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Include pcrreplicate_batch field in Control Results Report
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@aaronstephenson
aaronstephenson committed Jun 7, 2019
1 parent 37bfe10 commit 9f0f431
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Showing 2 changed files with 20 additions and 10 deletions.
2 changes: 1 addition & 1 deletion code.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
"name": "lide",
"organization": "U.S. Geological Survey",
"description": "Web services for LILI (LIDE (Laboratory for Infectious Disease and the Environment) Information Management System)",
"version": "v0.99.3",
"version": "v0.99.4",
"status": "Release Candidate",

"permissions": {
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28 changes: 19 additions & 9 deletions lideservices/views.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1717,6 +1717,7 @@ def post(self, request):
"analysis_batch": ext_neg['extraction_batch__analysis_batch'],
"extraction_number": ext_neg['extraction_batch__extraction_number'],
# "replicate_number": ext_neg['replicate_number'],
"pcrreplicate_batch": ext_neg['pcrreplicate_batch'],
ext_neg['target__name']: ext_neg['result']
}
ext_neg_results[ext_neg['extraction_batch__id']] = data
Expand All @@ -1731,7 +1732,8 @@ def post(self, request):
ext_neg_result_ids = OrderedDict({
"analysis_batch": ext_neg_result.pop('analysis_batch'),
"analysis_batch_string": ext_neg_result.pop('analysis_batch_string'),
"extraction_number": ext_neg_result.pop('extraction_number')
"extraction_number": ext_neg_result.pop('extraction_number'),
"pcrreplicate_batch": ext_neg_result.pop('pcrreplicate_batch')
})
ext_neg_result_targets = OrderedDict(sorted(ext_neg_result.items()))
ext_neg_results_list_ordered.append(OrderedDict(**ext_neg_result_ids, **ext_neg_result_targets))
Expand Down Expand Up @@ -1763,6 +1765,7 @@ def post(self, request):
"analysis_batch": pcr_neg['extraction_batch__analysis_batch'],
"extraction_number": pcr_neg['extraction_batch__extraction_number'],
# "replicate_number": pcr_neg['replicate_number'],
"pcrreplicate_batch": pcr_neg['pcrreplicate_batch'],
pcr_neg['target__name']: pcr_neg['result']
}
pcr_neg_results[pcr_neg['extraction_batch__id']] = data
Expand All @@ -1777,7 +1780,8 @@ def post(self, request):
pcr_neg_result_ids = OrderedDict({
"analysis_batch": pcr_neg_result.pop('analysis_batch'),
"analysis_batch_string": pcr_neg_result.pop('analysis_batch_string'),
"extraction_number": pcr_neg_result.pop('extraction_number')
"extraction_number": pcr_neg_result.pop('extraction_number'),
"pcrreplicate_batch": pcr_neg_result.pop('pcrreplicate_batch')
})
pcr_neg_result_targets = OrderedDict(sorted(pcr_neg_result.items()))
pcr_neg_results_list_ordered.append(OrderedDict(**pcr_neg_result_ids, **pcr_neg_result_targets))
Expand Down Expand Up @@ -1808,7 +1812,8 @@ def post(self, request):
"analysis_batch_string": pcr_pos['extraction_batch__analysis_batch__name'],
"analysis_batch": pcr_pos['extraction_batch__analysis_batch'],
"extraction_number": pcr_pos['extraction_batch__extraction_number'],
# "replicate_number": pcr_neg['replicate_number'],
# "replicate_number": pcr_pos['replicate_number'],
"pcrreplicate_batch": pcr_pos['pcrreplicate_batch'],
pcr_pos['target__name']: pcr_pos['result']
}
pcr_pos_results[pcr_pos['extraction_batch__id']] = data
Expand All @@ -1823,16 +1828,18 @@ def post(self, request):
pcr_pos_result_ids = OrderedDict({
"analysis_batch": pcr_pos_result.pop('analysis_batch'),
"analysis_batch_string": pcr_pos_result.pop('analysis_batch_string'),
"extraction_number": pcr_pos_result.pop('extraction_number')
"extraction_number": pcr_pos_result.pop('extraction_number'),
"pcrreplicate_batch": pcr_pos_result.pop('pcrreplicate_batch')
})
pcr_pos_result_targets = OrderedDict(sorted(pcr_pos_result.items()))
pcr_pos_results_list_ordered.append(OrderedDict(**pcr_pos_result_ids, **pcr_pos_result_targets))

# ExtractionBatch-level controls
# Ext Pos
ext_poss = PCRReplicateBatch.objects.all().annotate(
ext_pos_rna_rt_cq_value=Max('extraction_batch__reversetranscriptions__ext_pos_rna_rt_cq_value',
filter=Q(extraction_batch__reversetranscriptions__re_rt__isnull=True))
ext_poss = PCRReplicateBatch.objects.filter(
extraction_batch__reversetranscriptions__re_rt__isnull=True
).annotate(
ext_pos_rna_rt_cq_value=F('extraction_batch__reversetranscriptions__ext_pos_rna_rt_cq_value')
).annotate(
result=Case(
When(ext_pos_rna_rt_cq_value__gt=0, then=Value(pos)),
Expand All @@ -1843,6 +1850,7 @@ def post(self, request):
'extraction_batch__id', 'extraction_batch__analysis_batch', 'extraction_batch__analysis_batch__name',
'extraction_batch__extraction_number', 'replicate_number', 'target__name', 'pcrreplicate_batch', 'result'
).order_by('extraction_batch__analysis_batch', 'extraction_batch__id')
print(ext_poss.query)
if sample_ids:
ext_poss = ext_poss.filter(pcrreplicates__sample_extraction__sample__in=sample_ids)
if target_ids:
Expand All @@ -1859,7 +1867,8 @@ def post(self, request):
"analysis_batch_string": ext_pos['extraction_batch__analysis_batch__name'],
"analysis_batch": ext_pos['extraction_batch__analysis_batch'],
"extraction_number": ext_pos['extraction_batch__extraction_number'],
# "replicate_number": pcr_neg['replicate_number'],
"pcrreplicate_batch": ext_pos['pcrreplicate_batch'],
# "replicate_number": ext_pos['replicate_number'],
ext_pos['target__name']: ext_pos['result']
}
ext_pos_results[ext_pos['extraction_batch__id']] = data
Expand All @@ -1874,7 +1883,8 @@ def post(self, request):
ext_pos_result_ids = OrderedDict({
"analysis_batch": ext_pos_result.pop('analysis_batch'),
"analysis_batch_string": ext_pos_result.pop('analysis_batch_string'),
"extraction_number": ext_pos_result.pop('extraction_number')
"extraction_number": ext_pos_result.pop('extraction_number'),
"pcrreplicate_batch": ext_pos_result.pop('pcrreplicate_batch')
})
ext_pos_result_targets = OrderedDict(sorted(ext_pos_result.items()))
ext_pos_results_list_ordered.append(OrderedDict(**ext_pos_result_ids, **ext_pos_result_targets))
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