onconova.oncology.controllers.genomic_signature

AnyPayloadSchemas module-attribute

AnyResponseSchemas module-attribute

PAYLOAD_SCHEMAS module-attribute

RESPONSE_SCHEMAS module-attribute

GenomicSignatureController

Bases: ControllerBase

create_genomic_signature(payload)

Source code in onconova/oncology/controllers/genomic_signature.py

@route.post(
    path="",
    response={201: ModifiedResourceSchema, **COMMON_HTTP_ERRORS},
    permissions=[perms.CanManageCases],
    operation_id="createGenomicSignature",
)
def create_genomic_signature(self, payload: AnyPayloadSchemas):  # type: ignore
    return 201, payload.model_dump_django()

delete_genomic_signature(genomicSignatureId)

Source code in onconova/oncology/controllers/genomic_signature.py

@route.delete(
    path="/{genomicSignatureId}",
    response={204: None, 404: None, **COMMON_HTTP_ERRORS},
    permissions=[perms.CanManageCases],
    operation_id="deleteGenomicSignatureById",
)
def delete_genomic_signature(self, genomicSignatureId: str):
    instance = get_object_or_404(orm.GenomicSignature, id=genomicSignatureId)
    instance.delete()
    return 204, None

get_all_genomic_signature_history_events(genomicSignatureId)

Source code in onconova/oncology/controllers/genomic_signature.py

@route.get(
    path="/{genomicSignatureId}/history/events",
    response={200: Paginated[HistoryEvent], 404: None, **COMMON_HTTP_ERRORS},
    permissions=[perms.CanViewCases],
    operation_id="getAllGenomicSignatureHistoryEvents",
)
@paginate()
@ordering()
def get_all_genomic_signature_history_events(self, genomicSignatureId: str):
    instance = get_object_or_404(orm.GenomicSignature, id=genomicSignatureId)
    return pghistory.models.Events.objects.tracks(instance).all()  # type: ignore

get_all_genomic_signatures_matching_the_query(query)

Source code in onconova/oncology/controllers/genomic_signature.py

@route.get(
    path="",
    response={
        200: Paginated[AnyResponseSchemas],
        **COMMON_HTTP_ERRORS,
    },
    exclude_none=True,
    permissions=[perms.CanViewCases],
    operation_id="getGenomicSignatures",
)
@paginate()
@ordering()
@anonymize()
def get_all_genomic_signatures_matching_the_query(self, query: Query[scm.GenomicSignatureFilters]):  # type: ignore
    queryset = orm.GenomicSignature.objects.all().order_by("-date")
    return [
        cast_to_model_schema(
            genomic_signature.get_discriminated_genomic_signature(),
            RESPONSE_SCHEMAS,
        )
        for genomic_signature in query.filter(queryset)
    ]

get_genomic_signature_by_id(genomicSignatureId)

Source code in onconova/oncology/controllers/genomic_signature.py

@route.get(
    path="/{genomicSignatureId}",
    response={200: AnyResponseSchemas, 404: None},
    exclude_none=True,
    permissions=[perms.CanViewCases],
    operation_id="getGenomicSignatureById",
)
@anonymize()
def get_genomic_signature_by_id(self, genomicSignatureId: str):
    instance = get_object_or_404(orm.GenomicSignature, id=genomicSignatureId)
    return cast_to_model_schema(
        instance.get_discriminated_genomic_signature(), RESPONSE_SCHEMAS
    )

get_genomic_signature_history_event_by_id(genomicSignatureId, eventId)

Source code in onconova/oncology/controllers/genomic_signature.py

@route.get(
    path="/{genomicSignatureId}/history/events/{eventId}",
    response={200: HistoryEvent, 404: None, **COMMON_HTTP_ERRORS},
    permissions=[perms.CanViewCases],
    operation_id="getGenomicSignatureHistoryEventById",
)
def get_genomic_signature_history_event_by_id(
    self, genomicSignatureId: str, eventId: str
):
    instance = get_object_or_404(orm.GenomicSignature, id=genomicSignatureId)
    event = instance.parent_events.filter(pgh_id=eventId).first()  # type: ignore
    if not event and hasattr(instance, "events"):
        event = instance.events.filter(pgh_id=eventId).first()
    if not event:
        return 404, None
    return get_object_or_404(
        pghistory.models.Events.objects.tracks(instance), pgh_id=eventId  # type: ignore
    )

revert_genomic_signature_to_history_event(genomicSignatureId, eventId)

Source code in onconova/oncology/controllers/genomic_signature.py

@route.put(
    path="/{genomicSignatureId}/history/events/{eventId}/reversion",
    response={201: ModifiedResourceSchema, 404: None, **COMMON_HTTP_ERRORS},
    permissions=[perms.CanManageCases],
    operation_id="revertGenomicSignatureToHistoryEvent",
)
def revert_genomic_signature_to_history_event(
    self, genomicSignatureId: str, eventId: str
):
    instance = get_object_or_404(orm.GenomicSignature, id=genomicSignatureId)
    instance = instance.get_discriminated_genomic_signature()
    try:
        return 201, revert_multitable_model(instance, eventId)
    except ObjectDoesNotExist:
        return 404, None

update_genomic_signature(genomicSignatureId, payload)

Source code in onconova/oncology/controllers/genomic_signature.py

@route.put(
    path="/{genomicSignatureId}",
    response={200: ModifiedResourceSchema, 404: None, **COMMON_HTTP_ERRORS},
    permissions=[perms.CanManageCases],
    operation_id="updateGenomicSignatureById",
)
def update_genomic_signature(self, genomicSignatureId: str, payload: AnyPayloadSchemas):  # type: ignore
    instance = get_object_or_404(
        orm.GenomicSignature, id=genomicSignatureId
    ).get_discriminated_genomic_signature()
    return payload.model_dump_django(instance=instance)

cast_to_model_schema(model_instance, schemas, payload=None)

Source code in onconova/oncology/controllers/genomic_signature.py

def cast_to_model_schema(model_instance, schemas, payload=None):
    return next(
        (
            schema.model_validate(payload or model_instance)
            for schema in schemas
            if (payload or model_instance).genomic_signature_type
            == schema.model_fields["category"].default
        )
    )

2025-10-172025-10-17runner