def mutate(
args: Dict,
info: graphql.execution.base.ResolveInfo,
user_study: InputUserStudy,
):
""" Upserts a `ModelUserStudy` record based on the `user_study` input.
Returns
MutationUserStudyUpsert: The result of the mutation.
"""
# Cleanup the Auth0 user ID.
auth0_user_id = clean_auth0_user_id(auth0_user_id=str(
user_study.auth0_user_id), )
# Retrieve the NCT ID of the defined study.
nct_id = str(user_study.nct_id)
# Check that the requesting user is authorized to upsert the user with
# the given Auth0 ID.
check_auth(info=info, auth0_user_id=auth0_user_id)
# Retrieve the session out of the context as the `get_query` method
# automatically selects the model.
session = info.context.get("session") # type: sqlalchemy.orm.Session
# Retrieve the `ModelUser` record object.
user = get_user(session=session, auth0_user_id=auth0_user_id)
# Raise an exception if the requested user could not be found.
if not user:
msg = "User with Auth0 ID '{}' could not be found."
msg_fmt = msg.format(auth0_user_id)
raise graphql.GraphQLError(message=msg_fmt)
# Retrieve the `ModelStudy` record object.
study = get_study(session=session, nct_id=nct_id)
# Raise an exception if the requested study could not be found.
if not study:
msg = "Study with NCT ID '{}' could not be found."
msg_fmt = msg.format(nct_id)
raise graphql.GraphQLError(message=msg_fmt)
# Upsert the `ModelUserStudy` record.
statement = insert(ModelUserStudy,
values={
"user_id": user.user_id,
"study_id": study.study_id,
}).on_conflict_do_nothing() # type: Insert
# Execute the upsert.
result = session.execute(statement) # type: ResultProxy
# Retrieve the newly upserted `ModelUser` record object.
obj = get_user(session=session, auth0_user_id=auth0_user_id)
session.commit()
return MutationUserStudyUpsert(user=obj)
def mutate(
args: Dict,
info: graphql.execution.base.ResolveInfo,
auth0_user_id: str,
):
""" Deletes a `ModelUser` record based on the `user` input.
Returns
MutationUserDelete: The result of the mutation.
"""
# Cleanup the Auth0 user ID.
auth0_user_id = clean_auth0_user_id(auth0_user_id=str(auth0_user_id))
# Check that the requesting user is authorized to upsert the user with
# the given Auth0 ID.
check_auth(info=info, auth0_user_id=auth0_user_id)
# Retrieve the session out of the context as the `get_query` method
# automatically selects the model.
session = info.context.get("session") # type: sqlalchemy.orm.Session
# Retrieve the `ModelUser` record object.
query = session.query(ModelUser)
query = query.filter(ModelUser.auth0_user_id == auth0_user_id)
obj = query.one_or_none() # type: ModelUser
# Raise an exception if the requested user could not be found.
if not obj:
msg = "User with Auth0 ID '{}' could not be found."
msg_fmt = msg.format(auth0_user_id)
raise graphql.GraphQLError(message=msg_fmt)
# Delete the `ModelSearch` records related to this user as well as all
# `ModelUserSearch` and `ModelSearchDescriptor` records related to
# those searches.
delete_user_searches(session=session, user_id=obj.user_id)
# Delete all `ModelUserStudy` records related to this user.
query = session.query(ModelUserStudy)
query = query.filter(ModelUserStudy.user_id == obj.user_id)
query.delete()
# Delete all `ModelUserCitation` records related to this user.
query = session.query(ModelUserCitation)
query = query.filter(ModelUserCitation.user_id == obj.user_id)
query.delete()
# Delete the `ModelUser` record.
session.delete(obj)
session.commit()
return MutationUserDelete(user=obj)
def resolve_by_search_uuid(
args: dict,
info: graphene.ResolveInfo,
auth0_user_id: str,
search_uuid: str,
) -> ModelSearch:
""" Retrieves a `ModelUser` record object through its Auth0 IDs.
Args:
args (dict): The resolver arguments.
info (graphene.ResolveInfo): The resolver info.
auth0_user_id (str): The Auth0 ID of the user to which the search
belongs.
search_uuid (uuid.UUID): The search UUID for which the
`ModelSearch` record object will be retrieved.
Returns:
ModelSearch: The retrieved `ModelSearch` record object or `None`
if no matches were found.
"""
# Cleanup the Auth0 user ID.
auth0_user_id = clean_auth0_user_id(auth0_user_id=str(auth0_user_id))
# Check that the requesting user is authorized to retrieve the user with
# the given Auth0 ID.
check_auth(info=info, auth0_user_id=auth0_user_id)
# Retrieve the query on `ModelSearch`.
query = TypeSearch.get_query(
info=info,
) # type: sqlalchemy.orm.query.Query
# Filter to the `ModelSearch` record matching the `search_uuid`.
query = query.filter(ModelSearch.search_uuid == search_uuid)
# Limit query to fields requested in the GraphQL query adding
# `load_only` and `joinedload` options as required.
query = apply_requested_fields(
info=info,
query=query,
orm_class=ModelSearch,
)
obj = query.one_or_none()
# Raise an exception if the requested search could not be found.
if not obj:
msg = "Search with UUID '{}' could not be found."
msg_fmt = msg.format(search_uuid)
raise graphql.GraphQLError(message=msg_fmt)
return obj
def mutate(
args: Dict,
info: graphql.execution.base.ResolveInfo,
auth0_user_id: str,
search_uuid: uuid.UUID,
):
""" Deletes a `ModelSearch` record and all its `ModelSearchDescriptor`
records.
Returns
MutationSearchUpsert: The result of the mutation.
"""
# Cleanup the Auth0 user ID.
auth0_user_id = clean_auth0_user_id(auth0_user_id=str(auth0_user_id))
# Check that the requesting user is authorized to make changes to the
# user with the given Auth0 ID.
check_auth(info=info, auth0_user_id=auth0_user_id)
# Retrieve the session out of the context as the `get_query` method
# automatically selects the model.
session = info.context.get("session") # type: sqlalchemy.orm.Session
# Retrieve the `ModelUser` record object.
user = get_user(session=session, auth0_user_id=auth0_user_id)
# Raise an exception if the requested user could not be found.
if not user:
raise graphql.GraphQLError(
message=f"User with Auth0 ID '{auth0_user_id}' could not be "
f"found.")
# Retrieve the `ModelSearch` record object.
search = get_search(session=session, search_uuid=search_uuid)
# Raise an exception if the requested search could not be found.
if not search:
raise graphql.GraphQLError(
message=f"Search with UUID '{search_uuid}' under user with "
f"Auth0 ID '{auth0_user_id}' could not be found.")
# Delete the `ModelSearch` record and all its related `ModelUserSearch`
# and `ModelSearchDescriptor` records.
delete_search(session=session, search_id=search.search_id)
session.commit()
return MutationSearchDelete(search=search)
def mutate(
args: Dict,
info: graphql.execution.base.ResolveInfo,
user: InputUser,
):
""" Upserts a `ModelUser` record based on the `user` input.
Returns
MutationUserUpsert: The result of the mutation.
"""
# Cleanup the Auth0 user ID.
auth0_user_id = clean_auth0_user_id(auth0_user_id=str(
user.auth0_user_id), )
# Check that the requesting user is authorized to upsert the user with
# the given Auth0 ID.
check_auth(info=info, auth0_user_id=auth0_user_id)
# Retrieve the session out of the context as the `get_query` method
# automatically selects the model.
session = info.context.get("session") # type: sqlalchemy.orm.Session
# Upsert the `ModelUser` record.
statement = insert(ModelUser,
values={
"auth0_user_id": user.auth0_user_id,
"email": user.email,
}).on_conflict_do_nothing() # type: Insert
# Execute the upsert.
result = session.execute(statement) # type: ResultProxy
# Retrieve the newly upserted `ModelUser` record object.
obj = get_user(session=session, auth0_user_id=auth0_user_id)
session.commit()
return MutationUserUpsert(user=obj)
def mutate(
args: Dict,
info: graphql.execution.base.ResolveInfo,
user_citation: InputUserCitation,
):
""" Deletes a `ModelUserCitation` record based on the `user_citation`
input.
Returns
MutationUserCitationDelete: The result of the mutation.
"""
# Cleanup the Auth0 user ID.
auth0_user_id = clean_auth0_user_id(auth0_user_id=str(
user_citation.auth0_user_id), )
# Retrieve the PubMed ID of the defined study.
pmid = int(str(user_citation.pmid))
# Check that the requesting user is authorized to upsert the user with
# the given Auth0 ID.
check_auth(info=info, auth0_user_id=auth0_user_id)
# Retrieve the session out of the context as the `get_query` method
# automatically selects the model.
session = info.context.get("session") # type: sqlalchemy.orm.Session
# Retrieve the `ModelUser` record object.
user = get_user(session=session, auth0_user_id=auth0_user_id)
# Raise an exception if the requested user could not be found.
if not user:
msg = "User with Auth0 ID '{}' could not be found."
msg_fmt = msg.format(auth0_user_id)
raise graphql.GraphQLError(message=msg_fmt)
# Retrieve the `ModelCitation` record object.
citation = get_citation(session=session, pmid=pmid)
# Raise an exception if the requested citation could not be found.
if not citation:
msg = "Citation with PubMed ID '{}' could not be found."
msg_fmt = msg.format(pmid)
raise graphql.GraphQLError(message=msg_fmt)
# Retrieve the `ModelUserCitation` record object.
query = session.query(ModelUserCitation)
query = query.filter(ModelUserCitation.user_id == user.user_id)
query = query.filter(
ModelUserCitation.citation_id == citation.citation_id, )
user_citation = query.one_or_none()
# Raise an exception if the requested user-citation could not be found.
if not user_citation:
msg = ("User-citation for user with Auth0 ID '{} and PubMed "
"ID '{}' could not be found.")
msg_fmt = msg.format(auth0_user_id, pmid)
raise graphql.GraphQLError(message=msg_fmt)
# Delete the `ModelUserCitation` record.
session.delete(user_citation)
# Retrieve the newly upserted `ModelUser` record object.
obj = get_user(session=session, auth0_user_id=auth0_user_id)
session.commit()
return MutationUserCitationDelete(user=obj)
def mutate(
args: Dict,
info: graphql.execution.base.ResolveInfo,
user_study: InputUserStudy,
):
""" Deletes a `ModelUserStudy` record based on the `user_study` input.
Returns
MutationUserStudyDelete: The result of the mutation.
"""
# Cleanup the Auth0 user ID.
auth0_user_id = clean_auth0_user_id(auth0_user_id=str(
user_study.auth0_user_id), )
# Retrieve the NCT ID of the defined study.
nct_id = str(user_study.nct_id)
# Check that the requesting user is authorized to upsert the user with
# the given Auth0 ID.
check_auth(info=info, auth0_user_id=auth0_user_id)
# Retrieve the session out of the context as the `get_query` method
# automatically selects the model.
session = info.context.get("session") # type: sqlalchemy.orm.Session
# Retrieve the `ModelUser` record object.
user = get_user(session=session, auth0_user_id=auth0_user_id)
# Raise an exception if the requested user could not be found.
if not user:
msg = "User with Auth0 ID '{}' could not be found."
msg_fmt = msg.format(auth0_user_id)
raise graphql.GraphQLError(message=msg_fmt)
# Retrieve the `ModelStudy` record object.
study = get_study(session=session, nct_id=nct_id)
# Raise an exception if the requested study could not be found.
if not study:
msg = "Study with NCT ID '{}' could not be found."
msg_fmt = msg.format(nct_id)
raise graphql.GraphQLError(message=msg_fmt)
# Retrieve the `ModelUserStudy` record object.
query = session.query(ModelUserStudy)
query = query.filter(ModelUserStudy.user_id == user.user_id)
query = query.filter(ModelUserStudy.study_id == study.study_id)
user_study = query.one_or_none()
# Raise an exception if the requested user-study could not be found.
if not user_study:
msg = ("User-study for user with Auth0 ID '{} and NCT ID '{}' "
"could not be found.")
msg_fmt = msg.format(auth0_user_id, nct_id)
raise graphql.GraphQLError(message=msg_fmt)
# Delete the `ModelUserStudy` record.
session.delete(user_study)
# Retrieve the newly upserted `ModelUser` record object.
obj = get_user(session=session, auth0_user_id=auth0_user_id)
session.commit()
return MutationUserStudyDelete(user=obj)
def mutate(
args: Dict,
info: graphql.execution.base.ResolveInfo,
auth0_user_id: str,
search: InputSearch,
mesh_descriptor_ids: List[int],
):
""" Upserts a `ModelSearch` record based on the `search` input.
Returns
MutationSearchUpsert: The result of the mutation.
"""
# Cleanup the Auth0 user ID.
auth0_user_id = clean_auth0_user_id(auth0_user_id=str(auth0_user_id))
# Check that the requesting user is authorized to make changes to the
# user with the given Auth0 ID.
check_auth(info=info, auth0_user_id=auth0_user_id)
# Retrieve the session out of the context as the `get_query` method
# automatically selects the model.
session = info.context.get("session") # type: sqlalchemy.orm.Session
# Retrieve the `ModelUser` record object.
user = get_user(session=session, auth0_user_id=auth0_user_id)
# Raise an exception if the requested user could not be found.
if not user:
raise graphql.GraphQLError(
message=f"User with Auth0 ID '{auth0_user_id}' could not be "
f"found.")
# Upsert the `ModelSearch` record.
statement = insert(
ModelSearch,
values={
"search_uuid":
search.search_uuid,
"title":
search.title,
"gender":
EnumGender.get_member(
value=str(search.gender)) if search.gender else None,
"year_beg":
search.year_beg,
"year_end":
search.year_end,
"age_beg":
search.age_beg,
"age_end":
search.age_end,
}).on_conflict_do_nothing() # type: Insert
# Execute the upsert.
session.execute(statement) # type: ResultProxy
# Retrieve the newly upserted `ModelSearch` record object.
search = get_search(session=session, search_uuid=search.search_uuid)
# Upsert a `ModelUserSearch` record.
statement = insert(ModelUserSearch,
values={
"user_id": user.user_id,
"search_id": search.search_id,
}).on_conflict_do_nothing() # type: Insert
# Execute the upsert.
session.execute(statement) # type: ResultProxy
# Delete all existing `ModelSearchDescriptor` records for the given
# search so they can be replaced with new ones.
delete_search_descriptors(session=session, search_id=search.search_id)
# Upsert a `ModelSearchDescriptor` record for each of the defined
# descriptors.
for mesh_descriptor_id in mesh_descriptor_ids:
statement = insert(ModelSearchDescriptor,
values={
"search_id": search.search_id,
"descriptor_id": mesh_descriptor_id,
}).on_conflict_do_nothing() # type: Insert
# Execute the upsert.
session.execute(statement) # type: ResultProxy
session.commit()
return MutationSearchUpsert(search=search)
