def crud_get_users(
item_to_dict,
enforcer: casbin.Enforcer,
db: Session,
current_user: Auth0ClaimsPatched,
archived: Optional[bool] = None,
page: Optional[int] = None,
per_page: Optional[int] = None,
) -> List[dict]:
return paginatify(
items_label='users',
items=[
user for user in all_users(db, archived).order_by(
User.created_on.desc())
if check_access(enforcer,
user=current_user.username,
path=f"/user/{str(user.id)}",
method="GET") and user and user.current
],
item_to_dict=item_to_dict,
page=page,
per_page=per_page,
)
def crud_get_runs(
item_to_dict,
enforcer: casbin.Enforcer,
db: Session,
current_user: Auth0ClaimsPatched,
protocol: Optional[int] = None,
run: Optional[int] = None,
plate: Optional[str] = None,
reagent: Optional[str] = None,
sample: Optional[str] = None,
creator: Optional[str] = None,
archived: Optional[bool] = None,
page: Optional[int] = None,
per_page: Optional[int] = None,
) -> List[dict]:
runs_queries = []
# Add filter specific queries. These will be intersected later on.
if protocol:
runs_queries.append(
all_runs(db, archived)\
.join(ProtocolVersion, ProtocolVersion.id == Run.protocol_version_id)\
.filter(ProtocolVersion.protocol_id == protocol)
)
if run:
runs_queries.append(
all_runs(db, archived)\
.filter(Run.id == run)
)
if plate:
run_version_query = all_runs(db, archived)\
.join(RunVersion, RunVersion.id == Run.version_id)
runs_subquery = filter_by_plate_label(run_version_query, plate)
runs_queries.append(runs_subquery)
if reagent:
run_version_query = all_runs(db, archived)\
.join(RunVersion, RunVersion.id == Run.version_id)
runs_subquery = filter_by_reagent_label(run_version_query, reagent)
runs_queries.append(runs_subquery)
if sample:
run_version_query = all_runs(db, archived)\
.join(RunVersion, RunVersion.id == Run.version_id)
runs_subquery = filter_by_sample_label(run_version_query, sample)
runs_queries.append(runs_subquery)
if creator:
runs_queries.append(
all_runs(db, archived)\
# .filter(Run.id == run)
.filter(Run.created_by == creator)
)
# Add a basic non-deleted items query if no filters were specified.
if len(runs_queries) == 0:
runs_queries.append(all_runs(db, archived))
# Only return the intersection of all queries.
runs_query = reduce(lambda a, b: a.intersect(b), runs_queries)
return paginatify(
items_label='runs',
items=[
run
for run in runs_query.distinct().order_by(Run.created_on.desc())
if check_access(enforcer,
user=current_user.username,
path=f"/run/{str(run.id)}",
method="GET") and run and run.current
],
item_to_dict=lambda run: item_to_dict(fix_plate_markers_run(db, run)),
page=page,
per_page=per_page,
)
def crud_get_run_samples(
item_to_dict,
enforcer: casbin.Enforcer,
db: Session,
current_user: Auth0ClaimsPatched,
run_id: Optional[int] = None,
protocol: Optional[int] = None,
plate: Optional[str] = None,
reagent: Optional[str] = None,
creator: Optional[str] = None,
archived: Optional[bool] = None,
page: Optional[int] = None,
per_page: Optional[int] = None,
) -> List[dict]:
if not check_access(enforcer,
user=current_user.username,
path=f"/run/{str(run_id)}",
method="GET"):
raise HTTPException(status_code=403, detail='Insufficient Permissions')
run = db.query(Run).get(run_id)
if not run or run.is_deleted:
raise HTTPException(status_code=404, detail='Run Not Found')
samples_queries = []
# Add filter specific queries. These will be intersected later on.
if protocol:
samples_queries.append(
all_samples(db, run, archived)\
.join(ProtocolVersion, ProtocolVersion.id == Sample.protocol_version_id)\
.filter(ProtocolVersion.protocol_id == protocol)
)
if plate:
samples_queries.append(
all_samples(db, run, archived)\
.filter(Sample.plate_id == plate)
)
if reagent:
run_version_query = all_samples(db, run, archived)\
.join(RunVersion, RunVersion.id == Sample.run_version_id)
samples_subquery = filter_by_reagent_label(run_version_query, reagent)
samples_queries.append(samples_subquery)
if creator:
samples_queries.append(
all_samples(db, run, archived)\
.filter(Sample.created_by == creator)
)
# Add a basic non-deleted items query if no filters were specified.
if len(samples_queries) == 0:
samples_queries.append(all_samples(db, run, archived))
# Only return the intersection of all queries.
samples_query = reduce(lambda a, b: a.intersect(b), samples_queries)
return paginatify(
items_label='samples',
items=[
sample for sample in samples_query.distinct().order_by(
Sample.sample_id.asc())
],
item_to_dict=item_to_dict,
page=page,
per_page=per_page,
)
def graphql_crud_get_samples(
enforcer: casbin.Enforcer,
current_user: Auth0CurrentUserPatched,
info: ResolveInfo,
# Search parameters
protocol: Optional[int] = None,
run: Optional[int] = None,
plate: Optional[str] = None,
reagent: Optional[str] = None,
sample: Optional[str] = None,
creator: Optional[str] = None,
archived: Optional[bool] = None,
# Paging parameters
page: Optional[int] = None,
per_page: Optional[int] = None,
):
# Calculate which top level fields to remove.
top_level_ignore = {
'sample_id', 'plate_id', 'run_version_id', 'protocol_version_id',
'created_by', 'created_on', 'updated_by', 'updated_on', 'run_id',
'protocol_id'
}
# Flatten `info` parameter into jsonb_query_path statements.
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) > 3 and result_parts[3] not in top_level_ignore:
top_level.add(result_parts[3])
jsonb_fields = [
'sample_id',
'sampleID',
'plate_id',
'plateID',
'run_version_id',
'protocol_version_id',
'created_by',
'created_on',
'updated_by',
'updated_on',
'run_id',
'runID',
'protocol_id',
'protocolID',
]
select_args = [
Sample.sample_id.label('sample_id'),
Sample.sample_id.label('sampleID'),
Sample.plate_id.label('plate_id'),
Sample.plate_id.label('plateID'),
Sample.run_version_id.label('run_version_id'),
Sample.protocol_version_id.label('protocol_version_id'),
Sample.created_by.label('created_by'),
Sample.created_on.label('created_on'),
SampleVersion.updated_by.label('updated_by'),
SampleVersion.updated_on.label('updated_on'),
RunVersion.run_id.label('run_id'),
RunVersion.run_id.label('runID'),
ProtocolVersion.protocol_id.label('protocol_id'),
ProtocolVersion.protocol_id.label('protocolID'),
]
for field in top_level:
jsonb_fields.append(field)
select_args.append(SampleVersion.data[field].label(field))
db = get_session(info)
# Join with additional tables as necessary for search params.
from_tables = OrderedDict()
filters = []
if protocol:
filters.append(ProtocolVersion.protocol_id == protocol)
if run:
filters.append(RunVersion.run_id == run)
if plate:
filters.append(Sample.plate_id.like(f"%{plate}%"))
if reagent:
filters.append(filter_by_reagent_label_filter(reagent))
if sample:
filters.append(Sample.sample_id.like(f"%{sample}%"))
if creator:
filters.append(Sample.created_by == creator)
if archived is None or archived == False:
filters.append(Sample.is_deleted == False)
query = db.query(*select_args)\
.select_from(Sample)\
.join(SampleVersion, SampleVersion.id == Sample.version_id)\
.join(RunVersion, RunVersion.id == Sample.run_version_id)\
.join(ProtocolVersion, ProtocolVersion.id == Sample.protocol_version_id)
for join_cls, join_filter in from_tables.items():
query = query.join(join_cls, join_filter)
# Apply search filters.
for search_filter in filters:
query = query.filter(search_filter)
# Get results
query = query.distinct().order_by(Sample.created_on.desc())
rows = [
sample for sample in query
if check_access(enforcer,
user=current_user.username,
path=f"/run/{str(sample.run_id)}",
method="GET")
]
return paginatify(
items_label='samples',
items=rows,
item_to_dict=lambda sample: SampleResult.parse_obj(
add_sample_id(sample._asdict())),
page=page,
per_page=per_page,
)