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%)

0.0 hits per line

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0.0

/arnold/api/api_v1/endpoints/plots.py

import datetime as dt
from typing import Optional, List, Literal
from pydantic import BaseModel

from arnold.adapter import ArnoldAdapter

from fastapi import APIRouter, Depends, status
from fastapi.responses import JSONResponse
import logging
from arnold.settings import get_arnold_adapter

LOG = logging.getLogger(__name__)

router = APIRouter()


class ReceivedPlotDatapointsModel(BaseModel):
    tag: Optional[str]
    priority: Optional[str]
    total: int


class ReceivedPlotModel(BaseModel):
    date: str
    datapoints: List[ReceivedPlotDatapointsModel]


@router.get("/received", response_model=List[ReceivedPlotModel], response_model_exclude_none=True)
def received(
    adapter: ArnoldAdapter = Depends(get_arnold_adapter),
    date_min: Optional[dt.date] = dt.date.min,
    date_max: Optional[dt.date] = dt.date.max,
):
    samples = adapter.sample_collection.aggregate(
        [
            {
                "$match": {
                    "delivery_date": {"$exists": 1},
                    "received_date": {
                        "$gte": dt.datetime.fromordinal(date_min.toordinal()),
                        "$lte": dt.datetime.fromordinal(date_max.toordinal()),
                    },
                }
            },
            {
                "$project": {
                    "received_date": 1,
                    "sample_id": 1,
                    "tag": {"$substr": ["$application", 0, 3]},
                    "received_year": {"$year": "$received_date"},
                    "received_month": {"$month": "$received_date"},
                }
            },
            {
                "$group": {
                    "_id": {"tag": "$tag", "year": "$received_year", "month": "$received_month"},
                    "total": {"$sum": 1},
                }
            },
            {
                "$project": {
                    "year": "$_id.year",
                    "month": "$_id.month",
                    "date": {
                        "$concat": [
                            {"$substr": ["$_id.year", 0, -1]},
                            "/",
                            {"$substr": ["$_id.month", 0, -1]},
                        ]
                    },
                    "tag": "$_id.tag",
                    "total": "$total",
                    "_id": 0,
                }
            },
            {
                "$group": {
                    "_id": {"date": "$date", "year": "$year", "month": "$month"},
                    "datapoints": {"$push": "$$ROOT"},
                }
            },
            {
                "$project": {
                    "date": "$_id.date",
                    "year": "$_id.year",
                    "month": "$_id.month",
                    "datapoints": "$datapoints",
                    "_id": 0,
                }
            },
            {"$unset": ["datapoints.date", "datapoints.year", "datapoints.month"]},
            {"$sort": {"year": -1, "month": -1}},
            {"$unset": ["year", "month"]},
        ]
    )
    return list(samples)


@router.get("/turnaround", response_model=List[ReceivedPlotModel], response_model_exclude_none=True)
def turnaround(
    adapter: ArnoldAdapter = Depends(get_arnold_adapter),
    date_min: Optional[dt.date] = dt.date.min,
    date_max: Optional[dt.date] = dt.date.max,
    group: Optional[Literal["priority", "tag"]] = "tag",
):
    samples = adapter.sample_collection.aggregate(
        [
            {
                "$match": {
                    "delivery_date": {"$exists": 1},
                    "received_date": {
                        "$gte": dt.datetime.fromordinal(date_min.toordinal()),
                        "$lte": dt.datetime.fromordinal(date_max.toordinal()),
                    },
                }
            },
            {
                "$project": {
                    "received_date": 1,
                    "delivery_date": 1,
                    "sample_id": 1,
                    "tag": {"$substr": ["$application", 0, 3]},
                    "received_year": {"$year": "$received_date"},
                    "received_month": {"$month": "$received_date"},
                    "priority": "$priority",
                    "turnaround_time": {
                        "$divide": [{"$subtract": ["$delivery_date", "$received_date"]}, 86400000]
                    },
                }
            },
            {"$match": {"turnaround_time": {"$gt": 0}}},
            {
                "$group": {
                    "_id": {
                        f"{group}": f"${group}",
                        "year": "$received_year",
                        "month": "$received_month",
                    },
                    "total": {"$avg": "$turnaround_time"},
                }
            },
            {
                "$project": {
                    "year": "$_id.year",
                    "month": "$_id.month",
                    "date": {
                        "$concat": [
                            {"$substr": ["$_id.year", 0, -1]},
                            "/",
                            {"$substr": ["$_id.month", 0, -1]},
                        ]
                    },
                    f"{group}": f"$_id.{group}",
                    "total": {"$round": ["$total", 0]},
                    "_id": 0,
                }
            },
            {
                "$group": {
                    "_id": {"date": "$date", "year": "$year", "month": "$month"},
                    "datapoints": {"$push": "$$ROOT"},
                }
            },
            {
                "$project": {
                    "date": "$_id.date",
                    "year": "$_id.year",
                    "month": "$_id.month",
                    "datapoints": "$datapoints",
                    "_id": 0,
                }
            },
            {"$unset": ["datapoints.date", "datapoints.year", "datapoints.month"]},
            {"$sort": {"year": -1, "month": -1}},
            {"$unset": ["year", "month"]},
        ]
    )
    return list(samples)

1	import datetime as dt	×
2	from typing import Optional, List, Literal	×
3	from pydantic import BaseModel	×
4
5	from arnold.adapter import ArnoldAdapter	×
6
7	from fastapi import APIRouter, Depends, status	×
8	from fastapi.responses import JSONResponse	×
9	import logging	×
10	from arnold.settings import get_arnold_adapter	×
11
12	LOG = logging.getLogger(__name__)	×
13
14	router = APIRouter()	×
15
16
17	class ReceivedPlotDatapointsModel(BaseModel):	×
18	tag: Optional[str]	×
19	priority: Optional[str]	×
20	total: int	×
21
22
23	class ReceivedPlotModel(BaseModel):	×
24	date: str	×
25	datapoints: List[ReceivedPlotDatapointsModel]	×
26
27
28	@router.get("/received", response_model=List[ReceivedPlotModel], response_model_exclude_none=True)	×
29	def received(	×
30	adapter: ArnoldAdapter = Depends(get_arnold_adapter),
31	date_min: Optional[dt.date] = dt.date.min,
32	date_max: Optional[dt.date] = dt.date.max,
33	):
34	samples = adapter.sample_collection.aggregate(	×
35	[
36	{
37	"$match": {
38	"delivery_date": {"$exists": 1},
39	"received_date": {
40	"$gte": dt.datetime.fromordinal(date_min.toordinal()),
41	"$lte": dt.datetime.fromordinal(date_max.toordinal()),
42	},
43	}
44	},
45	{
46	"$project": {
47	"received_date": 1,
48	"sample_id": 1,
49	"tag": {"$substr": ["$application", 0, 3]},
50	"received_year": {"$year": "$received_date"},
51	"received_month": {"$month": "$received_date"},
52	}
53	},
54	{
55	"$group": {
56	"_id": {"tag": "$tag", "year": "$received_year", "month": "$received_month"},
57	"total": {"$sum": 1},
58	}
59	},
60	{
61	"$project": {
62	"year": "$_id.year",
63	"month": "$_id.month",
64	"date": {
65	"$concat": [
66	{"$substr": ["$_id.year", 0, -1]},
67	"/",
68	{"$substr": ["$_id.month", 0, -1]},
69	]
70	},
71	"tag": "$_id.tag",
72	"total": "$total",
73	"_id": 0,
74	}
75	},
76	{
77	"$group": {
78	"_id": {"date": "$date", "year": "$year", "month": "$month"},
79	"datapoints": {"$push": "$$ROOT"},
80	}
81	},
82	{
83	"$project": {
84	"date": "$_id.date",
85	"year": "$_id.year",
86	"month": "$_id.month",
87	"datapoints": "$datapoints",
88	"_id": 0,
89	}
90	},
91	{"$unset": ["datapoints.date", "datapoints.year", "datapoints.month"]},
92	{"$sort": {"year": -1, "month": -1}},
93	{"$unset": ["year", "month"]},
94	]
95	)
96	return list(samples)	×
97
98
99	@router.get("/turnaround", response_model=List[ReceivedPlotModel], response_model_exclude_none=True)	×
100	def turnaround(	×
101	adapter: ArnoldAdapter = Depends(get_arnold_adapter),
102	date_min: Optional[dt.date] = dt.date.min,
103	date_max: Optional[dt.date] = dt.date.max,
104	group: Optional[Literal["priority", "tag"]] = "tag",
105	):
106	samples = adapter.sample_collection.aggregate(	×
107	[
108	{
109	"$match": {
110	"delivery_date": {"$exists": 1},
111	"received_date": {
112	"$gte": dt.datetime.fromordinal(date_min.toordinal()),
113	"$lte": dt.datetime.fromordinal(date_max.toordinal()),
114	},
115	}
116	},
117	{
118	"$project": {
119	"received_date": 1,
120	"delivery_date": 1,
121	"sample_id": 1,
122	"tag": {"$substr": ["$application", 0, 3]},
123	"received_year": {"$year": "$received_date"},
124	"received_month": {"$month": "$received_date"},
125	"priority": "$priority",
126	"turnaround_time": {
127	"$divide": [{"$subtract": ["$delivery_date", "$received_date"]}, 86400000]
128	},
129	}
130	},
131	{"$match": {"turnaround_time": {"$gt": 0}}},
132	{
133	"$group": {
134	"_id": {
135	f"{group}": f"${group}",
136	"year": "$received_year",
137	"month": "$received_month",
138	},
139	"total": {"$avg": "$turnaround_time"},
140	}
141	},
142	{
143	"$project": {
144	"year": "$_id.year",
145	"month": "$_id.month",
146	"date": {
147	"$concat": [
148	{"$substr": ["$_id.year", 0, -1]},
149	"/",
150	{"$substr": ["$_id.month", 0, -1]},
151	]
152	},
153	f"{group}": f"$_id.{group}",
154	"total": {"$round": ["$total", 0]},
155	"_id": 0,
156	}
157	},
158	{
159	"$group": {
160	"_id": {"date": "$date", "year": "$year", "month": "$month"},
161	"datapoints": {"$push": "$$ROOT"},
162	}
163	},
164	{
165	"$project": {
166	"date": "$_id.date",
167	"year": "$_id.year",
168	"month": "$_id.month",
169	"datapoints": "$datapoints",
170	"_id": 0,
171	}
172	},
173	{"$unset": ["datapoints.date", "datapoints.year", "datapoints.month"]},
174	{"$sort": {"year": -1, "month": -1}},
175	{"$unset": ["year", "month"]},
176	]
177	)
178	return list(samples)	×

Clinical-Genomics / arnold / 7102454002

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