7102454002

Committed 05 Dec 2023 02:52PM UTC coverage: 0.0%. Remained the same

Build # 7102454002

Build Type

push

github

Committed by

web-flow

Commit Message

Update to pydantic v2 (#47) (patch)

Added
Move the models to pydantic v2

add Codeowners for automatic reviewer tagging

Run Details

0 of 89 new or added lines in 5 files covered. (0.0%)

28 existing lines in 5 files now uncovered.

0 of 699 relevant lines covered (0.0%)

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/arnold/crud/read/plot/trend_step_fields.py

from typing import Optional

from arnold.adapter import ArnoldAdapter
from arnold.crud.read.plot.format_plot_data import format_grouped_plot_data, format_plot_data


def trend_step_fields(
    adapter: ArnoldAdapter,
    year: int,
    workflow: str,
    step_type: str,
    field: str,
    group: Optional[str],
) -> list:
    lookup = {
        "$lookup": {
            "from": "sample",
            "localField": "sample_id",
            "foreignField": "_id",
            "as": "sample",
        }
    }
    unwind = {"$unwind": {"path": "$sample"}}
    match = {
        "$match": {
            "date_run": {"$exists": "True"},
            field: {"$exists": "True"},
            "workflow": workflow,
            "step_type": step_type,
        }
    }
    project = {
        "$project": {
            "month": {"$month": "$date_run"},
            "year": {"$year": "$date_run"},
            field: 1,
        }
    }
    match_year = {"$match": {"year": year}}
    field_replaced_dot = field.split(".")[1]
    group_by = {
        "$group": {
            "_id": {"month": "$month"},
            field_replaced_dot: {"$push": f"${field}"},
        }
    }
    add_average = {
        "$addFields": {f"average_{field_replaced_dot}": {"$avg": f"${field_replaced_dot}"}}
    }

    if group:
        match["$match"][f"sample.{group}"] = {"$exists": "True"}
        project["$project"][group] = f"$sample.{group}"
        group_by["$group"]["_id"][group] = f"${group}"

    pipe = [lookup, unwind, match, project, match_year, group_by, add_average]

    data = list(adapter.step_collection.aggregate(pipe))
    return (
        format_grouped_plot_data(
            plot_data=data, group_field=group, trend_field=f"average_{field_replaced_dot}"
        )
        if group
        else format_plot_data(plot_data=data, trend_field=f"average_{field_replaced_dot}")
    )

1	from typing import Optional	×
2
3	from arnold.adapter import ArnoldAdapter	×
4	from arnold.crud.read.plot.format_plot_data import format_grouped_plot_data, format_plot_data	×
5
6
7	def trend_step_fields(	×
8	adapter: ArnoldAdapter,
9	year: int,
10	workflow: str,
11	step_type: str,
12	field: str,
13	group: Optional[str],
14	) -> list:
15	lookup = {	×
16	"$lookup": {
17	"from": "sample",
18	"localField": "sample_id",
19	"foreignField": "_id",
20	"as": "sample",
21	}
22	}
23	unwind = {"$unwind": {"path": "$sample"}}	×
UNCOV 24	match = {	×
25	"$match": {
26	"date_run": {"$exists": "True"},
27	field: {"$exists": "True"},
28	"workflow": workflow,
29	"step_type": step_type,
30	}
31	}
UNCOV 32	project = {	×
33	"$project": {
34	"month": {"$month": "$date_run"},
35	"year": {"$year": "$date_run"},
36	field: 1,
37	}
38	}
39	match_year = {"$match": {"year": year}}	×
40	field_replaced_dot = field.split(".")[1]	×
UNCOV 41	group_by = {	×
42	"$group": {
43	"_id": {"month": "$month"},
44	field_replaced_dot: {"$push": f"${field}"},
45	}
46	}
UNCOV 47	add_average = {	×
48	"$addFields": {f"average_{field_replaced_dot}": {"$avg": f"${field_replaced_dot}"}}
49	}
50
51	if group:	×
52	match["$match"][f"sample.{group}"] = {"$exists": "True"}	×
53	project["$project"][group] = f"$sample.{group}"	×
UNCOV 54	group_by["$group"]["_id"][group] = f"${group}"	×
55
UNCOV 56	pipe = [lookup, unwind, match, project, match_year, group_by, add_average]	×
57
58	data = list(adapter.step_collection.aggregate(pipe))	×
UNCOV 59	return (	×
60	format_grouped_plot_data(
61	plot_data=data, group_field=group, trend_field=f"average_{field_replaced_dot}"
62	)
63	if group
64	else format_plot_data(plot_data=data, trend_field=f"average_{field_replaced_dot}")
65	)

Clinical-Genomics / arnold / 7102454002

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