_current_user_from_request(info.context['request'])
if current_user is None:
raise HTTPException(401, "Unauthorized")
# Calculate which top level fields to remove.
top_level_ignore = {'id', 'protocol_id', 'created_by', 'created_on', 'updated_by', 'updated_on'}
select_args = []
top_level = set()
for result in graphql_ast_flatten_field(info.field_asts[0], info.fragments, info.return_type, info.schema):
result_parts = result.split('.')
if len(result_parts) > 1 and result_parts[1] not in top_level_ignore:
top_level.add(result_parts[1])
jsonb_fields = [
'id',
'protocol_id',
'created_by',
'created_on',
'updated_by',
'updated_on',
]
select_args = [
Protocol.id.label('id'),
Protocol.id.label('protocol_id'),
Protocol.created_by.label('created_by'),
Protocol.created_on.label('created_on'),
ProtocolVersion.updated_by.label('updated_by'),
ProtocolVersion.updated_on.label('updated_on'),
]
for field in top_level:
jsonb_fields.append(field)
select_args.append(ProtocolVersion.data[field].label(field))
db = get_session(info)
row_version = db.query(*select_args)\
.select_from(ProtocolVersion)\
.join(Run, and_(
Run.id == root.id,
Run.protocol_version_id == ProtocolVersion.id,
))\
.join(Protocol, Protocol.id == ProtocolVersion.protocol_id)\
.first()
return ProtocolModel.parse_obj(row_version._asdict())
def resolve_user(root, info: ResolveInfo, id: str, version_id: Optional[int]):
enforcer = get_enforcer_from_request(info.context['request'])
current_user = get_current_user_from_request(info.context['request'])
if current_user is None:
raise HTTPException(401, "Unauthorized")
db = get_session(info)
model_dict = crud_get_user(
item_to_dict=lambda user: add_ids(versioned_row_to_dict(user, user.current), user_id=user.id),
enforcer=enforcer,
db=db,
current_user=current_user,
user_id=id,
version_id=version_id,
)
return UserModel.parse_obj(model_dict)
def resolve_protocol(root, info: ResolveInfo, id: int, version_id: Optional[int]):
enforcer = get_enforcer_from_request(info.context['request'])
current_user = get_current_user_from_request(info.context['request'])
if current_user is None:
raise HTTPException(401, "Unauthorized")
db = get_session(info)
model_dict = crud_get_protocol(
item_to_dict=lambda protocol: add_ids(versioned_row_to_dict(protocol, protocol.current), protocol_id=protocol.id),
enforcer=enforcer,
db=db,
current_user=current_user,
protocol_id=id,
version_id=version_id,
)
return ProtocolModel.parse_obj(model_dict)
def resolve_sample(root, info: ResolveInfo, sample_id: str, plate_id: str, run_version_id: int, protocol_version_id: int, version_id: Optional[int]):
enforcer = get_enforcer_from_request(info.context['request'])
current_user = get_current_user_from_request(info.context['request'])
if current_user is None:
raise HTTPException(401, "Unauthorized")
db = get_session(info)
model_dict = crud_get_sample(
item_to_dict=lambda sample: versioned_row_to_dict(sample, sample.current),
enforcer=enforcer,
db=db,
current_user=current_user,
sample_id=sample_id,
plate_id=plate_id,
run_version_id=run_version_id,
protocol_version_id=protocol_version_id,
version_id=version_id,
)
return SampleResult.parse_obj(model_dict)
def resolve_run(
root,
info: ResolveInfo,
id: int,
version_id: int,
):
enforcer = get_enforcer_from_request(info.context['request'])
current_user = get_current_user_from_request(info.context['request'])
if current_user is None:
raise HTTPException(401, "Unauthorized")
db = get_session(info)
model_dict = crud_get_run(
item_to_dict=lambda run: add_ids(versioned_row_to_dict(run, run.current), run_id=run.id),
enforcer=enforcer,
db=db,
current_user=current_user,
run_id=id,
version_id=version_id,
)
return RunModel.parse_obj(model_dict)