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/models/database/flow_cell.py

from typing import Optional, List
from datetime import datetime

from pydantic import BaseModel


class Lane(BaseModel):
    name: Optional[str]
    percent_aligned_r1: Optional[float] = None
    percent_aligned_r2: Optional[float] = None
    percent_bases_q30_r1: Optional[float] = None
    percent_bases_q30_r2: Optional[float] = None
    percent_error_rate_r1: Optional[float] = None
    percent_error_rate_r2: Optional[float] = None
    percent_phasing_r1: Optional[float] = None
    percent_prephasing_r1: Optional[float] = None
    percent_prephasing_r2: Optional[float] = None
    percentpf_r1: Optional[float] = None
    percentpf_r2: Optional[float] = None
    cluster_density_r1: Optional[float] = None
    cluster_density_r2: Optional[float] = None
    intensity_cycle_1_r1: Optional[float] = None
    intensity_cycle_1_r2: Optional[float] = None
    reads_pf_millions_r1: Optional[int] = None
    reads_pf_millions_r2: Optional[int] = None
    yield_pf_giga_bases_r1: Optional[float] = None
    yield_pf_giga_bases_r2: Optional[float] = None
    percent_phasing_r2: Optional[float] = None


class FlowCell(BaseModel):
    instrument: Optional[str]
    date: Optional[datetime]
    done: Optional[bool]
    buffer_expiration_date: Optional[datetime]
    buffer_lot_number: Optional[str]
    buffer_part_number: Optional[str]
    buffer_serial_barcode: Optional[str]
    flow_cell_expiration_date: Optional[datetime]
    flow_cell_id: Optional[str]
    flow_cell_lot_number: Optional[str]
    flow_cell_mode: Optional[str]
    flow_cell_part_number: Optional[str]
    pe_cycle_kit: Optional[str]
    pe_expiration_date: Optional[datetime]
    pe_lot_number: Optional[str]
    pe_part_number: Optional[str]
    pe_serial_barcode: Optional[str]
    run_id: Optional[str]
    sbs_cycle_kit: Optional[str]
    sbs_expiration_date: Optional[datetime]
    sbs_lot_number: Optional[str]
    sbs_part_number: Optional[str]
    sbs_serial_barcode: Optional[str]
    lanes: Optional[List[Lane]]

1	from typing import Optional, List	×
2	from datetime import datetime	×
3
4	from pydantic import BaseModel	×
5
6
7	class Lane(BaseModel):	×
8	name: Optional[str]	×
NEW 9	percent_aligned_r1: Optional[float] = None	×
NEW 10	percent_aligned_r2: Optional[float] = None	×
NEW 11	percent_bases_q30_r1: Optional[float] = None	×
NEW 12	percent_bases_q30_r2: Optional[float] = None	×
NEW 13	percent_error_rate_r1: Optional[float] = None	×
NEW 14	percent_error_rate_r2: Optional[float] = None	×
NEW 15	percent_phasing_r1: Optional[float] = None	×
NEW 16	percent_prephasing_r1: Optional[float] = None	×
NEW 17	percent_prephasing_r2: Optional[float] = None	×
NEW 18	percentpf_r1: Optional[float] = None	×
NEW 19	percentpf_r2: Optional[float] = None	×
NEW 20	cluster_density_r1: Optional[float] = None	×
NEW 21	cluster_density_r2: Optional[float] = None	×
NEW 22	intensity_cycle_1_r1: Optional[float] = None	×
NEW 23	intensity_cycle_1_r2: Optional[float] = None	×
NEW 24	reads_pf_millions_r1: Optional[int] = None	×
NEW 25	reads_pf_millions_r2: Optional[int] = None	×
NEW 26	yield_pf_giga_bases_r1: Optional[float] = None	×
NEW 27	yield_pf_giga_bases_r2: Optional[float] = None	×
NEW 28	percent_phasing_r2: Optional[float] = None	×
29
30
31	class FlowCell(BaseModel):	×
32	instrument: Optional[str]	×
33	date: Optional[datetime]	×
34	done: Optional[bool]	×
35	buffer_expiration_date: Optional[datetime]	×
36	buffer_lot_number: Optional[str]	×
37	buffer_part_number: Optional[str]	×
38	buffer_serial_barcode: Optional[str]	×
39	flow_cell_expiration_date: Optional[datetime]	×
40	flow_cell_id: Optional[str]	×
41	flow_cell_lot_number: Optional[str]	×
42	flow_cell_mode: Optional[str]	×
43	flow_cell_part_number: Optional[str]	×
44	pe_cycle_kit: Optional[str]	×
45	pe_expiration_date: Optional[datetime]	×
46	pe_lot_number: Optional[str]	×
47	pe_part_number: Optional[str]	×
48	pe_serial_barcode: Optional[str]	×
49	run_id: Optional[str]	×
50	sbs_cycle_kit: Optional[str]	×
51	sbs_expiration_date: Optional[datetime]	×
52	sbs_lot_number: Optional[str]	×
53	sbs_part_number: Optional[str]	×
54	sbs_serial_barcode: Optional[str]	×
55	lanes: Optional[List[Lane]]	×

Clinical-Genomics / arnold / 7102454002

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