def resolve_by_ui(args: dict, info: graphene.ResolveInfo,
ui: str) -> ModelDescriptor:
"""Retrieves a `ModelDescriptor` object through its UI.
Args:
args (dict): The resolver arguments.
info (graphene.ResolveInfo): The resolver info.
ui (str): The UI of the `ModelDescriptor` to retrieve.
Returns:
DescriptorModel: The retrieved `ModelDescriptor` object or `None`
if no match was not found.
"""
# Retrieve the query on `ModelDescriptor`.
query = TypeDescriptor.get_query(info=info,
) # type: sqlalchemy.orm.query.Query
# Filter to the `ModelDescriptor` record matching `ui`.
query = query.filter(ModelDescriptor.ui == ui)
# 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=ModelDescriptor,
)
obj = query.first()
return obj
def resolve_by_group_name(args: dict, info: graphene.ResolveInfo,
group_name: str) -> List[ModelHealthTopic]:
""" Retrieves `ModelHealthTopic` record objects through their group
name.
Args:
args (dict): The resolver arguments.
info (graphene.ResolveInfo): The resolver info.
group_name (str): The name of the health-topic group to retrieve
health-topics for.
Returns:
List[ModelHealthTopic]: The retrieved `ModelHealthTopic` record
objects or an empty list if no matches were found.
"""
# Retrieve the query on `ModelHealthTopic`.
query = TypeHealthTopic.get_query(
info=info) # type: sqlalchemy.orm.query.Query
# Filter to the `ModelHealthTopic` records matching the given
# group.
query = query.join(ModelHealthTopic.health_topic_groups)
query = query.filter(ModelHealthTopicGroup.name == group_name)
# 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=ModelHealthTopic)
objs = query.all()
return objs
def resolve_by_synonym(
args: Dict,
info: graphene.ResolveInfo,
synonym: str,
limit: Union[int, None] = None,
) -> List[ModelDescriptor]:
"""Retrieves a list of `ModelDescriptor` objects with a tree-number
prefix-matching `tree_number_prefix`.
Args:
args (dict): The resolver arguments.
info (graphene.ResolveInfo): The resolver info.
synonym (str): The synonym query by which to perform the search.
limit (int, optional): The number of closest-matching descriptors
to return. Defaults to `None`.
Returns:
list[DescriptorModel]: The list of matched `ModelDescriptor`
objects or an empty list if no match was found.
"""
# 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
# Define a function to calculate the maximum similarity between a
# descriptor's synonyms and the synonym query.
func_similarity = sqlalchemy_func.max(
sqlalchemy_func.similarity(
ModelDescriptorSynonym.synonym,
synonym,
)).label("synonym_similarity")
# Query out `ModelDescriptor`.
query = session.query(ModelDescriptor) # type: sqlalchemy.orm.Query
query = query.join(ModelDescriptor.synonyms)
query = query.filter(ModelDescriptorSynonym.synonym.op("%%")(synonym))
query = query.order_by(func_similarity.desc())
query = query.group_by(ModelDescriptor.descriptor_id)
if limit is not None:
query = query.limit(limit=limit)
# 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=ModelDescriptor,
)
objs = query.all()
return objs
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 resolve_by_tree_number_prefix(
args: dict, info: graphene.ResolveInfo,
tree_number_prefix: str) -> List[ModelDescriptor]:
"""Retrieves a list of `ModelDescriptor` objects with a tree-number
prefix-matching `tree_number_prefix`.
Args:
args (dict): The resolver arguments.
info (graphene.ResolveInfo): The resolver info.
tree_number_prefix (str): The tree-number prefix to match against.
Returns:
list[DescriptorModel]: The list of matched `ModelDescriptor`
objects or an empty list if no match was found.
"""
# 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
# Query out `ModelDescriptor`.
query = session.query(ModelDescriptor) # type: sqlalchemy.orm.Query
query = query.join(ModelDescriptor.tree_numbers)
# Filter down to `ModelDescriptor` objects with a tree-number
# prefix-matching `tree_number_prefix`.
query = query.filter(
ModelTreeNumber.tree_number.like(
"{}%".format(tree_number_prefix)), )
# 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=ModelDescriptor,
)
objs = query.all()
return objs
def resolve_by_id(
args: dict,
info: graphene.ResolveInfo,
citation_ids: List[int],
) -> List[ModelCitation]:
"""Retrieves `ModelCitation` record objects through their IDs.
Args:
args (dict): The resolver arguments.
info (graphene.ResolveInfo): The resolver info.
citation_ids (List[str]): The IDs for which `ModelCitation` record
objects will be retrieved.
Returns:
List[ModelCitation]: The retrieved `ModelCitation` record objects
or an empty list if no matches were found.
"""
# Retrieve the query on `ModelCitation`.
query = TypeCitation.get_query(
info=info,
) # type: sqlalchemy.orm.query.Query
# Filter to the `ModelCitation` records matching any of the
# `citation_ids`.
query = query.filter(ModelCitation.citation_id.in_(citation_ids))
# 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=ModelCitation,
)
objs = query.all()
return objs
def resolve_filter(
args: dict,
info: graphene.ResolveInfo,
study_ids: List[int],
overall_statuses: Optional[List[EnumOverallStatus]] = None,
cities: Optional[List[str]] = None,
states: Optional[List[str]] = None,
countries: Optional[List[str]] = None,
facility_canonical_ids: Optional[List[int]] = None,
current_location_longitude: Optional[float] = None,
current_location_latitude: Optional[float] = None,
distance_max_km: Optional[int] = None,
intervention_types: Optional[List[EnumIntervention]] = None,
phases: Optional[List[EnumPhase]] = None,
study_types: Optional[List[EnumStudy]] = None,
gender: Optional[EnumGender] = None,
year_beg: Optional[int] = None,
year_end: Optional[int] = None,
age_beg: Optional[int] = None,
age_end: Optional[int] = None,
order_by: Optional[str] = None,
order: Optional[TypeEnumOrder] = None,
offset: Optional[int] = None,
limit: Optional[int] = None,
) -> List[ModelStudy]:
# 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
query = session.query(ModelStudy) # type: sqlalchemy.orm.query.Query
# 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=ModelStudy,
)
# Apply the different optional filters to the query.
query = TypeStudies._apply_query_filters(
query=query,
study_ids=study_ids,
overall_statuses=overall_statuses,
cities=cities,
states=states,
countries=countries,
facility_canonical_ids=facility_canonical_ids,
current_location_longitude=current_location_longitude,
current_location_latitude=current_location_latitude,
distance_max_km=distance_max_km,
intervention_types=intervention_types,
phases=phases,
study_types=study_types,
gender=gender,
year_beg=year_beg,
year_end=year_end,
age_beg=age_beg,
age_end=age_end,
)
# Apply order (if defined).
if order_by:
# Convert the order-by field to snake-case. This allows for fields
# to be defined in camel-case but won't error-out if the fields are
# already in snake-case.
order_by = to_snake_case(order_by)
if order and order == TypeEnumOrder.DESC.value:
query = query.order_by(getattr(ModelStudy, order_by).desc())
else:
query = query.order_by(getattr(ModelStudy, order_by).asc())
query = query.group_by(ModelStudy.study_id)
# Apply offset (if defined).
if offset:
query = query.offset(offset=offset)
# Apply limit (if defined).
if limit:
query = query.limit(limit=limit)
objs = query.all()
return objs
def resolve_search(
args: dict,
info: graphene.ResolveInfo,
mesh_descriptor_ids: List[int],
gender: Optional[EnumGender] = None,
year_beg: Optional[int] = None,
year_end: Optional[int] = None,
age_beg: Optional[int] = None,
age_end: Optional[int] = None,
do_include_children: Optional[bool] = True,
) -> List[ModelStudy]:
"""Retrieves a list of `ModelStudy` objects matching several optional
filters.
Args:
args (dict): The resolver arguments.
info (graphene.ResolveInfo): The resolver info.
mesh_descriptor_ids (List[int]): A list of MeSH descriptor IDs of
the descriptors tagged against the study.
gender (Optional[EnumGender] = None): The patient gender to search
by.
year_beg (Optional[int] = None): The minimum year the start date a
matched `ModelStudy` may have.
year_end (Optional[int] = None): The maximum year the start date a
matched `ModelStudy` may have.
age_beg (Optional[int] = None): The minimum eligibility age date a
matched `ModelStudy` may have.
age_end (Optional[int] = None): The maximum eligibility age date a
matched `ModelStudy` may have.
do_include_children (Optional[bool] = True): Whether to search for
and include in the search the children MeSH descriptors of the
provided descriptors.
Returns:
List[StudyModel]: The list of matched `ModelStudy` objects or an
empty list if no match was found.
"""
# 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
# If the search is to account for the provided descriptors and their
# children then find all the children descriptor IDs. Otherwise only
# use the provided ones.
if do_include_children:
# Retrieve all tree-numbers for the specified MeSH descriptors.
query_tns = session.query(
ModelTreeNumber.tree_number,
ModelDescriptorTreeNumber.descriptor_id,
)
query_tns = query_tns.join(ModelTreeNumber.descriptor_tree_numbers)
query_tns = query_tns.filter(
ModelDescriptorTreeNumber.descriptor_id.in_(
mesh_descriptor_ids, ), )
# Retrieve the tree-numbers and associate them with each provided
# descriptor ID in `map_descriptor_tns`.
map_descriptor_tns = {}
tree_numbers_all = []
for tree_number, descriptor_id in query_tns.all():
map_descriptor_tns.setdefault(
descriptor_id,
[],
).append(tree_number)
tree_numbers_all.append(tree_number)
# Deduplicate the tree-numbers.
tree_numbers_all = list(set(tree_numbers_all))
# If no tree-numbers have been found return an empty list.
if not tree_numbers_all:
return []
# Query out the IDs of all children descriptors of all provided
# descriptors based on the retrieved tree-numbers.
query_descs = session.query(
ModelDescriptor.descriptor_id,
ModelTreeNumber.tree_number,
)
query_descs = query_descs.join(ModelDescriptor.tree_numbers)
# Children descriptors are found by retrieving all descriptors
# with any tree number prefixed by one of the previously found
# tree-numbers.
query_descs = query_descs.filter(
ModelTreeNumber.tree_number.like(
sqlalchemy.any_(
postgresql.array(
tuple([
"{}%".format(tn) for tn in tree_numbers_all
])))))
# Retrieve the children descriptor IDs and associate them with each
# provided descriptor ID in `map_descriptor_children`.
map_descriptor_children = {}
for child_descriptor_id, tree_number in query_descs.all():
for descriptor_id, tree_numbers in map_descriptor_tns.items():
for tree_number_prefix in tree_numbers:
if tree_number.startswith(tree_number_prefix):
map_descriptor_children.setdefault(
descriptor_id,
[descriptor_id],
).append(child_descriptor_id)
# Unique the descriptor IDs under each provided descriptor ID.
for descriptor_id, tree_numbers in map_descriptor_children.items():
map_descriptor_children[descriptor_id] = list(
set(tree_numbers))
else:
map_descriptor_children = {
descriptor_id: [descriptor_id]
for descriptor_id in mesh_descriptor_ids
}
# If no descriptor IDs have been found return an empty list.
if not map_descriptor_children:
return []
# Create a function to aggregate the MeSH descriptor IDs of queried
# studies into an array.
array_descriptors = sqlalchemy_func.array_agg(
ModelDescriptor.descriptor_id, )
# Find all clinical-trial studies associated with the MeSH descriptors
# found prior.
query = session.query(ModelStudy)
# Filter studies by associated mesh-descriptors.
query = query.join(ModelStudy.descriptors)
# Filter studies the year of their start-date.
if year_beg:
query = query.filter(
ModelStudy.start_date >= datetime.date(year_beg, 1, 1))
if year_end:
query = query.filter(
ModelStudy.start_date <= datetime.date(year_end, 12, 31))
# Join on the `eligibility` relationship if any of the fiters that
# require it are defined.
if gender or age_beg or age_end:
query = query.join(ModelStudy.eligibility)
# Apply a gender filter if defined.
if gender:
if gender == EnumGender.ALL:
query = query.filter(
ModelEligibility.gender == EnumGender.ALL.value, )
elif gender in [EnumGender.FEMALE, EnumGender.MALE]:
_value = EnumGender.get_member(value=str(gender))
query = query.filter(
sqlalchemy.or_(
ModelEligibility.gender == EnumGender.ALL.value,
ModelEligibility.gender == _value,
))
# Filter studies by eligibility age.
if age_beg or age_end:
query = TypeStudies._apply_age_filter(query=query,
age_beg=age_beg,
age_end=age_end)
# Group by study ID assembling the MeSH descriptor IDs of each study
# into arrays. Each study will pass the filters if it has at least one
# of the descriptors under the provided descriptors (which will be
# multiple if children descriptors are used). This is achieved through
# the overlap `&&` operator which returns `true` if one array shares at
# least one element with the other.
query = query.group_by(ModelStudy.study_id)
query = query.having(
sqlalchemy.and_(*[
array_descriptors.op("&&")(sqlalchemy_func.cast(
descriptor_ids,
postgresql.ARRAY(postgresql.BIGINT),
)) for descriptor_ids in map_descriptor_children.values()
]))
# Limit query to fields requested in the GraphQL query.
query = apply_requested_fields(
info=info,
query=query,
orm_class=ModelStudy,
)
objs = query.all()
return objs
def resolve_search(
args: dict,
info: graphene.ResolveInfo,
mesh_descriptor_ids: List[int],
year_beg: Optional[int] = None,
year_end: Optional[int] = None,
do_include_children: Optional[bool] = True,
) -> List[ModelCitation]:
"""Retrieves a list of `ModelCitation` objects matching several optional
filters.
Args:
args (dict): The resolver arguments.
info (graphene.ResolveInfo): The resolver info.
mesh_descriptor_ids (List[int]): A list of MeSH descriptor IDs of
the descriptors tagged against the study.
year_beg (Optional[int]): The minimum year the publication date the
article of a matched `ModelCitation` may have.
year_end (Optional[int]): The maximum year the publication date the
article of a matched `ModelCitation` may have.
do_include_children (Optional[bool]): Whether to search for and
include in the search the children MeSH descriptors of the
provided descriptors.
Returns:
List[ModelCitation]: The list of matched `ModelCitation` objects
or an empty list if no match was found.
"""
# 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
# If the search is to account for the provided descriptors and their
# children then find all the children descriptor IDs. Otherwise only
# use the provided ones.
if do_include_children:
# Retrieve all tree-numbers for the specified MeSH descriptors.
query_tns = session.query(
ModelTreeNumber.tree_number,
ModelDescriptorTreeNumber.descriptor_id,
)
query_tns = query_tns.join(ModelTreeNumber.descriptor_tree_numbers)
query_tns = query_tns.filter(
ModelDescriptorTreeNumber.descriptor_id.in_(
mesh_descriptor_ids,
),
)
# Retrieve the tree-numbers and associate them with each provided
# descriptor ID in `map_descriptor_tns`.
map_descriptor_tns = {}
tree_numbers_all = []
for tree_number, descriptor_id in query_tns.all():
map_descriptor_tns.setdefault(
descriptor_id,
[],
).append(tree_number)
tree_numbers_all.append(tree_number)
# Deduplicate the tree-numbers.
tree_numbers_all = list(set(tree_numbers_all))
# If no tree-numbers have been found return an empty list.
if not tree_numbers_all:
return []
# Query out the IDs of all children descriptors of all provided
# descriptors based on the retrieved tree-numbers.
query_descs = session.query(
ModelDescriptor.descriptor_id,
ModelTreeNumber.tree_number,
)
query_descs = query_descs.join(ModelDescriptor.tree_numbers)
# Children descriptors are found by retrieving all descriptors
# with any tree number prefixed by one of the previously found
# tree-numbers.
query_descs = query_descs.filter(
ModelTreeNumber.tree_number.like(
sqlalchemy.any_(postgresql.array(
tuple([
"{}%".format(tn)
for tn in tree_numbers_all
])
))
)
)
# Retrieve the children descriptor IDs and associate them with each
# provided descriptor ID in `map_descriptor_children`.
map_descriptor_children = {}
for child_descriptor_id, tree_number in query_descs.all():
for descriptor_id, tree_numbers in map_descriptor_tns.items():
for tree_number_prefix in tree_numbers:
if tree_number.startswith(tree_number_prefix):
map_descriptor_children.setdefault(
descriptor_id,
[descriptor_id],
).append(child_descriptor_id)
# Unique the descriptor IDs under each provided descriptor ID.
for descriptor_id, tree_numbers in map_descriptor_children.items():
map_descriptor_children[descriptor_id] = list(set(tree_numbers))
else:
map_descriptor_children = {
descriptor_id: [descriptor_id]
for descriptor_id in mesh_descriptor_ids
}
# If no descriptor IDs have been found return an empty list.
if not map_descriptor_children:
return []
# Create a function to aggregate the MeSH descriptor IDs of queried
# citations into an array.
array_descriptors = sqlalchemy_func.array_agg(
ModelDescriptor.descriptor_id,
)
# Find all PubMed citations associated with the MeSH descriptors found
# prior.
query = session.query(ModelCitation)
# Filter citations by associated mesh-descriptors.
query = query.join(ModelCitation.descriptors)
if year_beg or year_end:
query = query.join(ModelCitation.article)
# Filter studies the year of their start-date.
if year_beg:
query = query.filter(
ModelArticle.publication_year >= year_beg
)
if year_end:
query = query.filter(
ModelArticle.publication_year <= year_end
)
# Group by citation ID assembling the MeSH descriptor IDs of each study
# into arrays. Each citation will pass the filters if it has at least
# one of the descriptors under the provided descriptors (which will be
# multiple if children descriptors are used). This is achieved through
# the overlap `&&` operator which returns `true` if one array shares at
# least one element with the other.
query = query.group_by(ModelCitation.citation_id)
query = query.having(
sqlalchemy.and_(
*[
array_descriptors.op("&&")(
sqlalchemy_func.cast(
descriptor_ids,
postgresql.ARRAY(postgresql.BIGINT),
)
)
for descriptor_ids in map_descriptor_children.values()
]
)
)
# Limit query to fields requested in the GraphQL query.
query = apply_requested_fields(
info=info,
query=query,
orm_class=ModelCitation,
)
objs = query.all()
return objs
def resolve_count_citations_by_qualifier(
args: dict,
info: graphene.ResolveInfo,
citation_ids: List[int],
limit: Optional[int] = None,
) -> List[TypeCountCitationsQualifier]:
"""Creates a list of `TypeCountCitationsQualifier` objects with the
number of citations per qualifier.
Args:
args (dict): The resolver arguments.
info (graphene.ResolveInfo): The resolver info.
citation_ids (List[int]): A list of citation IDs.
limit (Optional[int]): The number of results to return. Defaults to
`None` in which case all results are returned.
Returns:
list[TypeCountCitationsQualifier]: The list of
`TypeCountCitationsQualifier` objects with the results of the
aggregation.
"""
# 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
# Define the `COUNT(citations.citation_id)` function.
func_count_citations = sqlalchemy_func.count(
sqlalchemy_func.distinct(
ModelCitationDescriptorQualifier.citation_id), )
# Query out the count of citations by country.
query = session.query(
ModelQualifier,
func_count_citations,
) # type: sqlalchemy.orm.Query
query = query.join(
ModelCitationDescriptorQualifier,
ModelCitationDescriptorQualifier.qualifier_id ==
ModelQualifier.qualifier_id,
)
query = query.filter(
ModelCitationDescriptorQualifier.citation_id.in_(citation_ids), )
# Group by qualifier.
query = query.group_by(ModelQualifier.qualifier_id, )
# Order by the number of studies.
query = query.order_by(func_count_citations.desc())
# Extract the fields requested in the GraphQL query.
fields = extract_requested_fields(
info=info,
fields=info.field_asts,
do_convert_to_snake_case=True,
)["count_citations_by_qualifier"]["qualifier"]
# Limit query to `ModelQualifier` fields requested in the GraphQL
# query.
query = apply_requested_fields(
info=info,
query=query,
orm_class=ModelQualifier,
fields={"qualifier": fields},
)
# Apply limit (if defined).
if limit:
query = query.limit(limit=limit)
results = query.all()
# Wrap the results of the aggregation in `TypeCountCitationsQualifier`
# objects.
objs = [
TypeCountCitationsQualifier(qualifier=result[0],
count_citations=result[1])
for result in results
]
return objs