From 7df7637c2b35129a3f51c71b8f46aaec3942b47d Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Fri, 18 Oct 2024 09:15:49 -0400 Subject: [PATCH] remove duplicative nested dichotomous fields / add BMDU / add tests (#68) * remove duplicative nested dichotomous fields * add nested dichotomous bmdu visualization * add a few more tests --- .../src/components/IndividualModel/Summary.js | 1 + .../Output/FrequentistResultTable.js | 9 +- .../NestedDichotomous/BootstrapResults.js | 2 +- tests/analysis/test_api.py | 6 + tests/analysis/test_models.py | 26 ++ tests/analysis/test_views.py | 2 +- tests/data/db.yaml | 223 +++++++++++++++++- 7 files changed, 255 insertions(+), 14 deletions(-) diff --git a/frontend/src/components/IndividualModel/Summary.js b/frontend/src/components/IndividualModel/Summary.js index 2e498af8..a934437c 100644 --- a/frontend/src/components/IndividualModel/Summary.js +++ b/frontend/src/components/IndividualModel/Summary.js @@ -17,6 +17,7 @@ class Summary extends Component { data = [ ["BMD", ff(model.results.bmd), model.results.bmd], ["BMDL", ff(model.results.bmdl), model.results.bmdl], + ["BMDU", ff(model.results.bmdu), model.results.bmdu], ["AIC", ff(model.results.aic), model.results.aic], [ diff --git a/frontend/src/components/Output/FrequentistResultTable.js b/frontend/src/components/Output/FrequentistResultTable.js index 947e44b3..dce5cb52 100644 --- a/frontend/src/components/Output/FrequentistResultTable.js +++ b/frontend/src/components/Output/FrequentistResultTable.js @@ -83,7 +83,9 @@ const getModelBinLabel = function(output, index) { }, getColWidths = function(store) { if (store.isNestedDichotomous) { - return store.recommendationEnabled ? [20, 12, 12, 12, 12, 32] : [20, 20, 20, 20, 20]; + return store.recommendationEnabled + ? [20, 11, 11, 11, 11, 11, 25] + : [20, 16, 16, 16, 16, 16]; } else { return store.recommendationEnabled ? [12, 8, 8, 8, 8, 8, 10, 10, 28] @@ -248,6 +250,9 @@ class FrequentistRow extends Component { + + + {ff(results.combined_pvalue)} @@ -341,7 +346,7 @@ class FrequentistResultTable extends Component { Model BMDL BMD - {isNestedDichotomous ? null : BMDU} + BMDU P-Value diff --git a/frontend/src/components/Output/NestedDichotomous/BootstrapResults.js b/frontend/src/components/Output/NestedDichotomous/BootstrapResults.js index f38c7633..3cae34f8 100644 --- a/frontend/src/components/Output/NestedDichotomous/BootstrapResults.js +++ b/frontend/src/components/Output/NestedDichotomous/BootstrapResults.js @@ -13,7 +13,7 @@ class BootstrapResult extends Component { ["# Iterations", settings.bootstrap_iterations], ["Bootstrap Seed", ff(settings.bootstrap_seed)], ["Log-likelihood", ff(results.ll)], - ["Observed Chi²", ff(results.obs_chi_sq)], + ["Observed Chi²", ff(results.chi_squared)], [ Combined P-Value diff --git a/tests/analysis/test_api.py b/tests/analysis/test_api.py index 507c673d..34a8e140 100644 --- a/tests/analysis/test_api.py +++ b/tests/analysis/test_api.py @@ -75,6 +75,12 @@ def test_auth(self, complete_continuous): response = client.patch(write_url, payload, format="json") assert response.status_code == 200 + def test_default_input(self): + client = APIClient() + url = reverse("api:analysis-default") + response = client.get(url, format="json") + assert response.json()["dataset_type"] == "C" + def test_patch_auth(self): client = APIClient() analysis = Analysis.objects.create() diff --git a/tests/analysis/test_models.py b/tests/analysis/test_models.py index 445b907e..c33f556c 100644 --- a/tests/analysis/test_models.py +++ b/tests/analysis/test_models.py @@ -13,6 +13,32 @@ def write_excel(data: dict, path: Path): df.to_excel(writer, sheet_name=name, index=False) +@pytest.mark.django_db() +class TestAnalysis: + def test_maybe_hanging(self): + qs = Analysis.maybe_hanging(queryset=Analysis.objects.all()) + assert qs.count() == 1 + assert str(qs[0].id) == "bb5ada91-8f32-4a24-aedf-dcecbe5044f6" + + def test_model_class_label(self): + a = Analysis.objects.get(id="cc3ca355-a57a-4fba-9dc3-99657562df68") + assert a.model_class_label == "Continuous" + + def test_timestamp(self): + a = Analysis.objects.get(id="cc3ca355-a57a-4fba-9dc3-99657562df68") + assert str(a.timestamp) == "2021-12-15 18:42:49.109397+00:00" + + def test_delete_old_analyses(self): + n_before = Analysis.objects.count() + assert Analysis.objects.filter(id="1b4360dd-27ae-46f1-ad7e-45796d44be8c").exists() + + Analysis.delete_old_analyses() + + n_after = Analysis.objects.count() + assert n_before - n_after == 1 + assert not Analysis.objects.filter(id="1b4360dd-27ae-46f1-ad7e-45796d44be8c").exists() + + @pytest.mark.django_db() class TestExecution: def test_continuous(self, complete_continuous, data_path, rewrite_data_files): diff --git a/tests/analysis/test_views.py b/tests/analysis/test_views.py index ae3f624c..72f79a07 100644 --- a/tests/analysis/test_views.py +++ b/tests/analysis/test_views.py @@ -68,7 +68,7 @@ def test_context(self): "deleteUrl": f"http://testserver/analysis/{pk}/{pw}/delete/", "executeUrl": f"/api/v1/analysis/{pk}/execute/", "executeResetUrl": f"/api/v1/analysis/{pk}/execute-reset/", - "deleteDateStr": "June 14, 2022", + "deleteDateStr": "December 31, 2045", "collections": [{"id": 1, "name": "Label #1"}], }, } diff --git a/tests/data/db.yaml b/tests/data/db.yaml index dacf9f6a..c1191ef2 100644 --- a/tests/data/db.yaml +++ b/tests/data/db.yaml @@ -1763,12 +1763,12 @@ created: 2021-12-15 18:42:28.857142+00:00 started: 2021-12-15 18:42:48.876358+00:00 ended: 2021-12-15 18:42:49.109397+00:00 - deletion_date: 2022-06-14 18:42:49.109397+00:00 + deletion_date: 2045-12-31 23:23:23.232323+00:00 - model: analysis.analysis pk: ded15870-8986-4d5b-b924-ef9036b2e17e fields: created: 2024-05-14 19:17:13.442351+00:00 - deletion_date: 2024-11-10 19:18:13.839491+00:00 + deletion_date: 2045-12-31 23:23:23.232323+00:00 ended: 2024-05-14 19:18:13.839482+00:00 errors: [] inputs: @@ -10294,7 +10294,6 @@ bmd: 13.190689586371025 cov: [] dof: 36.0 - max: 0.0 bmdl: 9.824944175804669 bmdu: -9999.0 litter: @@ -10855,7 +10854,6 @@ - 0.995 - 0.9973333333333333 fixed_lsc: 11.692307692307692 - obs_chi_sq: 0.0 parameters: - 0.144138836294475 - -4.7767358236974005 @@ -10956,7 +10954,6 @@ bmd: 13.190689586371025 cov: [] dof: 36.0 - max: 0.0 bmdl: 9.824944175804765 bmdu: -9999.0 litter: @@ -11517,7 +11514,6 @@ - 0.995 - 0.9973333333333333 fixed_lsc: 11.692307692307692 - obs_chi_sq: 0.0 parameters: - 0.144138836294475 - -4.7767358236974005 @@ -11618,7 +11614,6 @@ bmd: 12.951178803705256 cov: [] dof: 35.0 - max: 0.0 bmdl: 9.646361865829302 bmdu: -9999.0 litter: @@ -12179,7 +12174,6 @@ - 0.994 - 0.996 fixed_lsc: 11.692307692307692 - obs_chi_sq: 0.0 parameters: - 0.08472920680181548 - -4.1096589164749755 @@ -12280,7 +12274,6 @@ bmd: 12.951182313338903 cov: [] dof: 35.0 - max: 0.0 bmdl: 9.646362099673082 bmdu: -9999.0 litter: @@ -12841,7 +12834,6 @@ - 0.999 - 0.9996666666666667 fixed_lsc: 11.692307692307692 - obs_chi_sq: 0.0 parameters: - 0.08472962434038567 - -4.1096619680341115 @@ -14548,6 +14540,217 @@ deletion_date: null starred: false collections: [1] +- model: analysis.analysis + pk: 1b4360dd-27ae-46f1-ad7e-45796d44be8c + fields: + password: 8t47uf4epmuf + inputs: + analysis_name: should be deleted (expired) + dataset_options: + - dataset_id: 0 + degree: 3 + enabled: true + dataset_type: D + datasets: + - doses: + - 0 + - 50 + - 100 + - 200 + - 400 + dtype: D + incidences: + - 0 + - 0 + - 1 + - 4 + - 11 + metadata: + dose_name: Dose + dose_units: '' + id: 0 + name: 'Dataset #1' + response_name: Incidence + response_units: '' + ns: + - 20 + - 20 + - 20 + - 20 + - 20 + models: + bayesian: + - model: Multistage + prior_weight: 1 + frequentist_restricted: + - LogLogistic + frequentist_unrestricted: + - LogProbit + options: + - bmr_type: 1 + bmr_value: 0.1 + confidence_level: 0.95 + recommender: + enabled: true + recommend_questionable: false + recommend_viable: true + rules: + - enabled_continuous: true + enabled_dichotomous: true + enabled_nested: true + failure_bin: 1 + rule_class: gof + threshold: 0.1 + - enabled_continuous: true + enabled_dichotomous: true + enabled_nested: true + failure_bin: 1 + rule_class: dof_zero + threshold: null + - enabled_continuous: true + enabled_dichotomous: true + enabled_nested: true + failure_bin: 0 + rule_class: high_bmd + threshold: 1 + - enabled_continuous: false + enabled_dichotomous: false + enabled_nested: false + failure_bin: 1 + rule_class: warnings + threshold: null + - enabled_continuous: true + enabled_dichotomous: true + enabled_nested: true + failure_bin: 0 + rule_class: high_bmdl + threshold: 1 + - enabled_continuous: true + enabled_dichotomous: true + enabled_nested: true + failure_bin: 1 + rule_class: roi_large + threshold: 2 + - enabled_continuous: false + enabled_dichotomous: false + enabled_nested: false + failure_bin: 1 + rule_class: gof_cancer + threshold: 0.05 + - enabled_continuous: true + enabled_dichotomous: true + enabled_nested: true + failure_bin: 2 + rule_class: aic_missing + threshold: null + - enabled_continuous: true + enabled_dichotomous: true + enabled_nested: true + failure_bin: 2 + rule_class: bmd_missing + threshold: null + - enabled_continuous: true + enabled_dichotomous: true + enabled_nested: true + failure_bin: 2 + rule_class: roi_missing + threshold: null + - enabled_continuous: true + enabled_dichotomous: true + enabled_nested: true + failure_bin: 2 + rule_class: bmdl_missing + threshold: null + - enabled_continuous: false + enabled_dichotomous: false + enabled_nested: false + failure_bin: 1 + rule_class: bmdu_missing + threshold: null + - enabled_continuous: true + enabled_dichotomous: true + enabled_nested: true + failure_bin: 1 + rule_class: low_bmd_fail + threshold: 10 + - enabled_continuous: true + enabled_dichotomous: true + enabled_nested: true + failure_bin: 0 + rule_class: low_bmd_warn + threshold: 3 + - enabled_continuous: true + enabled_dichotomous: false + enabled_nested: false + failure_bin: 1 + rule_class: variance_fit + threshold: 0.05 + - enabled_continuous: true + enabled_dichotomous: true + enabled_nested: true + failure_bin: 1 + rule_class: low_bmdl_fail + threshold: 10 + - enabled_continuous: true + enabled_dichotomous: true + enabled_nested: true + failure_bin: 0 + rule_class: low_bmdl_warn + threshold: 3 + - enabled_continuous: false + enabled_dichotomous: false + enabled_nested: false + failure_bin: 1 + rule_class: variance_type + threshold: 0.05 + - enabled_continuous: true + enabled_dichotomous: false + enabled_nested: false + failure_bin: 0 + rule_class: control_stdev_fit + threshold: 1.5 + - enabled_continuous: true + enabled_dichotomous: true + enabled_nested: true + failure_bin: 1 + rule_class: bmd_bmdl_ratio_fail + threshold: 20 + - enabled_continuous: true + enabled_dichotomous: true + enabled_nested: true + failure_bin: 0 + rule_class: bmd_bmdl_ratio_warn + threshold: 3 + - enabled_continuous: true + enabled_dichotomous: true + enabled_nested: true + failure_bin: 0 + rule_class: control_residual_high + threshold: 2 + sufficiently_close_bmdl: 3 + outputs: {} + errors: [] + created: 2024-08-22 01:23:45.123456+00:00 + last_updated: 2024-08-22 01:23:45.123456+00:00 + started: 2024-08-22 01:23:45.123456+00:00 + ended: 2024-08-22 01:23:45.123456+00:00 + deletion_date: 2024-08-22 01:23:45.123456+00:00 + starred: false + collections: [] +- model: analysis.analysis + pk: bb5ada91-8f32-4a24-aedf-dcecbe5044f6 + fields: + password: u1c1ekxgu1uq + inputs: {} + outputs: {} + errors: [] + created: 2024-08-22 01:23:45.123456+00:00 + last_updated: 2024-08-22 01:23:45.123456+00:00 + started: 2024-08-22 01:23:45.123456+00:00 + ended: null + deletion_date: null + starred: false + collections: [] - model: analysis.collection pk: 1 fields: