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onconova.research.controllers.analysis

CohortAnalysisController

Bases: ControllerBase

get_cohort_line_progression_free_survival_by_categories(cohortId, therapyLine, categorization)

Source code in onconova/research/controllers/analysis.py 
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@route.get(
    path="/{cohortId}/analysis/{therapyLine}/progression-free-survivals/categories",
    response={
        200: CategorizedSurvivals,
        404: None,
        422: None,
        **COMMON_HTTP_ERRORS,
    },
    permissions=[perms.CanViewCohorts],
    operation_id="getCohortLineProgressionFreeSurvivalsByCategories",
)
def get_cohort_line_progression_free_survival_by_categories(
    self,
    cohortId: str,
    therapyLine: str,
    categorization: Literal["therapies"] | Literal["drugs"],
):
    cohort = get_nonempty_cohort_or_error(cohortId)
    return CategorizedSurvivals.calculate(
        cohort=cohort,
        therapyLine=therapyLine,
        categorization=categorization,
    ).add_metadata(cohort)

get_cohort_line_progression_free_survival_curve(cohortId, therapyLine, confidence=0.95)

Source code in onconova/research/controllers/analysis.py 
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@route.get(
    path="/{cohortId}/analysis/{therapyLine}/progression-free-survival/kaplan-meier",
    response={200: KaplanMeierCurve, 404: None, 422: None, **COMMON_HTTP_ERRORS},
    permissions=[perms.CanViewCohorts],
    operation_id="getCohortLineProgressionFreeSurvivalCurve",
)
def get_cohort_line_progression_free_survival_curve(
    self, cohortId: str, therapyLine: str, confidence: float = 0.95
):
    cohort = get_nonempty_cohort_or_error(cohortId)
    therapy_line_survivals = (
        cohort.valid_cases.annotate(
            progression_free_survival=Subquery(
                TherapyLine.objects.filter(
                    case_id=OuterRef("id"), label=therapyLine
                )
                .annotate(pfs=F("progression_free_survival"))
                .values_list("pfs", flat=True)[:1]
            )
        )
        .filter(progression_free_survival__isnull=False)
        .values_list("progression_free_survival", flat=True)
    )
    if not therapy_line_survivals:
        raise EmptyCohortException
    return 200, KaplanMeierCurve.calculate(
        survivals=list(therapy_line_survivals),
        confidence_level=confidence,
    ).add_metadata(cohort)

get_cohort_line_property_distribution(cohortId, therapyLine, property)

Source code in onconova/research/controllers/analysis.py 
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@route.get(
    path="/{cohortId}/analysis/{therapyLine}/distribution",
    response={200: Distribution, 404: None, 422: None, **COMMON_HTTP_ERRORS},
    permissions=[perms.CanViewCohorts],
    operation_id="getCohortLinePropertyDistribution",
)
def get_cohort_line_property_distribution(
    self, cohortId: str, therapyLine: str, property: Literal["cases", "responses"]
):
    cohort = get_nonempty_cohort_or_error(cohortId)
    if property == "cases":
        return TherapyLineCasesDistribution.calculate(
            cohort, therapyLine
        ).add_metadata(cohort)
    elif property == "responses":
        return TherapyLineResponseDistribution.calculate(
            cohort, therapyLine
        ).add_metadata(cohort)

get_cohort_oncoplot_dataset(cohortId)

Source code in onconova/research/controllers/analysis.py 
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@route.get(
    path="/{cohortId}/analysis/oncoplot",
    response={200: OncoplotDataset, 404: None, 422: None, **COMMON_HTTP_ERRORS},
    permissions=[perms.CanViewCohorts],
    operation_id="getCohortOncoplot",
)
def get_cohort_oncoplot_dataset(self, cohortId: str):
    cohort = get_nonempty_cohort_or_error(cohortId)
    return OncoplotDataset.calculate(cohort.valid_cases.all()).add_metadata(cohort)

get_cohort_overall_survival_curve(cohortId, confidence=0.95)

Source code in onconova/research/controllers/analysis.py 
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@route.get(
    path="/{cohortId}/analysis/overall-survical/kaplan-meier",
    response={200: KaplanMeierCurve, 404: None, 422: None, **COMMON_HTTP_ERRORS},
    permissions=[perms.CanViewCohorts],
    operation_id="getCohortOverallSurvivalCurve",
)
def get_cohort_overall_survival_curve(
    self, cohortId: str, confidence: float = 0.95
):
    cohort = get_nonempty_cohort_or_error(cohortId)
    return KaplanMeierCurve.calculate(
        survivals=list(
            cohort.valid_cases.annotate(overall_survival=F("overall_survival"))
            .filter(overall_survival__isnull=False)
            .values_list("overall_survival", flat=True)
        ),
        confidence_level=confidence,
    ).add_metadata(cohort)

get_cohort_property_distribution(cohortId, property)

Source code in onconova/research/controllers/analysis.py 
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@route.get(
    path="/{cohortId}/analysis/distribution",
    response={200: Distribution, 404: None, 422: None, **COMMON_HTTP_ERRORS},
    permissions=[perms.CanViewCohorts],
    operation_id="getCohortPropertyDistribution",
)
def get_cohort_property_distribution(
    self,
    cohortId: str,
    property: Literal[
        "gender", "age", "ageAtDiagnosis", "neoplasticSites", "vitalStatus"
    ],
):
    cohort = get_nonempty_cohort_or_error(cohortId)
    return Distribution.calculate(cohort, property).add_metadata(cohort)

get_nonempty_cohort_or_error(cohortId)

Source code in onconova/research/controllers/analysis.py 
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def get_nonempty_cohort_or_error(cohortId: str) -> Cohort:
    cohort = get_object_or_404(Cohort, id=cohortId)
    if not cohort.valid_cases.exists():
        raise EmptyCohortException
    return cohort
runner