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Fix sample matching and data retrieval in dashboard graph for percentage of reads #298

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Merged
merged 3 commits into from
Jun 6, 2025
Merged

Fix sample matching and data retrieval in dashboard graph for percentage of reads #298

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d18bd91
Fix data reload when json_date is empty
Aberdur Jun 5, 2025
55d8e7c
Fix sequenced base pairs vs PCR Ct values data generation
Aberdur Jun 5, 2025
7d9e4aa
Fix linting
Aberdur Jun 5, 2025
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27 changes: 17 additions & 10 deletions dashboard/utils/generic_process_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -395,21 +395,29 @@ 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)
Expand All @@ -425,7 +433,6 @@ def pre_proc_based_pairs_sequenced():
"graphic_data": based_pairs,
}
)

return {"SUCCESS": "Success"}


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2 changes: 1 addition & 1 deletion dashboard/utils/met_sequencing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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 = (
Expand Down