From d18bd91b1b9bfbf508ed41e2d91422c4388eecf7 Mon Sep 17 00:00:00 2001 From: Alejandro Date: Thu, 5 Jun 2025 12:07:52 +0200 Subject: [PATCH 1/3] Fix data reload when json_date is empty --- dashboard/utils/met_sequencing.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dashboard/utils/met_sequencing.py b/dashboard/utils/met_sequencing.py index 745bd938..4cfc0126 100644 --- a/dashboard/utils/met_sequencing.py +++ b/dashboard/utils/met_sequencing.py @@ -18,7 +18,7 @@ def get_pre_proc_data(graphic_name, out_format): json_data = dashboard.utils.generic_graphic_data.get_graphic_json_data( graphic_name ) - if json_data is None: + if json_data is None or json_data == {}: # Execute the pre-processed task to get the data if graphic_name == "library_kit_pcr_1": result = ( From 55d8e7c88ee2b428d3943b320becba3cf1196554 Mon Sep 17 00:00:00 2001 From: Alejandro Date: Thu, 5 Jun 2025 12:08:29 +0200 Subject: [PATCH 2/3] Fix sequenced base pairs vs PCR Ct values data generation --- dashboard/utils/generic_process_data.py | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/dashboard/utils/generic_process_data.py b/dashboard/utils/generic_process_data.py index 27024dee..45a557a7 100644 --- a/dashboard/utils/generic_process_data.py +++ b/dashboard/utils/generic_process_data.py @@ -395,21 +395,24 @@ def pre_proc_based_pairs_sequenced(): pcr_ct_1_values = core.utils.rest_api.get_sample_parameter_data( {"sample_project_name": "Relecov", "parameter": "diagnostic_pcr_Ct_value_1"} ) - samps_db = core.models.Sample.objects.all().values_list("collecting_lab_sample_id") + samps_db = set(x[0] for x in core.models.Sample.objects.all().values_list("collecting_lab_sample_id")) if "ERROR" in pcr_ct_1_values: return pcr_ct_1_values for ct_value in pcr_ct_1_values: sample_name = ct_value["Sample name"] + if sample_name not in samps_db: continue - base_value = ( - core.models.BioinfoAnalysisValue.objects.filter( - bioinfo_analysis_fieldID__property_name__exact="number_of_reads_sequenced", - sample__collecting_lab_sample_id__exact=sample_name, - ) - .last() - .get_value() - ) + + base_value_qs = core.models.BioinfoAnalysisValue.objects.filter( + bioinfo_analysis_fieldID__property_name__exact="number_of_reads_sequenced", + sample__collecting_lab_sample_id__exact=sample_name, + ).last() + + if base_value_qs is None: + continue + + base_value = base_value_qs.get_value() try: float_base_value = float(ct_value["diagnostic_pcr_Ct_value_1"]) base_value_int = int(base_value) @@ -425,7 +428,6 @@ def pre_proc_based_pairs_sequenced(): "graphic_data": based_pairs, } ) - return {"SUCCESS": "Success"} From 7d9e4aa4ce293fe3506e47c48a7385feea20a519 Mon Sep 17 00:00:00 2001 From: Alejandro Date: Thu, 5 Jun 2025 12:15:08 +0200 Subject: [PATCH 3/3] Fix linting --- dashboard/utils/generic_process_data.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/dashboard/utils/generic_process_data.py b/dashboard/utils/generic_process_data.py index 45a557a7..bb01e2f1 100644 --- a/dashboard/utils/generic_process_data.py +++ b/dashboard/utils/generic_process_data.py @@ -395,7 +395,12 @@ def pre_proc_based_pairs_sequenced(): pcr_ct_1_values = core.utils.rest_api.get_sample_parameter_data( {"sample_project_name": "Relecov", "parameter": "diagnostic_pcr_Ct_value_1"} ) - samps_db = set(x[0] for x in core.models.Sample.objects.all().values_list("collecting_lab_sample_id")) + samps_db = set( + x[0] + for x in core.models.Sample.objects.all().values_list( + "collecting_lab_sample_id" + ) + ) if "ERROR" in pcr_ct_1_values: return pcr_ct_1_values for ct_value in pcr_ct_1_values: