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/sample.py

from typing import Optional
from pydantic import Field, BaseModel, validator
from datetime import datetime


class Sample(BaseModel):
    """LIMS Sample Collection"""

    sample_id: str
    id: Optional[str] = Field(..., alias="_id")
    ticket: Optional[str] = None
    received_date: Optional[datetime] = None
    delivery_date: Optional[datetime] = None
    sequenced_date: Optional[datetime] = None
    prepared_date: Optional[datetime] = None
    collection_date: Optional[datetime] = None
    category: Optional[str] = None
    sequenced_to_delivered: Optional[int] = None
    prepped_to_sequenced: Optional[int] = None
    received_to_prepped: Optional[int] = None
    received_to_delivered: Optional[int] = None
    initial_qc: Optional[str] = None
    library_qc: Optional[str] = None
    prep_method: Optional[str] = None
    application: Optional[str] = None
    bait_set: Optional[str] = None
    capture_kit: Optional[str] = None
    comment: Optional[str] = None
    concentration: Optional[float] = None
    concentration_sample: Optional[float] = None
    customer: Optional[str] = None
    data_analysis: Optional[str] = None
    data_delivery: Optional[str] = None
    elution_buffer: Optional[str] = None
    extraction_method: Optional[str] = None
    family_name: Optional[str] = None
    formalin_fixation_time: Optional[float] = None
    index: Optional[str] = None
    index_number: Optional[str] = None
    lab_code: Optional[str] = None
    organism: Optional[str] = None
    organism_other: Optional[str] = None
    original_lab: Optional[str] = None
    original_lab_address: Optional[str] = None
    pool: Optional[str] = None
    post_formalin_fixation_time: Optional[float] = None
    pre_processing_method: Optional[str] = None
    priority: Optional[str] = None
    quantity: Optional[str] = None
    reference_genome: Optional[str] = None
    region: Optional[str] = None
    region_code: Optional[str] = None
    require_qcok: Optional[str] = None
    rml_plate_name: Optional[str] = None
    selection_criteria: Optional[str] = None
    sequencing_qc_pass: Optional[str] = None
    sex: Optional[str] = None
    source: Optional[str] = None
    target_reads: Optional[float] = None
    tissue_block_size: Optional[str] = None
    tumour: Optional[str] = None
    tumour_purity: Optional[int] = None
    verified_organism: Optional[str] = None
    volume: Optional[float] = None
    well_position_rml: Optional[str] = None

    @validator("id", always=True)
    def set_id(cls, v, values: dict) -> str:
        """sett _id to prep_id"""

        return values.get("sample_id")

    class Config:
        populate_by_name = True

1	from typing import Optional	×
2	from pydantic import Field, BaseModel, validator	×
3	from datetime import datetime	×
4
5
6	class Sample(BaseModel):	×
7	"""LIMS Sample Collection"""
8
9	sample_id: str	×
10	id: Optional[str] = Field(..., alias="_id")	×
NEW 11	ticket: Optional[str] = None	×
NEW 12	received_date: Optional[datetime] = None	×
NEW 13	delivery_date: Optional[datetime] = None	×
NEW 14	sequenced_date: Optional[datetime] = None	×
NEW 15	prepared_date: Optional[datetime] = None	×
NEW 16	collection_date: Optional[datetime] = None	×
NEW 17	category: Optional[str] = None	×
NEW 18	sequenced_to_delivered: Optional[int] = None	×
NEW 19	prepped_to_sequenced: Optional[int] = None	×
NEW 20	received_to_prepped: Optional[int] = None	×
NEW 21	received_to_delivered: Optional[int] = None	×
NEW 22	initial_qc: Optional[str] = None	×
NEW 23	library_qc: Optional[str] = None	×
NEW 24	prep_method: Optional[str] = None	×
NEW 25	application: Optional[str] = None	×
NEW 26	bait_set: Optional[str] = None	×
NEW 27	capture_kit: Optional[str] = None	×
NEW 28	comment: Optional[str] = None	×
NEW 29	concentration: Optional[float] = None	×
NEW 30	concentration_sample: Optional[float] = None	×
NEW 31	customer: Optional[str] = None	×
NEW 32	data_analysis: Optional[str] = None	×
NEW 33	data_delivery: Optional[str] = None	×
NEW 34	elution_buffer: Optional[str] = None	×
NEW 35	extraction_method: Optional[str] = None	×
NEW 36	family_name: Optional[str] = None	×
NEW 37	formalin_fixation_time: Optional[float] = None	×
NEW 38	index: Optional[str] = None	×
NEW 39	index_number: Optional[str] = None	×
NEW 40	lab_code: Optional[str] = None	×
NEW 41	organism: Optional[str] = None	×
NEW 42	organism_other: Optional[str] = None	×
NEW 43	original_lab: Optional[str] = None	×
NEW 44	original_lab_address: Optional[str] = None	×
NEW 45	pool: Optional[str] = None	×
NEW 46	post_formalin_fixation_time: Optional[float] = None	×
NEW 47	pre_processing_method: Optional[str] = None	×
NEW 48	priority: Optional[str] = None	×
NEW 49	quantity: Optional[str] = None	×
NEW 50	reference_genome: Optional[str] = None	×
NEW 51	region: Optional[str] = None	×
NEW 52	region_code: Optional[str] = None	×
NEW 53	require_qcok: Optional[str] = None	×
NEW 54	rml_plate_name: Optional[str] = None	×
NEW 55	selection_criteria: Optional[str] = None	×
NEW 56	sequencing_qc_pass: Optional[str] = None	×
NEW 57	sex: Optional[str] = None	×
NEW 58	source: Optional[str] = None	×
NEW 59	target_reads: Optional[float] = None	×
NEW 60	tissue_block_size: Optional[str] = None	×
NEW 61	tumour: Optional[str] = None	×
NEW 62	tumour_purity: Optional[int] = None	×
NEW 63	verified_organism: Optional[str] = None	×
NEW 64	volume: Optional[float] = None	×
NEW 65	well_position_rml: Optional[str] = None	×
66
67	@validator("id", always=True)	×
68	def set_id(cls, v, values: dict) -> str:	×
69	"""sett _id to prep_id"""
70
71	return values.get("sample_id")	×
72
73	class Config:	×
NEW 74	populate_by_name = True	×

Clinical-Genomics / arnold / 7102454002

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