Skip to content

Optimize stats-info aggregation queries #395

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
Aberdur merged 2 commits into from
Apr 16, 2026
Merged

Optimize stats-info aggregation queries #395

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
debb24d
Optimize stats-info aggregation queries
Aberdur Apr 16, 2026
e63c3b9
Fix linting
Aberdur Apr 16, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
118 changes: 56 additions & 62 deletions wetlab/api/utils/sample.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
from datetime import datetime
from collections import defaultdict

from django.db.models import Count
import core.models
import core.utils.samples
import core.core_config
Expand Down Expand Up @@ -520,62 +522,45 @@ def collect_statistics_information(data):

if len(query_params) > 2:
return {"ERROR": ""}
stats_data = {}
par1_values = (
core.models.SampleProjectsFieldsValue.objects.filter(
sample_project_field_id__sample_projects_id=s_project_obj,
sample_project_field_id__sample_project_field_name__iexact=query_params[
0
],
)
.values_list("sample_project_field_value", flat=True)
.distinct()
base_values = core.models.SampleProjectsFieldsValue.objects.filter(
sample_project_field_id__sample_projects_id=s_project_obj
)

if len(query_params) == 2:
for par1_val in par1_values:
stats_data[par1_val] = {}

samples = core.models.SampleProjectsFieldsValue.objects.filter(
sample_project_field_id__sample_projects_id=s_project_obj,
sample_project_field_id__sample_project_field_name__iexact=query_params[
0
],
sample_project_field_value__exact=par1_val,
).values_list("sample_id", flat=True)
par2_values = (
core.models.SampleProjectsFieldsValue.objects.filter(
sample_id__in=samples,
sample_project_field_id__sample_project_field_name__iexact=query_params[
1
],
par1_rows = base_values.filter(
sample_project_field_id__sample_project_field_name__iexact=query_params[
0
]
).values_list("sample_id", "sample_project_field_value")
par2_rows = base_values.filter(
sample_project_field_id__sample_project_field_name__iexact=query_params[
1
]
).values_list("sample_id", "sample_project_field_value")

par1_by_sample = defaultdict(list)
for sample_id, par1_val in par1_rows:
par1_by_sample[sample_id].append(par1_val)

stats_data = defaultdict(dict)
for sample_id, par2_val in par2_rows:
for par1_val in par1_by_sample.get(sample_id, []):
stats_data[par1_val][par2_val] = (
stats_data[par1_val].get(par2_val, 0) + 1
)
.values_list("sample_project_field_value", flat=True)
.distinct()
)
for par2_val in par2_values:
value = core.models.SampleProjectsFieldsValue.objects.filter(
sample_id__in=samples,
sample_project_field_id__sample_project_field_name=query_params[
1
],
sample_project_field_value__exact=par2_val,
).count()
if value > 0:
stats_data[par1_val][par2_val] = value
else:
for par1_val in par1_values:
stats_data[par1_val] = (
core.models.SampleProjectsFieldsValue.objects.filter(
sample_project_field_id__sample_projects_id=s_project_obj,
sample_project_field_id__sample_project_field_name__iexact=query_params[
0
],
sample_project_field_value=par1_val,
).count()
)
return dict(stats_data)

return stats_data
counts = (
base_values.filter(
sample_project_field_id__sample_project_field_name__iexact=query_params[
0
]
)
.values("sample_project_field_value")
.annotate(count=Count("id"))
)
return {
item["sample_project_field_value"]: item["count"] for item in counts
}
else: # Collect info stats for all fields
# Collect the fields utilization for sample projects
stats_data = {
Expand All @@ -591,21 +576,30 @@ def collect_statistics_information(data):
s_project_field_objs = core.models.SampleProjectsFields.objects.filter(
sample_projects_id=s_project_obj
)
field_ids = list(s_project_field_objs.values_list("id", flat=True))
total_counts = dict(
core.models.SampleProjectsFieldsValue.objects.filter(
sample_project_field_id__in=field_ids
)
.values_list("sample_project_field_id")
.annotate(total=Count("id"))
)
not_none_counts = dict(
core.models.SampleProjectsFieldsValue.objects.filter(
sample_project_field_id__in=field_ids
)
.exclude(sample_project_field_value__in=["None", ""])
.values_list("sample_project_field_id")
.annotate(total=Count("id"))
)
for s_project_field_obj in s_project_field_objs:
f_name = s_project_field_obj.get_field_name()
if not core.models.SampleProjectsFieldsValue.objects.filter(
sample_project_field_id=s_project_field_obj
).exists():
total_count = total_counts.get(s_project_field_obj.pk, 0)
if total_count == 0:
stats_data["never_used"].append(f_name)
stats_data["fields_value"][f_name] = 0
continue
count_not_none = (
core.models.SampleProjectsFieldsValue.objects.filter(
sample_project_field_id=s_project_field_obj
)
.exclude(sample_project_field_value__in=["None", ""])
.count()
)
count_not_none = not_none_counts.get(s_project_field_obj.pk, 0)
stats_data["fields_value"][f_name] = count_not_none
if count_not_none == 0:
stats_data["always_none"].append(f_name)
Expand Down
Loading